Data Analysis: Call Distribution Across Datasets

Analyze the distribution of cell types across different datasets by processing all files in the data/data-processed-nodes-with-harmonized-cell-types directory.

import numpy as np
import pandas as pd
import os
import json
import requests
import shutil
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.preprocessing import normalize
import plotly.express as px

# NOTE: If you are using Plotly within the VS Code Notebook Editor you will need to add a line of code to ensure that your plots can be seen both within VS Code and when rendered to HTML by Quarto.
import plotly.io as pio
pio.renderers.default = "plotly_mimetype+notebook_connected" 

pd.set_option('display.max_columns', None)
pd.set_option('display.max_rows', None)

# suppress warnings
import warnings
warnings.filterwarnings("ignore")

basepath = "/u/yashjain/hra-cell-distance-analysis/data"
data_filedir = "data-processed-nodes-with-harmonized-cell-types"
figures_output_dir = "generated-figures"

# Function to load your data
def load_data(path):
    data = pd.read_csv(path)
    return data

# Function to read all files ending with "-nodes.csv" in the `data_filedir` directory into a single DataFrame. 
# An additional column `Tissue Type` is added to identify the dataset each row belongs to which comes from the subdirectory name in `data_filedir` that the file belongs to. 
# Another additional column `Dataset` is added to identify the dataset name which comes from the filename befrore the `-nodes.csv` suffix.
def read_all_datasets(basepath, data_filedir):
    all_files = []
    for subdir, dirs, files in os.walk(os.path.join(basepath, data_filedir)):
        for file in files:
            if file.endswith("-nodes.csv"):
                file_path = os.path.join(subdir, file)
                tissue_type = os.path.basename(subdir)
                dataset_name = file.replace("-nodes.csv", "")
                df = load_data(file_path)
                df['Tissue Type'] = tissue_type
                df['Dataset'] = dataset_name
                all_files.append(df)

    merged = pd.concat(all_files, ignore_index=True)
    # reset index after concatenation
    # merged.reset_index(drop=True, inplace=True)
    return merged

def create_directory(directory):
    if not os.path.exists(directory):
        os.makedirs(directory)
        print(f"Directory '{directory}' created successfully.")
    else:
        print(f"Directory '{directory}' already exists.")

print(len(os.listdir(os.path.join(basepath, data_filedir))))

14

# Create destination directory. Overwrite if it exists.
if os.path.exists(os.path.join(basepath, figures_output_dir)):
    shutil.rmtree(os.path.join(basepath, figures_output_dir))
    print(f"Directory '{figures_output_dir}' already exists and has been removed. New directory will be created.")
else:
    print(f"Directory '{figures_output_dir}' does not exist and will be created.")
os.makedirs(os.path.join(basepath, figures_output_dir), exist_ok=False)

Directory 'generated-figures' already exists and has been removed. New directory will be created.

Per Dataset Cell Summary

# Call the function to read all datasets
df_all_data = read_all_datasets(basepath, data_filedir)

# Print the first few rows of the DataFrame
df_all_data.head(5)

	x	y	Original Cell Type	Level Three Cell Type	Level Three CL Label	Level Three CL ID	CL_Match/3	Level Two Cell Type	Level Two CL Label	Level Two CL ID	CL_Match/2	Level One Cell Type	Level One CL Label	Level One CL ID	CL_Match/1	Tissue Type	Dataset	z
0	1503.64128	1278.32154	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford	B004_Ascending	NaN
1	1958.05496	1553.46072	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford	B004_Ascending	NaN
2	2290.93940	1187.36332	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford	B004_Ascending	NaN
3	2863.48554	891.08862	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford	B004_Ascending	NaN
4	2563.43664	1468.54122	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford	B004_Ascending	NaN

# Print the total number of unique datasets per each tissue type
print("Total number of unique datasets per each tissue type:")
print(df_all_data.groupby('Tissue Type')['Dataset'].nunique())

# Print the sum of number of unique datasets overall.
print("\nTotal number of unique datasets overall:")
print(df_all_data['Dataset'].nunique())

Total number of unique datasets per each tissue type:
Tissue Type
bonemarrow-codex-chop                       20
colon-cycif-sorgerlab                       25
colon-xenium-stanford                       29
esophagus-codex-stanford                     1
intestine-codex-stanford                    64
lung-codex-urmc                              2
lymphnode-codex-yale                         5
maternalfetalinterface-mibitof-stanford    209
oralcavity-codex-czi                        13
pancreas-geomx-ufl                          12
skin-celldive-ge                            10
skin-confocal-sorgerlab                      2
spleen-codex-ufl                             6
tonsil-codex-stanford                        1
Name: Dataset, dtype: int64

Total number of unique datasets overall:
399

# Print the total number of cells per tissue type
print("Total number of cells per tissue type:")
tissue_counts = df_all_data.groupby('Tissue Type')['Original Cell Type'].count()
for tissue, count in tissue_counts.items():
    print(f"{tissue}: {count:,}")

# Print the sum of number of cells overall. Format the output number to be more readable.
print("\nTotal number of cells overall:")
print(f"{df_all_data['Original Cell Type'].count():,}")

Total number of cells per tissue type:
bonemarrow-codex-chop: 1,214,088
colon-cycif-sorgerlab: 12,758,141
colon-xenium-stanford: 2,639,215
esophagus-codex-stanford: 45,958
intestine-codex-stanford: 2,512,185
lung-codex-urmc: 1,209,309
lymphnode-codex-yale: 8,918,845
maternalfetalinterface-mibitof-stanford: 477,747
oralcavity-codex-czi: 1,412,189
pancreas-geomx-ufl: 14,891,875
skin-celldive-ge: 48,323
skin-confocal-sorgerlab: 55,255
spleen-codex-ufl: 992,398
tonsil-codex-stanford: 173,968

Total number of cells overall:
47,349,496

# Print the total number of unique cell types per tissue type. Compute separately for each cell type column (Level One Cell Type, Level Two Cell Type, Level Three Cell Type, Original Cell Type).
print("Total number of unique cell types per tissue type:")

# Create a summary table
tissue_types = df_all_data['Tissue Type'].unique()
columns = ['Original Cell Type', 'Level Three Cell Type', 'Level Two Cell Type', 'Level One Cell Type']

# Create a dictionary to store results
results = {}
for tissue in tissue_types:
    tissue_data = df_all_data[df_all_data['Tissue Type'] == tissue]
    results[tissue] = {}
    for col in columns:
        results[tissue][col] = tissue_data[col].nunique()

# Convert to DataFrame for better formatting
summary_df = pd.DataFrame(results).T
summary_df = summary_df[columns]  # Reorder columns

# Add a row for "Overall Unique Cell Types" which contains the total number of unique cell types across all tissue types from df_all_data for each column.
overall_unique = df_all_data[columns].nunique()
summary_df.loc['Total Unique Cell Types'] = overall_unique

summary_df

Total number of unique cell types per tissue type:

	Original Cell Type	Level Three Cell Type	Level Two Cell Type	Level One Cell Type
intestine-codex-stanford	25	25	17	5
tonsil-codex-stanford	10	10	8	5
esophagus-codex-stanford	12	12	11	5
colon-xenium-stanford	41	38	20	6
lymphnode-codex-yale	34	29	10	3
maternalfetalinterface-mibitof-stanford	26	23	11	5
oralcavity-codex-czi	39	28	20	6
pancreas-geomx-ufl	4	4	4	3
skin-celldive-ge	8	8	4	3
skin-confocal-sorgerlab	15	15	11	4
spleen-codex-ufl	12	12	9	3
lung-codex-urmc	54	20	17	7
bonemarrow-codex-chop	37	33	22	6
colon-cycif-sorgerlab	21	21	7	5
Total Unique Cell Types	295	161	57	8

# Extract the following columns from df_all_data: Original Cell Type, Level Three Cell Type, Level Three CL Label, Level Three CL ID, CL_Match/3, Level Two Cell Type, Level Two CL Label, Level Two CL ID, CL_Match/2, Level One Cell Type, Level One CL Label, Level One CL ID, CL_Match/1.
# Create a table containing these columns but have the rows be unique combinations of these columns.

columns = [
    'Original Cell Type',
    'Level Three Cell Type',
    'Level Three CL Label',
    'Level Three CL ID',
    'CL_Match/3',
    'Level Two Cell Type',
    'Level Two CL Label',
    'Level Two CL ID',
    'CL_Match/2',
    'Level One Cell Type',
    'Level One CL Label',
    'Level One CL ID',
    'CL_Match/1',
    'Tissue Type',
]

# Extract the unique combinations of these columns from df_all_data. Sort the DataFrame by 'Level Three Cell Type' in ascending order.
unique_combinations = df_all_data[columns].drop_duplicates().sort_values(by='Level Three Cell Type', ascending=True)

unique_combinations.reset_index(drop=True, inplace=True)

unique_combinations

	Original Cell Type	Level Three Cell Type	Level Three CL Label	Level Three CL ID	CL_Match/3	Level Two Cell Type	Level Two CL Label	Level Two CL ID	CL_Match/2	Level One Cell Type	Level One CL Label	Level One CL ID	CL_Match/1	Tissue Type
0	Acinar Cells	acinar cell of salivary gland	acinar cell of salivary gland	CL:0002623	skos:exactMatch	gland epithelium cell	glandular secretory epithelial cell	CL:0000150	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
1	Acini	acinar cell of salivary gland	acinar cell of salivary gland	CL:0002623	skos:exactMatch	gland epithelium cell	glandular secretory epithelial cell	CL:0000150	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
2	Adipocytes	adipocyte	adipocyte	CL:0000136	skos:exactMatch	adipocyte	adipocyte	CL:0000136	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	oralcavity-codex-czi
3	Adipocytes	adipocyte	adipocyte	CL:0000136	skos:exactMatch	adipocyte	adipocyte	CL:0000136	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
4	Adipocyte	adipocyte	adipocyte	CL:0000136	skos:exactMatch	adipocyte	adipocyte	CL:0000136	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	bonemarrow-codex-chop
5	B-Cells	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
6	B	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	tonsil-codex-stanford
7	B cell	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
8	B cells	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
9	B Cells	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
10	B cells	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
11	B	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
12	B cells, red pulp	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	spleen-codex-ufl
13	B_cell_1	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
14	B_activated	b cell:activated	B cell:activated	CL:0000236	skos:narrowMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
15	Fol B cells	b cell:follicular	follicular B cell	CL:0000843	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	spleen-codex-ufl
16	B_GC_DZ	b cell:germinal center	germinal center B cell	CL:0000844	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
17	B_GC_LZ	b cell:germinal center	germinal center B cell	CL:0000844	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
18	B_GC_prePB	b cell:germinal center pre-plasmablast	germinal center B cell:pre-plasmablast	CL:0000844	skos:narrowMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
19	Immature_B_Cell	b cell:immature	immature B cell	CL:0000816	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
20	B_IFN	b cell:interferon	B cell:interferon-stimulated	CL:0000236	skos:narrowMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
21	B_mem	b cell:memory	memory B cell	CL:0000787	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
22	Memory B	b cell:memory	memory B cell	CL:0000787	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
23	B_naive	b cell:naive	naive B cell	CL:0000788	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
24	Naive B	b cell:naive	naive B cell	CL:0000788	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
25	B_preGC	b cell:pre-germinal center	B cell:pre-germinal center	CL:0000236	skos:narrowMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
26	B_Cycling	b cell:proliferating	cycling B cell	CL:4033068	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
27	Beta cell	beta cell:pancreatic	type B pancreatic cell	CL:0000169	skos:exactMatch	beta cell	type B pancreatic cell	CL:0000169	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	pancreas-geomx-ufl
28	CD34+ CD61+	cell:cd34+ cd61+	leukocyte:cd34-positive cd61-positive	CL:0000738	skos:narrowMatch	megakaryocyte	megakaryocyte	CL:0000556	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
29	Ki67 proliferating	cell:proliferating	cell:proliferating	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	spleen-codex-ufl
30	DC	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
31	Dendritic cells	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
32	DC	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
33	DC	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
34	Dendritic Cells	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
35	CD11B+ CD11C- cells	dendritic cell:cd11b+	CD11b-positive dendritic cell	CL:0002465	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
36	DC_cDC1	dendritic cell:conventional 1	CD141-positive myeloid dendritic cell	CL:0002394	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
37	DC_cDC2	dendritic cell:conventional 2	CD1c-positive myeloid dendritic cell	CL:0002399	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
38	FDC	dendritic cell:follicular	follicular dendritic cell	CL:0000442	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	lymphnode-codex-yale
39	DC_CCR7+	dendritic cell:migratory	migratory dendtritic cell	CL:4047054	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
40	DC_pDC	dendritic cell:plasmacytoid	plasmacytoid dendritic cell	CL:0000784	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
41	pDC	dendritic cell:plasmacytoid	plasmacytoid dendritic cell	CL:0000784	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
42	Endosteal	endosteal cell	endosteal cell	CL:0002157	skos:exactMatch	skeletal stromal cell	bone cell:stromal	CL:0001035	skos:narrowMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	bonemarrow-codex-chop
43	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lymphnode-codex-yale
44	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	skin-celldive-ge
45	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	skin-confocal-sorgerlab
46	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	pancreas-geomx-ufl
47	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	intestine-codex-stanford
48	Endo_p	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lung-codex-urmc
49	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	tonsil-codex-stanford
50	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	colon-xenium-stanford
51	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	maternalfetalinterface-mibitof-stanford
52	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	colon-cycif-sorgerlab
53	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	esophagus-codex-stanford
54	ENDO_SMC	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lung-codex-urmc
55	Endo_2	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lung-codex-urmc
56	ENDO_1	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lung-codex-urmc
57	AEC	endothelial cell of artery	endothelial cell of artery	CL:1000413	skos:exactMatch	endothelial cell of artery	endothelial cell of artery	CL:1000413	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	bonemarrow-codex-chop
58	CAP_ENDO	endothelial cell of capillary	capillary endothelial cell	CL:0002144	skos:exactMatch	endothelial cell of capillary	capillary endothelial cell	CL:0002144	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lung-codex-urmc
59	Podoplanin	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	spleen-codex-ufl
60	Lymphatic endothelial cells	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	colon-xenium-stanford
61	Lymphatic	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	intestine-codex-stanford
62	Lymphatic_Endothelium	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lung-codex-urmc
63	lymphatic Endothelium	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lung-codex-urmc
64	Lymphatic Endothelial Cells	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	oralcavity-codex-czi
65	Lymphatic Vascular Cells	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell of lymphatic vessel	endothelial cell of lymphatic vessel	CL:0002138	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	oralcavity-codex-czi
66	SEC	endothelial cell of sinusoid	endothelial cell of sinusoid	CL:0002262	skos:exactMatch	endothelial cell of sinusoid	endothelial cell of sinusoid	CL:0002262	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	bonemarrow-codex-chop
67	Sinusoidal cells	endothelial cell of sinusoid	endothelial cell of sinusoid	CL:0002262	skos:exactMatch	endothelial cell of sinusoid	endothelial cell of sinusoid	CL:0002262	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	spleen-codex-ufl
68	Vascular Endothelial Cells	endothelial cell of vascular tree	endothelial cell of vascular tree	CL:0002139	skos:exactMatch	endothelial cell of vascular tree	endothelial cell of vascular tree	CL:0002139	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	oralcavity-codex-czi
69	blood endothelial	endothelial cell of vascular tree	endothelial cell of vascular tree	CL:0002139	skos:exactMatch	endothelial cell of vascular tree	endothelial cell of vascular tree	CL:0002139	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	spleen-codex-ufl
70	VEC Progen	endothelial cell of vascular tree	endothelial cell of vascular tree	CL:0002139	skos:exactMatch	endothelial cell of vascular tree	endothelial cell of vascular tree	CL:0002139	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	oralcavity-codex-czi
71	Enterocytes	enterocyte	enterocyte	CL:0000584	skos:exactMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
72	Enterocyte	enterocyte	enterocyte	CL:0000584	skos:exactMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
73	CD57+ Enterocyte	enterocyte:cd57+	CD57-positive enterocyte	CL:4033092	skos:exactMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
74	CD66+ Enterocyte	enterocyte:cd66+	enterocyte:cd66-positive	CL:0000584	skos:narrowMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
75	Immature Enterocytes	enterocyte:immature	enterocyte:immature	CL:0000584	skos:narrowMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
76	MUC1+ Enterocyte	enterocyte:muc1+	enterocyte:muc1-positive	CL:0000584	skos:narrowMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
77	Enterocyte Progenitors	enterocyte:progenitor	enterocyte:progenitor	CL:0000584	skos:narrowMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
78	Enteroendocrine	enteroendocrine cell	enteroendocrine cell	CL:0000164	skos:exactMatch	endocrine cell	endocrine cell	CL:0000163	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
79	Best4+ Enterocytes	enteroycte:best4+	BEST4+ enterocyte	CL:4030026	skos:exactMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
80	Epithelial	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
81	Ionocytes	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
82	Melanocytes	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
83	Lung_Epithelial_1	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
84	Lung_Epithelial_4	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
85	Merkel Cells	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
86	Lung_Epithelial_p	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
87	Ducts	epithelial cell:ductal	duct epithelial cell	CL:0000068	skos:exactMatch	gland epithelium cell	epithelial cell:gland	CL:0000066	skos:narrowMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
88	Ductal Epithelial Cells	epithelial cell:ductal	duct epithelial cell	CL:0000068	skos:exactMatch	gland epithelium cell	epithelial cell:gland	CL:0000066	skos:narrowMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
89	Ductal cell	epithelial cell:ductal	duct epithelial cell	CL:0000068	skos:exactMatch	gland epithelium cell	epithelial cell:gland	CL:0000066	skos:narrowMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	pancreas-geomx-ufl
90	Ki67+ Tumor/Epithelial	epithelial cell:ki67+ proliferating tumor	epithelial cell:ki67-positive proliferating tumor	CL:0000066	skos:narrowMatch	abnormal cell	abnormal cell	CL:0001061	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-cycif-sorgerlab
91	PDL1+ Tumor/Epithelial	epithelial cell:pdl1+ tumor	epithelial cell:pdl1-positive tumor	CL:0000066	skos:narrowMatch	abnormal cell	abnormal cell	CL:0001061	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-cycif-sorgerlab
92	Secretory_epithelial	epithelial cell:secretory	secretory epithelial cell	CL:1100001	skos:exactMatch	secretory cell of esophagus	glandular cell of esophagus	CL:0002657	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	esophagus-codex-stanford
93	Erythroblast	erythroblast	erythroblast	CL:0000765	skos:exactMatch	erythroid precursor	erythroid progenitor cell	CL:0000038	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
94	MEP/Early Erythroblast	erythroblast:basophilic	basophilic erythroblast	CL:0000549	skos:exactMatch	erythroid precursor	erythroid progenitor cell	CL:0000038	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
95	Erythroid	erythroid lineage cell	erythroid lineage cell	CL:0000764	skos:exactMatch	erythroid precursor	erythroid progenitor cell	CL:0000038	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
96	Fibroblasts	fibroblast	fibroblast	CL:0000057	skos:exactMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	oralcavity-codex-czi
97	Fibroblasts	fibroblast	fibroblast	CL:0000057	skos:exactMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	maternalfetalinterface-mibitof-stanford
98	Cancer Associated Fibroblasts	fibroblast:cancer associated	fibroblast:cancer associated	CL:0000057	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
99	Crypt Fibroblasts 1	fibroblast:crypt 1	crypt-top fibroblast:1	CL:4052009	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
100	Crypt Fibroblasts 2	fibroblast:crypt 2	crypt-top fibroblast:2	CL:4052009	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
101	Crypt Fibroblasts 3	fibroblast:crypt 3	crypt-top fibroblast:3	CL:4052009	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
102	Crypt Fibroblasts 4	fibroblast:crypt 4	crypt-top fibroblast:4	CL:4052009	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
103	Villus Fibroblasts WNT5B+	fibroblast:wnt5b+ villus	fibroblast:wnt5b+ villus	CL:0000057	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
104	Glandular_epi	glandular cell of esophagus	glandular cell of esophagus	CL:0002657	skos:exactMatch	gland epithelium cell	glandular secretory epithelial cell	CL:0000150	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	esophagus-codex-stanford
105	Glandular	glandular cell of placenta	glandular secretory epithelial cell:placenta	CL:0000150	skos:narrowMatch	gland epithelium cell	glandular secretory epithelial cell	CL:0000150	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	maternalfetalinterface-mibitof-stanford
106	Glia	glial cell	glial cell	CL:0000125	skos:exactMatch	neuroglial cell	glial cell	CL:0000125	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	colon-xenium-stanford
107	Glial/Neuron	glial cell/neuron	neural cell:glial/neuron	CL:0002319	skos:narrowMatch	neuroglial cell/neuron	neural cell:neuroglial/neuron	CL:0002319	skos:narrowMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	oralcavity-codex-czi
108	GC	goblet cell	goblet cell	CL:0000160	skos:exactMatch	goblet cell	goblet cell	CL:0000160	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
109	Goblet	goblet cell	goblet cell	CL:0000160	skos:exactMatch	goblet cell	goblet cell	CL:0000160	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
110	Goblet	goblet cell	goblet cell	CL:0000160	skos:exactMatch	goblet cell	goblet cell	CL:0000160	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
111	Immature Goblet	goblet cell:immature	goblet cell:immature	CL:0000160	skos:narrowMatch	goblet cell	goblet cell	CL:0000160	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
112	GMP	granulocyte monocyte progenitor cell	granulocyte monocyte progenitor cell	CL:0000557	skos:exactMatch	myeloid precursor	common myeloid progenitor	CL:0000049	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
113	GMP/Myeloblast	granulocyte monocyte progenitor cell/myeloblast	myeloid lineage restricted progenitor cell:gra...	CL:0000839	skos:narrowMatch	myeloid precursor	common myeloid progenitor	CL:0000049	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
114	SPINK2+ HSPC	hematopoietic stem and progenitor cell:spink2+	hematopoietic multipotent progenitor cell:spin...	CL:0000837	skos:narrowMatch	hematopoietic stem and progenitor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
115	HSC	hematopoietic stem cell	hematopoietic stem cell	CL:0000037	skos:exactMatch	stem cell	stem cell	CL:0000034	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
116	HSPC	hematopoietic stem cell	hematopoietic stem cell	CL:0000037	skos:exactMatch	stem cell	stem cell	CL:0000034	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
117	Placental_Mac	hofbauer cell	Hofbauer cell	CL:3000001	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
118	B_cell_macrophage_p?	immune cell	leukocyte	CL:0000738	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
119	ICC	interstitial cell of cajal	interstitial cell of Cajal	CL:0002088	skos:exactMatch	neurecto-epithelial cell	neurecto-epithelial cell	CL:0000710	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	intestine-codex-stanford
120	Keratinocyte	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
121	Basal Keratincytes	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
122	Suprabasal Keratinocytes	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
123	keratinocytes	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	skin-confocal-sorgerlab
124	DDB2	keratinocyte:ddb2+	keratinocyte:ddb2-positive	CL:0000312	skos:narrowMatch	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	skin-celldive-ge
125	KI67	keratinocyte:ki67+ proliferating	keratinocyte:ki67-positive proliferating	CL:0000312	skos:narrowMatch	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	skin-celldive-ge
126	P53	keratinocyte:p53+	keratinocyte:p53-positive	CL:0000312	skos:narrowMatch	keratinocyte	keratinocyte	CL:0000312	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	skin-celldive-ge
127	Langerhan cells	langerhans cell	Langerhans cell	CL:0000453	skos:exactMatch	langerhans cell	Langerhans cell	CL:0000453	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
128	Langerhans Cells	langerhans cell	Langerhans cell	CL:0000453	skos:exactMatch	langerhans cell	Langerhans cell	CL:0000453	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
129	Leukocyte	leukocyte	leukocyte	CL:0000738	skos:exactMatch	leukocyte	leukocyte	CL:0000738	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
130	Other Immune	leukocyte	leukocyte	CL:0000738	skos:exactMatch	leukocyte	leukocyte	CL:0000738	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
131	CD7+ Immune	lymphocyte:cd7+	CD7-positive lymphoid progenitor cell	CL:0001028	skos:exactMatch	lymphoid cell	lymphocyte	CL:0000542	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
132	DN Lymphocyte	lymphocyte:double-negative	double negative thymocyte	CL:0002489	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
133	DP Lymphocyte	lymphocyte:double-positive alpha-beta	double-positive, alpha-beta thymocyte	CL:0000809	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
134	Lymphocyte(III)	lymphocyte:iii	lymphocyte:III	CL:0000542	skos:narrowMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
135	PDL1+ lymphocyte	lymphocyte:pdl1+	lymphocyte:pdl1-positive	CL:0000542	skos:narrowMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
136	Innate	lymphoid cell:innate	innate lymphoid cell	CL:0001065	skos:exactMatch	lymphoid cell	lymphocyte	CL:0000542	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	tonsil-codex-stanford
137	ILC	lymphoid cell:innate	innate lymphoid cell	CL:0001065	skos:exactMatch	lymphoid cell	lymphocyte	CL:0000542	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
138	Innate	lymphoid cell:innate	innate lymphoid cell	CL:0001065	skos:exactMatch	lymphoid cell	lymphocyte	CL:0000542	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	esophagus-codex-stanford
139	ILCs	lymphoid cell:innate	innate lymphoid cell	CL:0001065	skos:exactMatch	lymphoid cell	lymphocyte	CL:0000542	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
140	CLP	lymphoid progenitor cell:common	common lymphoid progenitor	CL:0000051	skos:exactMatch	progenitor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
141	Macrophages_M2	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
142	M2 Macrophage	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
143	Macrophage	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
144	macrophage_CD1c+_myeloidDC	macrophage	alveolar macrophage	CL:0000583	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
145	Macrophages	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
146	Macrophages	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
147	CD68	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-celldive-ge
148	Macrophage	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
149	macrophage	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
150	macrophage_3	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
151	macrophage_2	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
152	Macrophages_M1	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
153	Macrophages	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	spleen-codex-ufl
154	macrophage_p	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
155	Mac1a	macrophage:1a	macrophage:1a	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
156	Mac1b	macrophage:1b	macrophage:1b	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
157	Mac2a	macrophage:2a	macrophage:2a	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
158	Mac2b	macrophage:2b	macrophage:2b	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
159	Mac2c	macrophage:2c	macrophage:2c	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
160	Macrophage(I)	macrophage:i	macrophage:I	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
161	Macrophage(II)	macrophage:ii	macrophage:II	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
162	Macrophage(III)	macrophage:iii	macrophage:III	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
163	M1 Macrophage	macrophage:inflammatory	inflammatory macrophage	CL:0000863	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
164	lung Intersitial macrophage	macrophage:interstitial	lung interstitial macrophage	CL:4033043	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
165	Macrophage(IV)	macrophage:iv	macrophage:IV	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
166	PDL1+ Macrophage	macrophage:pdl1+	macrophage:pdl1-positive	CL:0000235	skos:narrowMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
167	Mast	mast cell	mast cell	CL:0000097	skos:exactMatch	mast cell	mast cell	CL:0000097	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
168	Mast Cells	mast cell	mast cell	CL:0000097	skos:exactMatch	mast cell	mast cell	CL:0000097	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
169	Mast	mast cell	mast cell	CL:0000097	skos:exactMatch	mast cell	mast cell	CL:0000097	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
170	Mast	mast cell	mast cell	CL:0000097	skos:exactMatch	mast cell	mast cell	CL:0000097	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
171	Mast cell	mast cell	mast cell	CL:0000097	skos:exactMatch	mast cell	mast cell	CL:0000097	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
172	megakaryocyte	megakaryocyte	megakaryocyte	CL:0000556	skos:exactMatch	megakaryocyte	megakaryocyte	CL:0000556	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	lung-codex-urmc
173	GATA1pos_Mks	megakaryocyte:gata1+	megakaryocyte:gata1-positive	CL:0000556	skos:narrowMatch	megakaryocyte	megakaryocyte	CL:0000556	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
174	GATA1neg_Mks	megakaryocyte:gata1-	megakaryocyte:gata1-negative	CL:0000556	skos:narrowMatch	megakaryocyte	megakaryocyte	CL:0000556	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
175	Adipo-MSC	mesenchymal stem cell of adipose tissue	mesenchymal stem cell of adipose tissue	CL:0002570	skos:exactMatch	mesenchymal stem cell	mesenchymal stem cell	CL:0000134	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	bonemarrow-codex-chop
176	THY1+ MSC	mesenchymal stem/stromal cell:thy1+	mesenchymal stem cell:thy1-positive	CL:0000134	skos:narrowMatch	mesenchymal stem/stromal cell	mesenchymal stem cell	CL:0000134	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
177	Lung_Epithelil_2_CD4+_T_cell	mixed t cell/epithelial cell population	cell:mixed t cell/epithelial cell population	CL:0000000	skos:narrowMatch	mixed t cell/epithelial cell population	T cell/epithelial cell	CL:0000084/CL:0000066	skos:narrowMatch	mixed immune/epithelial cell population	T cell/epithelial cell	CL:0000084/CL:0000066	skos:narrowMatch	lung-codex-urmc
178	Monocytes	monocyte	monocyte	CL:0000576	skos:exactMatch	monocyte	monocyte	CL:0000576	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
179	Monocytes	monocyte	monocyte	CL:0000576	skos:exactMatch	monocyte	monocyte	CL:0000576	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
180	Monocyte-Macrophage	monocyte	monocyte	CL:0000576	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
181	Non-Classical Monocyte	monocyte:non-classical	non-classical monocyte	CL:0000875	skos:exactMatch	monocyte	monocyte	CL:0000576	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
182	Mural Cells	mural cell	mural cell	CL:0008034	skos:exactMatch	perivascular cell	perivascular cell	CL:4033054	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	oralcavity-codex-czi
183	muscle	muscle cell	muscle cell	CL:0000187	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	maternalfetalinterface-mibitof-stanford
184	Skeletal Myocytes	muscle cell:skeletal	cell of skeletal muscle	CL:0000188	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	oralcavity-codex-czi
185	Smooth muscle	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	intestine-codex-stanford
186	SMC_1	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	lung-codex-urmc
187	VSMC	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	lymphnode-codex-yale
188	SMC_2	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	lung-codex-urmc
189	SmoothMuscle	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	tonsil-codex-stanford
190	smooth muscle_2	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	lung-codex-urmc
191	SmoothMuscle	muscle cell:smooth	smooth muscle cell of the esophagus	CL:0002599	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	esophagus-codex-stanford
192	VSMC	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	bonemarrow-codex-chop
193	smooth muscle 1	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	lung-codex-urmc
194	NPM1 Mutant Blast	mutant blast:npm1	NaN	NaN	NaN	abnormal cell	abnormal cell	CL:0001061	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
195	Myeloid	myeloid cell	myeloid cell	CL:0000763	skos:exactMatch	myeloid cell	myeloid cell	CL:0000763	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
196	Myeloid cells	myeloid cell	myeloid cell	CL:0000763	skos:exactMatch	myeloid cell	myeloid cell	CL:0000763	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	spleen-codex-ufl
197	Intermediate Myeloid	myeloid cell:intermediate	myeloid cell:intermediate	CL:0000763	skos:narrowMatch	myeloid precursor	common myeloid progenitor	CL:0000049	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
198	Mature Myeloid	myeloid cell:mature	myeloid cell:mature	CL:0000763	skos:narrowMatch	myeloid cell	myeloid cell	CL:0000763	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
199	Early Myeloid Progenitor	myeloid progenitor cell:common	common myeloid progenitor	CL:0000049	skos:exactMatch	progenitor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	hematopoietic precursor cell	hematopoietic precursor cell	CL:0008001	skos:exactMatch	bonemarrow-codex-chop
200	Myoepithelial Cells	myoepithelial cell	myoepithelial cell	CL:0000185	skos:exactMatch	myoepithelial cell	myoepithelial cell	CL:0000185	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	oralcavity-codex-czi
201	Muscle/Fibroblast	myofibroblast	myofibroblast cell	CL:0000186	skos:exactMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-cycif-sorgerlab
202	Myofibroblasts	myofibroblast	myofibroblast cell	CL:0000186	skos:exactMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	maternalfetalinterface-mibitof-stanford
203	myofibroblast	myofibroblast	myofibroblast cell	CL:0000186	skos:exactMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	oralcavity-codex-czi
204	Myofibroblasts/Smooth Muscle 1	myofibroblast cell:smooth muscle 1	myofibroblast cell:smooth muscle-like 1	CL:0000186	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
205	Myofibroblasts/Smooth Muscle 2	myofibroblast cell:smooth muscle 2	myofibroblast cell:smooth muscle-like 2	CL:0000186	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
206	Myofibroblasts/Smooth Muscle 3	myofibroblast cell:smooth muscle 3	myofibroblast cell:smooth muscle-like 3	CL:0000186	skos:narrowMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
207	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
208	NK1	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
209	NK2	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
210	NK3	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
211	NK4	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
212	NK Cells	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
213	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
214	Tumor/Epithelial	neoplastic cell	neoplastic cell	CL:0001063	skos:exactMatch	abnormal cell	abnormal cell	CL:0001061	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-cycif-sorgerlab
215	Neuroendocrine	neuroendocrine cell	neuroendocrine cell	CL:0000165	skos:exactMatch	endocrine cell	endocrine cell	CL:0000163	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
216	Nerve	neuron	neuron	CL:0000540	skos:exactMatch	neuron	neuron	CL:0000540	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	esophagus-codex-stanford
217	Neurons	neuron	neuron	CL:0000540	skos:exactMatch	neuron	neuron	CL:0000540	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	colon-xenium-stanford
218	Nerve	neuron	neuron	CL:0000540	skos:exactMatch	neuron	neuron	CL:0000540	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	tonsil-codex-stanford
219	Nerve	neuron	neuron	CL:0000540	skos:exactMatch	neuron	neuron	CL:0000540	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	intestine-codex-stanford
220	Neutrophil	neutrophil	neutrophil	CL:0000775	skos:exactMatch	neutrophil	neutrophil	CL:0000775	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
221	neutrophil_2	neutrophil	neutrophil	CL:0000775	skos:exactMatch	neutrophil	neutrophil	CL:0000775	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
222	Neutrophils	neutrophil	neutrophil	CL:0000775	skos:exactMatch	neutrophil	neutrophil	CL:0000775	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
223	neutrophil	neutrophil	neutrophil	CL:0000775	skos:exactMatch	neutrophil	neutrophil	CL:0000775	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
224	Neutrophils/Monocytes	neutrophil/monocyte	myeloid leukocyte:neutrophil/monocyte	CL:0000766	skos:narrowMatch	neutrophil	neutrophil	CL:0000775	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	spleen-codex-ufl
225	Paneth	paneth cell	paneth cell	CL:0000510	skos:exactMatch	paneth cell	paneth cell	CL:0000510	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
226	Paneth	paneth cell	paneth cell	CL:0000510	skos:exactMatch	paneth cell	paneth cell	CL:0000510	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	esophagus-codex-stanford
227	Pericytes	pericyte	pericyte	CL:0000669	skos:exactMatch	pericyte	pericyte	CL:0000669	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
228	Plasma Cells	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
229	B_plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
230	Plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	tonsil-codex-stanford
231	Plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
232	Plasma Cells	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
233	Plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
234	Plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	esophagus-codex-stanford
235	AT1_1	pneumocyte:type 1	pulmonary alveolar type 1 cell	CL:0002062	skos:exactMatch	type 1 pneumocyte	pulmonary alveolar type 1 cell	CL:0002062	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
236	AT1 _2	pneumocyte:type 1	pulmonary alveolar type 1 cell	CL:0002062	skos:exactMatch	type 1 pneumocyte	pulmonary alveolar type 1 cell	CL:0002062	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
237	AT2_p	pneumocyte:type 2	pulmonary alveolar type 2 cell	CL:0002063	skos:exactMatch	type 2 pneumocyte	pulmonary alveolar type 2 cell	CL:0002063	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
238	AT2_2	pneumocyte:type 2	pulmonary alveolar type 2 cell	CL:0002063	skos:exactMatch	type 2 pneumocyte	pulmonary alveolar type 2 cell	CL:0002063	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
239	AT2	pneumocyte:type 2	pulmonary alveolar type 2 cell	CL:0002063	skos:exactMatch	type 2 pneumocyte	pulmonary alveolar type 2 cell	CL:0002063	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
240	AT2_1	pneumocyte:type 2	pulmonary alveolar type 2 cell	CL:0002063	skos:exactMatch	type 2 pneumocyte	pulmonary alveolar type 2 cell	CL:0002063	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	lung-codex-urmc
241	Schwann Cells	schwann cell	Schwann cell	CL:0002573	skos:exactMatch	neuroglial cell	glial cell	CL:0000125	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	bonemarrow-codex-chop
242	Squamous_epithelial	squamous epithelial cell	squamous epithelial cell	CL:0000076	skos:exactMatch	squamous epithelial cell	squamous epithelial cell	CL:0000076	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	esophagus-codex-stanford
243	Squamous_epithelial	squamous epithelial cell	squamous epithelial cell	CL:0000076	skos:exactMatch	squamous epithelial cell	squamous epithelial cell	CL:0000076	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	tonsil-codex-stanford
244	Stem	stem cell	stem cell	CL:0000034	skos:exactMatch	stem cell	stem cell	CL:0000034	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
245	Stroma	stromal cell	stromal cell	CL:0000499	skos:exactMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	esophagus-codex-stanford
246	Stroma	stromal cell	stromal cell	CL:0000499	skos:exactMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	intestine-codex-stanford
247	Stroma	stromal cell	stromal cell	CL:0000499	skos:exactMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	tonsil-codex-stanford
248	PDPN	stromal cell:podoplanin+	stromal cell:podoplanin-positive	CL:0000499	skos:narrowMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	esophagus-codex-stanford
249	PDPN	stromal cell:podoplanin+	stromal cell:podoplanin-positive	CL:0000499	skos:narrowMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	tonsil-codex-stanford
250	T	t cell	T cell	CL:0000084	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	esophagus-codex-stanford
251	gd T Cells	t cell	T cell	CL:0000084	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
252	T	t cell	T cell	CL:0000084	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	tonsil-codex-stanford
253	CD8 T	t cell	T cell	CL:0000084	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
254	CD8+_T_cell_CD_4+_T_cell	t cell	T cell	CL:0000084	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
255	CD4 T Cells	t cell:cd4+	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
256	CD4 T	t cell:cd4+	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
257	CD4+ T cell	t cell:cd4+	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
258	Th	t cell:cd4+	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
259	T helper	t cell:cd4+	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
260	T-Helper	t cell:cd4+	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-celldive-ge
261	CD4+ T-Cell	t cell:cd4+ alpha-beta	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
262	CD4+	t cell:cd4+ alpha-beta	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
263	CD4+_T_cell_2	t cell:cd4+ alpha-beta	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
264	CD4+_T_cell_3	t cell:cd4+ alpha-beta	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
265	CD4_+_Tcell/macrophage	t cell:cd4+ alpha-beta	lung resident memory CD4-positive, alpha-beta ...	CL:4033038	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
266	CD4+_T_cell_1	t cell:cd4+ alpha-beta	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
267	CD4+ T cell	t cell:cd4+ alpha-beta	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
268	CD4T	t cell:cd4+ alpha-beta	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
269	T_CD4+	t cell:cd4+ alpha-beta effector	effector CD4-positive, alpha-beta T cell	CL:0001044	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
270	CD4 Memory T cells	t cell:cd4+ alpha-beta memory	CD4-positive, alpha-beta memory T cell	CL:0000897	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	spleen-codex-ufl
271	T_CD4+_naive	t cell:cd4+ alpha-beta naive thymus-derived	naive thymus-derived CD4-positive, alpha-beta ...	CL:0000895	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
272	PD1+ T helper	t cell:cd4+ pdl1+	CD4-positive, alpha-beta T cell:pdl1-positive	CL:0000624	skos:narrowMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
273	T-Killer	t cell:cd8+	CD8-positive, alpha-beta T cell	CL:0000625	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-celldive-ge
274	CD8+ T cell_2	t cell:cd8+	lung resident memory CD8-positive, alpha-beta ...	CL:4033039	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
275	CD8 T Cells	t cell:cd8+	CD8-positive, alpha-beta T cell	CL:0000625	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
276	CD8+_T_cell_1	t cell:cd8+	lung resident memory CD8-positive, alpha-beta ...	CL:4033039	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
277	T_CD8+_cytotoxic	t cell:cd8+	CD8-positive, alpha-beta T cell	CL:0000625	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
278	T_CD8+_naive	t cell:cd8+	CD8-positive, alpha-beta T cell	CL:0000625	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
279	Tc	t cell:cd8+	CD8-positive, alpha-beta T cell	CL:0000625	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
280	CD8 + T cell_1	t cell:cd8+	lung resident memory CD8-positive, alpha-beta ...	CL:4033039	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
281	CD8+_T_cell_3	t cell:cd8+	lung resident memory CD8-positive, alpha-beta ...	CL:4033039	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
282	Tc cell	t cell:cd8+	CD8-positive, alpha-beta T cell	CL:0000625	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
283	CD8+_T_cell_2	t cell:cd8+	lung resident memory CD8-positive, alpha-beta ...	CL:4033039	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
284	CD8+ T	t cell:cd8+ alpha-beta	CD8-positive, alpha-beta T cell	CL:0000625	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
285	CD8T	t cell:cd8+ alpha-beta	CD8-positive, alpha-beta T cell	CL:0000625	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
286	CD8+	t cell:cd8+ alpha-beta effector memory	effector memory CD8-positive, alpha-beta T cell	CL:0000913	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
287	CD8 Memory T cells	t cell:cd8+ alpha-beta memory	CD8-positive, alpha-beta memory T cell	CL:0000909	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	spleen-codex-ufl
288	CD8+ T-Cell	t cell:cd8+ alpha-beta regulatory	CD8-positive, alpha-beta regulatory T cell	CL:0000795	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
289	T_CD8+_CD161+	t cell:cd8+ cd161+	CD8-positive, alpha-beta T cell:CD161-positive	CL:0000625	skos:narrowMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
290	PD1+ Tc	t cell:cd8+ pdl1+	CD8-positive, alpha-beta T cell:pdl1-positive	CL:0000625	skos:narrowMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
291	T_CD4+_TfH_GC	t cell:follicular helper	T follicular helper cell	CL:0002038	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
292	T_CD4+_TfH	t cell:follicular helper	T follicular helper cell	CL:0002038	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
293	NKT	t cell:mature natural killer	mature NK T cell	CL:0000814	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
294	NKT	t cell:mature natural killer	mature NK T cell	CL:0000814	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
295	Tissue T	t cell:memory	memory T cell	CL:0000813	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
296	Naive T	t cell:naive	naive T cell	CL:0000898	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
297	T reg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
298	Treg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
299	Treg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
300	Treg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
301	T_Treg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
302	T-Reg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-celldive-ge
303	Tregs	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
304	T_TfR	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
305	T_TIM3+	t cell:tim3+	T cell:tim3-positive	CL:0000084	skos:narrowMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
306	DP	thymocyte:cd4-intermediate cd8+ double-positive	CD4-intermediate, CD8-positive double-positive...	CL:0002430	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
307	TA2	transit amplifying cell	transit amplifying cell	CL:0009010	skos:exactMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
308	TA	transit amplifying cell	transit amplifying cell	CL:0009010	skos:exactMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
309	TA1	transit amplifying cell	transit amplifying cell	CL:0009010	skos:exactMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
310	CyclingTA	transit amplifying cell:proliferating	transit amplifying cell:proliferating	CL:0009010	skos:narrowMatch	transit amplifying cell	transit amplifying cell	CL:0009010	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
311	Cycling TA	transit amplifying cell:proliferating	transit amplifying cell:proliferating	CL:0009010	skos:narrowMatch	enterocyte	enterocyte	CL:0000584	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
312	EVT2	trophoblast:hla-g minus, cd57- ck7 low extravi...	extravillous trophoblast:hla-g-negative cd57-n...	CL:0008036	skos:narrowMatch	trophoblast	trophoblast cell	CL:0000351	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	maternalfetalinterface-mibitof-stanford
313	EVT1c	trophoblast:hla-g+ cd56+ extravillous	extravillous trophoblast:hla-g-positive cd56-p...	CL:0008036	skos:narrowMatch	trophoblast	trophoblast cell	CL:0000351	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	maternalfetalinterface-mibitof-stanford
314	EVT1a	trophoblast:hla-g+ ck7+ extravillous	extravillous trophoblast:hla-g-positive ck7-po...	CL:0008036	skos:narrowMatch	trophoblast	trophoblast cell	CL:0000351	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	maternalfetalinterface-mibitof-stanford
315	EVT1b	trophoblast:hla-g+ ck7- extravillous	extravillous trophoblast:hla-g-positive ck7-ne...	CL:0008036	skos:narrowMatch	trophoblast	trophoblast cell	CL:0000351	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	maternalfetalinterface-mibitof-stanford
316	Tuft	tuft cell:intestinal	intestinal tuft cell	CL:0019032	skos:exactMatch	tuft cell	brush cell	CL:0002204	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
317	Tumor	tumor cell	neoplastic cell	CL:0001063	skos:exactMatch	abnormal cell	abnormal cell	CL:0001061	skos:exactMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	skin-confocal-sorgerlab
318	indistinct	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	spleen-codex-ufl
319	Others	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	oralcavity-codex-czi
320	UNK_3	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	lung-codex-urmc
321	UNK_2	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	lung-codex-urmc
322	UNK_5_ambiguous	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	lung-codex-urmc
323	UNK_1_APC	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	lung-codex-urmc
324	UNK_3_(col1a1-driven_cluster)	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	lung-codex-urmc
325	UNK_4_(col1a1_driven_cluster)	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	lung-codex-urmc
326	Unknown	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	colon-xenium-stanford
327	other	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	maternalfetalinterface-mibitof-stanford
328	UNK_1	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	lung-codex-urmc
329	Unknown_lowcount	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	colon-xenium-stanford
330	unknown	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	pancreas-geomx-ufl
331	Artifact	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	bonemarrow-codex-chop
332	Undetermined	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	bonemarrow-codex-chop
333	Autofluorescent	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	bonemarrow-codex-chop
334	CD44+ Undetermined	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	bonemarrow-codex-chop
335	Other	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	colon-cycif-sorgerlab
336	ENDO_CD8+_T_Cell	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	lung-codex-urmc
337	Unknown	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	skin-confocal-sorgerlab

# Save unique_combinations DataFrame to a CSV file in the data/mapping_files directory.
unique_combinations.to_csv(os.path.join(basepath, "mapping_files", "generated_cell_type_complete_crosswalk.csv"), index=False)

# Print if there are any duplicates in the Original Cell Type column of the unique combinations DataFrame.
if unique_combinations['Original Cell Type'].duplicated().any():
    print("There are duplicates in the Original Cell Type column of the unique combinations DataFrame. This is expected because same Original Cell Type can be in multiple Tissue Types.")

# Print the duplicate values with their row indices.
duplicates = unique_combinations[unique_combinations['Original Cell Type'].duplicated(keep=False)]
duplicates

There are duplicates in the Original Cell Type column of the unique combinations DataFrame. This is expected because same Original Cell Type can be in multiple Tissue Types.

	Original Cell Type	Level Three Cell Type	Level Three CL Label	Level Three CL ID	CL_Match/3	Level Two Cell Type	Level Two CL Label	Level Two CL ID	CL_Match/2	Level One Cell Type	Level One CL Label	Level One CL ID	CL_Match/1	Tissue Type
2	Adipocytes	adipocyte	adipocyte	CL:0000136	skos:exactMatch	adipocyte	adipocyte	CL:0000136	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	oralcavity-codex-czi
3	Adipocytes	adipocyte	adipocyte	CL:0000136	skos:exactMatch	adipocyte	adipocyte	CL:0000136	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	colon-xenium-stanford
6	B	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	tonsil-codex-stanford
8	B cells	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
10	B cells	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
11	B	b cell	B cell	CL:0000236	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
30	DC	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
32	DC	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
33	DC	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	dendritic cell	dendritic cell	CL:0000451	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
43	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	lymphnode-codex-yale
44	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	skin-celldive-ge
45	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	skin-confocal-sorgerlab
46	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	pancreas-geomx-ufl
47	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	intestine-codex-stanford
49	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	tonsil-codex-stanford
50	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	colon-xenium-stanford
51	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	maternalfetalinterface-mibitof-stanford
52	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	colon-cycif-sorgerlab
53	Endothelial	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	endothelial cell	endothelial cell	CL:0000115	skos:exactMatch	esophagus-codex-stanford
96	Fibroblasts	fibroblast	fibroblast	CL:0000057	skos:exactMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	oralcavity-codex-czi
97	Fibroblasts	fibroblast	fibroblast	CL:0000057	skos:exactMatch	fibroblast	fibroblast	CL:0000057	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	maternalfetalinterface-mibitof-stanford
109	Goblet	goblet cell	goblet cell	CL:0000160	skos:exactMatch	goblet cell	goblet cell	CL:0000160	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
110	Goblet	goblet cell	goblet cell	CL:0000160	skos:exactMatch	goblet cell	goblet cell	CL:0000160	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	colon-xenium-stanford
136	Innate	lymphoid cell:innate	innate lymphoid cell	CL:0001065	skos:exactMatch	lymphoid cell	lymphocyte	CL:0000542	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	tonsil-codex-stanford
138	Innate	lymphoid cell:innate	innate lymphoid cell	CL:0001065	skos:exactMatch	lymphoid cell	lymphocyte	CL:0000542	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	esophagus-codex-stanford
143	Macrophage	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
145	Macrophages	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
146	Macrophages	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
148	Macrophage	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	skin-confocal-sorgerlab
153	Macrophages	macrophage	macrophage	CL:0000235	skos:exactMatch	macrophage	macrophage	CL:0000235	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	spleen-codex-ufl
167	Mast	mast cell	mast cell	CL:0000097	skos:exactMatch	mast cell	mast cell	CL:0000097	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
169	Mast	mast cell	mast cell	CL:0000097	skos:exactMatch	mast cell	mast cell	CL:0000097	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
170	Mast	mast cell	mast cell	CL:0000097	skos:exactMatch	mast cell	mast cell	CL:0000097	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
178	Monocytes	monocyte	monocyte	CL:0000576	skos:exactMatch	monocyte	monocyte	CL:0000576	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
179	Monocytes	monocyte	monocyte	CL:0000576	skos:exactMatch	monocyte	monocyte	CL:0000576	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
187	VSMC	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	lymphnode-codex-yale
189	SmoothMuscle	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	tonsil-codex-stanford
191	SmoothMuscle	muscle cell:smooth	smooth muscle cell of the esophagus	CL:0002599	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	esophagus-codex-stanford
192	VSMC	muscle cell:smooth	smooth muscle cell	CL:0000192	skos:exactMatch	muscle cell	muscle cell	CL:0000187	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	bonemarrow-codex-chop
207	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
213	NK	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	natural killer cell	natural killer cell	CL:0000623	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
216	Nerve	neuron	neuron	CL:0000540	skos:exactMatch	neuron	neuron	CL:0000540	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	esophagus-codex-stanford
218	Nerve	neuron	neuron	CL:0000540	skos:exactMatch	neuron	neuron	CL:0000540	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	tonsil-codex-stanford
219	Nerve	neuron	neuron	CL:0000540	skos:exactMatch	neuron	neuron	CL:0000540	skos:exactMatch	neural cell	neural cell	CL:0002319	skos:exactMatch	intestine-codex-stanford
225	Paneth	paneth cell	paneth cell	CL:0000510	skos:exactMatch	paneth cell	paneth cell	CL:0000510	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	intestine-codex-stanford
226	Paneth	paneth cell	paneth cell	CL:0000510	skos:exactMatch	paneth cell	paneth cell	CL:0000510	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	esophagus-codex-stanford
228	Plasma Cells	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	bonemarrow-codex-chop
230	Plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	tonsil-codex-stanford
231	Plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-xenium-stanford
232	Plasma Cells	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
233	Plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
234	Plasma	plasma cell	plasma cell	CL:0000786	skos:exactMatch	b cell	B cell	CL:0000236	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	esophagus-codex-stanford
242	Squamous_epithelial	squamous epithelial cell	squamous epithelial cell	CL:0000076	skos:exactMatch	squamous epithelial cell	squamous epithelial cell	CL:0000076	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	esophagus-codex-stanford
243	Squamous_epithelial	squamous epithelial cell	squamous epithelial cell	CL:0000076	skos:exactMatch	squamous epithelial cell	squamous epithelial cell	CL:0000076	skos:exactMatch	epithelial cell	epithelial cell	CL:0000066	skos:exactMatch	tonsil-codex-stanford
245	Stroma	stromal cell	stromal cell	CL:0000499	skos:exactMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	esophagus-codex-stanford
246	Stroma	stromal cell	stromal cell	CL:0000499	skos:exactMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	intestine-codex-stanford
247	Stroma	stromal cell	stromal cell	CL:0000499	skos:exactMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	tonsil-codex-stanford
248	PDPN	stromal cell:podoplanin+	stromal cell:podoplanin-positive	CL:0000499	skos:narrowMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	esophagus-codex-stanford
249	PDPN	stromal cell:podoplanin+	stromal cell:podoplanin-positive	CL:0000499	skos:narrowMatch	stromal cell	stromal cell	CL:0000499	skos:exactMatch	mesenchymal cell	mesenchymal cell	CL:0008019	skos:exactMatch	tonsil-codex-stanford
250	T	t cell	T cell	CL:0000084	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	esophagus-codex-stanford
252	T	t cell	T cell	CL:0000084	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	tonsil-codex-stanford
257	CD4+ T cell	t cell:cd4+	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	intestine-codex-stanford
267	CD4+ T cell	t cell:cd4+ alpha-beta	CD4-positive, alpha-beta T cell	CL:0000624	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lung-codex-urmc
293	NKT	t cell:mature natural killer	mature NK T cell	CL:0000814	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	lymphnode-codex-yale
294	NKT	t cell:mature natural killer	mature NK T cell	CL:0000814	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
298	Treg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	oralcavity-codex-czi
299	Treg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	maternalfetalinterface-mibitof-stanford
300	Treg	t cell:regulatory	regulatory T cell	CL:0000815	skos:exactMatch	t cell	T cell	CL:0000084	skos:exactMatch	immune cell	leukocyte	CL:0000738	skos:exactMatch	colon-cycif-sorgerlab
326	Unknown	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	colon-xenium-stanford
337	Unknown	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	unknown cell	cell:unknown	CL:0000000	skos:narrowMatch	skin-confocal-sorgerlab

Heatmap for Cell Type Distribution at Different Levels of Cell Type Annotation Across Datasets

# Method to create a heatmap visualization of cell type distribution across datasets.
def create_heatmap(df, normalize_method='percent', cell_type_level='Level Three Cell Type'):
    """
    Create an aesthetically enhanced heatmap visualization.
    """
    # Set the style and font
    plt.style.use("seaborn-v0_8-white") 
    plt.rcParams["svg.fonttype"] = 'none'  # to store text as text, not as path
    
    # Transpose the dataframe and sort index (cell types) alphabetically
    df_plot = df
    df_plot = df_plot.sort_index(axis=1)
    
    # Normalize the data
    if normalize_method == 'percent':
        df_plot = df_plot.div(df_plot.sum(axis=1), axis=0) * 100
    
    # Create binary mask for coloring
    binary_mask = (df_plot > 0).astype(float)
    
    # Calculate figure size
    width = max(16, len(df_plot.columns) * 0.4)
    height = max(8, len(df_plot.index) * 0.4)
    
    # Create figure with higher DPI for better quality
    fig, ax = plt.subplots(figsize=(width, height), dpi=150)
    
    # Define custom colors
    bg_color = '#ffffff'  # Pure white background
    present_color = '#D5A023'  # Professional blue, #D5A023
    absent_color = '#f8f9fa'  # Very light gray
    text_color = '#333333'  # Dark gray for text
    grid_color = '#e6e6e6'  # Light gray for grid
    
    # Set figure background color
    fig.patch.set_facecolor(bg_color)
    ax.set_facecolor(bg_color)
    
    # Create custom colormap
    custom_cmap = sns.color_palette([absent_color, present_color], n_colors=2)
    
    # Create annotations with custom formatting (float for non-zero, integer for zero)
    annotations = df_plot.copy()
    for i in range(len(annotations)):
        for j in range(len(annotations.columns)):
            val = annotations.iloc[i, j]
            if val == 0:
                annotations.iloc[i, j] = '0'
            else:
                annotations.iloc[i, j] = f'{val:.1f}'
    
    # Create heatmap with enhanced styling
    ax = sns.heatmap(binary_mask,
                     cmap=custom_cmap,
                     annot=annotations,
                     fmt='',
                     cbar=False,
                     linewidths=0.5,
                     linecolor=grid_color,
                     annot_kws={
                         'size': 7,
                         'color': text_color,
                         'ha': 'center',
                         'va': 'center'
                     },
                     square=True)
    
    # Style the axis labels with better positioning
    plt.xticks(rotation=90, color=text_color, ha='center', va='top')
    plt.yticks(rotation=0, color=text_color, va='center')
    
    # Enhance axis labels with adjusted positioning
    ax.set_xlabel(cell_type_level, fontsize=11, fontweight='bold', color=text_color, labelpad=15)
    ax.set_ylabel('Tissue Type', fontsize=11, fontweight='bold', color=text_color, labelpad=10)
    
    # Add title with styling
    plt.title('Cell Type Distribution Across Datasets', 
             pad=20,
             fontsize=13,
             fontweight='bold',
             color=text_color)
    
    # Remove spines
    for spine in ax.spines.values():
        spine.set_visible(False)
    
    # Adjust layout with specific margins
    plt.tight_layout(pad=1.5)
    
    # Save figure with high quality
    plt.savefig(f'{os.path.join(basepath, figures_output_dir)}/cell_type_distribution_binary_heatmap_{cell_type_level}.png',
                dpi=300,
                bbox_inches='tight',
                pad_inches=0.5,
                facecolor=bg_color)
    
    # Save fig as svg
    plt.savefig(f'{os.path.join(basepath, figures_output_dir)}/cell_type_distribution_binary_heatmap_{cell_type_level}.svg',
                dpi=600,
                bbox_inches='tight',
                pad_inches=0.5,
                facecolor=bg_color)
    plt.show()

heatmap_df_loriginal = df_all_data.groupby(['Tissue Type', 'Original Cell Type']).size().unstack(fill_value=0)
# Create a heatmap of the summary DataFrame
create_heatmap(heatmap_df_loriginal, normalize_method='percent', cell_type_level='Original Cell Type')
heatmap_df_loriginal

Original Cell Type	AEC	AT1 _2	AT1_1	AT2	AT2_1	AT2_2	AT2_p	Acinar Cells	Acini	Adipo-MSC	Adipocyte	Adipocytes	Artifact	Autofluorescent	B	B Cells	B cell	B cells	B cells, red pulp	B-Cells	B_Cycling	B_GC_DZ	B_GC_LZ	B_GC_prePB	B_IFN	B_activated	B_cell_1	B_cell_macrophage_p?	B_mem	B_naive	B_plasma	B_preGC	Basal Keratincytes	Best4+ Enterocytes	Beta cell	CAP_ENDO	CD11B+ CD11C- cells	CD34+ CD61+	CD4 Memory T cells	CD4 T	CD4 T Cells	CD4+	CD4+ T cell	CD4+ T-Cell	CD4+_T_cell_1	CD4+_T_cell_2	CD4+_T_cell_3	CD44+ Undetermined	CD4T	CD4_+_Tcell/macrophage	CD57+ Enterocyte	CD66+ Enterocyte	CD68	CD7+ Immune	CD8 + T cell_1	CD8 Memory T cells	CD8 T	CD8 T Cells	CD8+	CD8+ T	CD8+ T cell_2	CD8+ T-Cell	CD8+_T_cell_1	CD8+_T_cell_2	CD8+_T_cell_3	CD8+_T_cell_CD_4+_T_cell	CD8T	CLP	Cancer Associated Fibroblasts	Crypt Fibroblasts 1	Crypt Fibroblasts 2	Crypt Fibroblasts 3	Crypt Fibroblasts 4	Cycling TA	CyclingTA	DC	DC_CCR7+	DC_cDC1	DC_cDC2	DC_pDC	DDB2	DN Lymphocyte	DP	DP Lymphocyte	Dendritic Cells	Dendritic cells	Ductal Epithelial Cells	Ductal cell	Ducts	ENDO_1	ENDO_CD8+_T_Cell	ENDO_SMC	EVT1a	EVT1b	EVT1c	EVT2	Early Myeloid Progenitor	Endo_2	Endo_p	Endosteal	Endothelial	Enterocyte	Enterocyte Progenitors	Enterocytes	Enteroendocrine	Epithelial	Erythroblast	Erythroid	FDC	Fibroblasts	Fol B cells	GATA1neg_Mks	GATA1pos_Mks	GC	GMP	GMP/Myeloblast	Glandular	Glandular_epi	Glia	Glial/Neuron	Goblet	HSC	HSPC	ICC	ILC	ILCs	Immature Enterocytes	Immature Goblet	Immature_B_Cell	Innate	Intermediate Myeloid	Ionocytes	KI67	Keratinocyte	Ki67 proliferating	Ki67+ Tumor/Epithelial	Langerhan cells	Langerhans Cells	Leukocyte	Lung_Epithelial_1	Lung_Epithelial_4	Lung_Epithelial_p	Lung_Epithelil_2_CD4+_T_cell	Lymphatic	Lymphatic Endothelial Cells	Lymphatic Vascular Cells	Lymphatic endothelial cells	Lymphatic_Endothelium	Lymphocyte(III)	M1 Macrophage	M2 Macrophage	MEP/Early Erythroblast	MUC1+ Enterocyte	Mac1a	Mac1b	Mac2a	Mac2b	Mac2c	Macrophage	Macrophage(I)	Macrophage(II)	Macrophage(III)	Macrophage(IV)	Macrophages	Macrophages_M1	Macrophages_M2	Mast	Mast Cells	Mast cell	Mature Myeloid	Melanocytes	Memory B	Merkel Cells	Monocyte-Macrophage	Monocytes	Mural Cells	Muscle/Fibroblast	Myeloid	Myeloid cells	Myoepithelial Cells	Myofibroblasts	Myofibroblasts/Smooth Muscle 1	Myofibroblasts/Smooth Muscle 2	Myofibroblasts/Smooth Muscle 3	NK	NK Cells	NK1	NK2	NK3	NK4	NKT	NPM1 Mutant Blast	Naive B	Naive T	Nerve	Neuroendocrine	Neurons	Neutrophil	Neutrophils	Neutrophils/Monocytes	Non-Classical Monocyte	Other	Other Immune	Others	P53	PD1+ T helper	PD1+ Tc	PDL1+ Macrophage	PDL1+ Tumor/Epithelial	PDL1+ lymphocyte	PDPN	Paneth	Pericytes	Placental_Mac	Plasma	Plasma Cells	Podoplanin	SEC	SMC_1	SMC_2	SPINK2+ HSPC	Schwann Cells	Secretory_epithelial	Sinusoidal cells	Skeletal Myocytes	Smooth muscle	SmoothMuscle	Squamous_epithelial	Stem	Stroma	Suprabasal Keratinocytes	T	T helper	T reg	T-Helper	T-Killer	T-Reg	TA	TA1	TA2	THY1+ MSC	T_CD4+	T_CD4+_TfH	T_CD4+_TfH_GC	T_CD4+_naive	T_CD8+_CD161+	T_CD8+_cytotoxic	T_CD8+_naive	T_TIM3+	T_TfR	T_Treg	Tc	Tc cell	Th	Tissue T	Treg	Tregs	Tuft	Tumor	Tumor/Epithelial	UNK_1	UNK_1_APC	UNK_2	UNK_3	UNK_3_(col1a1-driven_cluster)	UNK_4_(col1a1_driven_cluster)	UNK_5_ambiguous	Undetermined	Unknown	Unknown_lowcount	VEC Progen	VSMC	Vascular Endothelial Cells	Villus Fibroblasts WNT5B+	blood endothelial	gd T Cells	indistinct	keratinocytes	lung Intersitial macrophage	lymphatic Endothelium	macrophage	macrophage_2	macrophage_3	macrophage_CD1c+_myeloidDC	macrophage_p	megakaryocyte	muscle	myofibroblast	neutrophil	neutrophil_2	other	pDC	smooth muscle 1	smooth muscle_2	unknown
Tissue Type
bonemarrow-codex-chop	7127	0	0	0	0	0	0	0	0	7967	23798	0	28818	40530	0	0	0	0	0	67639	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	387	0	0	0	0	0	40122	0	0	0	1476	0	0	0	0	0	0	0	0	0	0	0	0	0	35078	0	0	0	0	0	165	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	81582	0	0	4026	0	0	0	0	0	0	23866	253710	0	0	0	3649	2635	0	945	1960	0	0	0	0	0	61	5130	0	0	0	0	0	11874	0	110357	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	558	0	0	0	0	0	0	0	0	0	0	0	27731	0	0	0	0	0	245083	0	0	0	0	46785	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	39861	0	0	0	0	0	0	0	0	6218	0	0	0	0	0	0	0	0	0	0	0	0	0	0	38853	0	24640	0	0	2250	52	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4846	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12570	0	0	0	2939	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8800	0	0	0
colon-cycif-sorgerlab	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	513904	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	46504	0	204156	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	870316	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	391199	0	0	0	0	0	0	0	0	0	0	0	0	864987	0	0	0	0	0	0	0	0	0	0	125601	43643	398528	192296	0	0	0	0	0	0	0	0	0	0	0	0	0	1517623	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	644325	0	0	0	162434	52444	128716	80686	31568	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	457493	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1105099	0	0	427925	0	0	0	4498694	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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skin-confocal-sorgerlab	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	257	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	751	0	0	8176	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	515	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5985	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2042	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2154	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	390	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1103	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1227	0	0	0	23908	0	0	0	0	0	0	0	0	0	7768	0	0	0	0	0	0	0	0	948	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
spleen-codex-ufl	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	56246	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53983	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	91948	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98430	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44566	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103112	0	0	0	0	0	0	0	0	0	0	0	0	0	0	72380	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	159397	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11069	0	0	0	0	0	0	191107	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	48199	0	61961	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
tonsil-codex-stanford	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31867	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3295	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61932	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	281	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11561	0	0	0	2243	0	0	0	0	0	0	0	0	0	0	0	152	5013	0	8946	0	48678	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

heatmap_df_l3 = df_all_data.groupby(['Tissue Type', 'Level Three Cell Type']).size().unstack(fill_value=0)
# Create a heatmap of the summary DataFrame
create_heatmap(heatmap_df_l3, normalize_method='percent', cell_type_level='Level Three Cell Type')
heatmap_df_l3

Level Three Cell Type	acinar cell of salivary gland	adipocyte	b cell	b cell:activated	b cell:follicular	b cell:germinal center	b cell:germinal center pre-plasmablast	b cell:immature	b cell:interferon	b cell:memory	b cell:naive	b cell:pre-germinal center	b cell:proliferating	beta cell:pancreatic	cell:cd34+ cd61+	cell:proliferating	dendritic cell	dendritic cell:cd11b+	dendritic cell:conventional 1	dendritic cell:conventional 2	dendritic cell:follicular	dendritic cell:migratory	dendritic cell:plasmacytoid	endosteal cell	endothelial cell	endothelial cell of artery	endothelial cell of capillary	endothelial cell of lymphatic vessel	endothelial cell of sinusoid	endothelial cell of vascular tree	enterocyte	enterocyte:cd57+	enterocyte:cd66+	enterocyte:immature	enterocyte:muc1+	enterocyte:progenitor	enteroendocrine cell	enteroycte:best4+	epithelial cell	epithelial cell:ductal	epithelial cell:ki67+ proliferating tumor	epithelial cell:pdl1+ tumor	epithelial cell:secretory	erythroblast	erythroblast:basophilic	erythroid lineage cell	fibroblast	fibroblast:cancer associated	fibroblast:crypt 1	fibroblast:crypt 2	fibroblast:crypt 3	fibroblast:crypt 4	fibroblast:wnt5b+ villus	glandular cell of esophagus	glandular cell of placenta	glial cell	glial cell/neuron	goblet cell	goblet cell:immature	granulocyte monocyte progenitor cell	granulocyte monocyte progenitor cell/myeloblast	hematopoietic stem and progenitor cell:spink2+	hematopoietic stem cell	hofbauer cell	immune cell	interstitial cell of cajal	keratinocyte	keratinocyte:ddb2+	keratinocyte:ki67+ proliferating	keratinocyte:p53+	langerhans cell	leukocyte	lymphocyte:cd7+	lymphocyte:double-negative	lymphocyte:double-positive alpha-beta	lymphocyte:iii	lymphocyte:pdl1+	lymphoid cell:innate	lymphoid progenitor cell:common	macrophage	macrophage:1a	macrophage:1b	macrophage:2a	macrophage:2b	macrophage:2c	macrophage:i	macrophage:ii	macrophage:iii	macrophage:inflammatory	macrophage:interstitial	macrophage:iv	macrophage:pdl1+	mast cell	megakaryocyte	megakaryocyte:gata1+	megakaryocyte:gata1-	mesenchymal stem cell of adipose tissue	mesenchymal stem/stromal cell:thy1+	mixed t cell/epithelial cell population	monocyte	monocyte:non-classical	mural cell	muscle cell	muscle cell:skeletal	muscle cell:smooth	mutant blast:npm1	myeloid cell	myeloid cell:intermediate	myeloid cell:mature	myeloid progenitor cell:common	myoepithelial cell	myofibroblast	myofibroblast cell:smooth muscle 1	myofibroblast cell:smooth muscle 2	myofibroblast cell:smooth muscle 3	natural killer cell	neoplastic cell	neuroendocrine cell	neuron	neutrophil	neutrophil/monocyte	paneth cell	pericyte	plasma cell	pneumocyte:type 1	pneumocyte:type 2	schwann cell	squamous epithelial cell	stem cell	stromal cell	stromal cell:podoplanin+	t cell	t cell:cd4+	t cell:cd4+ alpha-beta	t cell:cd4+ alpha-beta effector	t cell:cd4+ alpha-beta memory	t cell:cd4+ alpha-beta naive thymus-derived	t cell:cd4+ pdl1+	t cell:cd8+	t cell:cd8+ alpha-beta	t cell:cd8+ alpha-beta effector memory	t cell:cd8+ alpha-beta memory	t cell:cd8+ alpha-beta regulatory	t cell:cd8+ cd161+	t cell:cd8+ pdl1+	t cell:follicular helper	t cell:mature natural killer	t cell:memory	t cell:naive	t cell:regulatory	t cell:tim3+	thymocyte:cd4-intermediate cd8+ double-positive	transit amplifying cell	transit amplifying cell:proliferating	trophoblast:hla-g minus, cd57- ck7 low extravillous	trophoblast:hla-g+ cd56+ extravillous	trophoblast:hla-g+ ck7+ extravillous	trophoblast:hla-g+ ck7- extravillous	tuft cell:intestinal	tumor cell	unknown cell
Tissue Type
bonemarrow-codex-chop	0	23798	67639	0	0	0	0	11874	0	0	0	0	0	0	387	0	0	0	0	0	0	0	8800	4026	0	7127	0	0	24640	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23866	558	253710	0	0	0	0	0	0	0	0	0	0	0	0	0	945	1960	2250	5191	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	165	27731	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2635	3649	7967	4846	0	46785	6218	0	0	0	2939	39861	0	110357	245083	81582	0	0	0	0	0	0	0	0	0	0	0	0	0	38853	0	0	52	0	0	0	0	0	0	40122	0	0	0	0	0	0	0	0	35078	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	83394
colon-cycif-sorgerlab	0	0	513904	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	870316	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	391199	80686	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	46504	204156	864987	31568	0	0	0	0	0	0	0	0	125601	43643	398528	0	0	192296	128716	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1517623	0	0	0	0	4498694	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	457493	0	0	0	0	162434	1105099	0	0	0	0	0	52444	0	0	0	0	427925	0	0	0	0	0	0	0	0	0	0	644325
colon-xenium-stanford	0	19998	0	0	0	0	0	0	0	6071	18682	0	0	0	0	0	280	0	0	0	0	0	0	0	100459	0	0	1678	0	0	23276	0	0	84378	0	38052	8859	48830	0	0	0	0	0	0	0	0	0	174781	11540	1989	17393	21553	7787	0	0	23129	0	72513	688263	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	79329	0	0	0	0	0	0	0	0	0	0	0	0	57344	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	102913	5611	39474	0	0	0	1632	0	0	0	82636	43345	0	0	0	0	136725	0	0	0	0	55167	0	0	0	0	0	0	135197	0	0	0	0	0	0	0	6920	3800	0	0	267320	150379	0	0	0	0	15315	0	86576
esophagus-codex-stanford	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6181	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	658	0	0	0	0	0	0	0	0	0	0	14690	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4282	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9023	0	0	0	0	0	0	0	0	0	0	0	0	0	2047	0	0	275	0	1177	0	0	0	1077	0	4218	914	1416	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
intestine-codex-stanford	0	0	35506	0	0	0	0	0	0	0	0	0	0	0	0	0	32002	0	0	0	0	0	0	0	180762	0	0	64498	0	0	484864	1895	49441	0	17869	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	163170	0	0	0	0	0	0	0	33832	0	0	0	0	0	0	7174	0	0	0	0	0	0	112478	0	0	0	0	0	0	0	0	21825	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	375143	0	0	0	0	0	0	0	0	0	0	5027	0	14970	76903	14657	0	21381	0	128320	0	0	0	0	0	212937	0	0	117028	0	0	0	0	0	0	200401	0	0	0	0	0	0	0	0	0	0	0	0	57253	82849	0	0	0	0	0	0	0
lung-codex-urmc	0	0	1314	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	204947	0	46307	17253	0	0	0	0	0	0	0	0	0	0	64678	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	12297	0	0	0	0	0	0	0	163004	0	0	0	0	0	0	0	0	0	229	0	0	7495	5595	0	0	0	0	36072	0	0	0	0	0	84712	0	0	0	0	0	0	0	0	0	0	0	0	0	0	46560	0	0	0	0	44182	185250	0	0	0	0	0	7623	0	128883	0	0	0	0	75999	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	76899
lymphnode-codex-yale	0	0	0	126134	0	507360	13922	0	4815	1842344	673104	25059	511309	0	0	0	0	0	31899	45018	26871	7842	195456	0	303403	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	267761	0	150671	0	0	0	0	0	0	0	0	0	0	0	0	39333	0	0	0	0	0	0	263671	0	0	0	0	32155	0	0	0	0	0	0	0	0	0	0	390251	0	0	0	0	0	0	0	417145	0	0	0	0	0	0	0	0	0	0	256204	0	731555	0	711188	0	0	0	0	77613	0	812221	56189	0	0	377378	20974	0	0	0	0	0	0	0	0	0	0
maternalfetalinterface-mibitof-stanford	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1831	0	0	0	0	0	0	0	19045	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	153458	0	0	0	0	0	0	0	18065	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5857	9507	42881	1765	6739	0	0	0	0	0	0	0	678	0	0	0	0	0	0	0	0	0	3084	0	0	0	0	0	0	0	0	62218	0	0	0	59780	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1922	0	0	0	0	0	5962	0	0	0	0	0	0	3236	0	0	85	0	0	0	0	2044	3203	21598	18199	0	0	36589
oralcavity-codex-czi	236528	1357	13227	0	0	0	0	0	0	0	0	0	0	0	0	0	17028	0	0	0	0	0	0	0	0	0	0	12820	0	66969	0	0	0	0	0	0	0	0	61383	116523	0	0	0	0	0	0	272689	0	0	0	0	0	0	0	0	0	2525	0	0	0	0	0	0	0	0	0	20805	0	0	0	1421	0	0	0	0	0	0	0	0	46804	0	0	0	0	0	0	0	0	0	0	0	0	576	0	0	0	0	0	0	2580	0	6807	0	490	0	0	0	0	0	0	102636	26475	0	0	0	6936	0	0	0	45147	0	0	0	6376	0	0	0	0	0	0	0	2209	8856	0	0	0	0	0	15512	0	0	0	0	0	0	0	0	0	0	14360	0	6764	0	0	0	0	0	0	0	0	296386
pancreas-geomx-ufl	0	0	0	0	0	0	0	0	0	0	0	0	0	124066	0	0	0	0	0	0	0	0	0	0	3280557	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3339841	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8147411
skin-celldive-ge	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22427	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4126	6834	1447	0	0	0	0	0	0	0	0	0	1133	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10945	0	0	0	0	0	337	0	0	0	0	0	0	0	0	0	0	1074	0	0	0	0	0	0	0	0	0	0	0
skin-confocal-sorgerlab	0	0	257	0	0	0	0	0	0	0	0	0	0	0	0	0	5985	751	0	0	0	0	0	0	2042	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	948	0	0	0	13	390	0	0	0	0	0	0	0	2154	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	515	8176	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1227	0	1103	0	0	0	0	0	0	0	0	0	23908	7768
spleen-codex-ufl	0	0	56246	0	98430	0	0	0	0	0	0	0	0	0	0	44566	0	0	0	0	0	0	0	0	0	0	0	11069	191107	48199	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103112	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	72380	0	0	0	0	0	0	0	0	0	0	0	0	0	159397	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53983	0	0	0	0	0	91948	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61961
tonsil-codex-stanford	0	0	31867	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3295	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61932	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	152	0	0	0	0	0	0	0	0	0	0	0	0	0	281	0	0	0	0	2243	0	0	0	5013	0	8946	11561	48678	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

heatmap_df_l2 = df_all_data.groupby(['Tissue Type', 'Level Two Cell Type']).size().unstack(fill_value=0)
# Create a heatmap of the summary DataFrame
create_heatmap(heatmap_df_l2, normalize_method='percent', cell_type_level='Level Two Cell Type')
heatmap_df_l2

Level Two Cell Type	abnormal cell	adipocyte	b cell	beta cell	dendritic cell	endocrine cell	endothelial cell	endothelial cell of artery	endothelial cell of capillary	endothelial cell of lymphatic vessel	endothelial cell of sinusoid	endothelial cell of vascular tree	enterocyte	epithelial cell	erythroid precursor	fibroblast	gland epithelium cell	goblet cell	hematopoietic stem and progenitor cell	immune cell	keratinocyte	langerhans cell	leukocyte	lymphoid cell	macrophage	mast cell	megakaryocyte	mesenchymal stem cell	mesenchymal stem/stromal cell	mixed t cell/epithelial cell population	monocyte	muscle cell	myeloid cell	myeloid precursor	myoepithelial cell	natural killer cell	neurecto-epithelial cell	neuroglial cell	neuroglial cell/neuron	neuron	neutrophil	paneth cell	pericyte	perivascular cell	progenitor cell	secretory cell of esophagus	skeletal stromal cell	squamous epithelial cell	stem cell	stromal cell	t cell	transit amplifying cell	trophoblast	tuft cell	type 1 pneumocyte	type 2 pneumocyte	unknown cell
Tissue Type
bonemarrow-codex-chop	39861	23798	118366	0	8800	0	0	7127	0	0	24640	0	0	0	278134	0	0	0	2250	0	0	0	0	0	27731	0	6671	7967	4846	0	53003	2939	245083	113262	0	0	0	52	0	0	0	0	0	0	81747	0	4026	0	5191	0	75200	0	0	0	0	0	83394
colon-cycif-sorgerlab	4970579	0	513904	0	0	0	870316	0	0	0	0	0	0	0	0	1517623	0	0	0	0	0	0	0	0	888784	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3352610	0	0	0	0	0	644325
colon-xenium-stanford	0	19998	68098	0	280	8859	100459	0	0	1678	0	0	461856	0	0	383041	0	760776	0	0	0	0	0	21	79329	57344	0	0	0	0	0	0	0	0	0	0	0	23129	0	1632	0	0	82636	0	0	0	0	0	136725	0	201084	150379	0	15315	0	0	86576
esophagus-codex-stanford	0	0	1177	0	0	0	6181	0	0	0	0	0	0	0	0	0	14690	0	0	0	0	0	0	4282	0	0	0	0	0	0	0	9023	0	0	0	0	0	0	0	2047	0	275	0	0	0	658	0	1077	0	5132	1416	0	0	0	0	0	0
intestine-codex-stanford	0	0	163826	0	32002	14970	180762	0	0	64498	0	0	694171	0	0	0	0	163170	0	0	0	0	0	7174	134303	0	0	0	0	0	0	375143	0	0	0	5027	33832	0	0	76903	14657	21381	0	0	0	0	0	0	0	212937	317429	0	0	0	0	0	0
lung-codex-urmc	0	0	1314	0	0	0	204947	0	46307	17253	0	0	0	64678	0	0	0	0	0	10	0	0	12297	0	163233	7495	5595	0	0	36072	0	84712	0	0	0	0	0	0	0	0	46560	0	0	0	0	0	0	0	0	0	212505	0	0	0	44182	185250	76899
lymphnode-codex-yale	0	0	4121192	0	307086	0	303403	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	267761	150671	39333	0	0	0	0	263671	32155	0	0	0	390251	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3043322	0	0	0	0	0	0
maternalfetalinterface-mibitof-stanford	0	0	0	0	1831	0	19045	0	0	0	0	0	0	0	0	215676	18065	0	0	0	0	0	0	0	66750	678	0	0	0	0	0	3084	0	0	0	59780	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11205	0	45044	0	0	0	36589
oralcavity-codex-czi	0	1357	19603	0	17028	0	0	0	0	12820	0	66969	0	61383	0	299164	353051	0	0	0	20805	1421	0	0	49384	576	0	0	0	0	0	490	0	0	102636	6936	0	0	2525	0	45147	0	0	6807	0	0	0	0	0	0	47701	0	0	0	0	0	296386
pancreas-geomx-ufl	0	0	0	124066	0	0	3280557	0	0	0	0	0	0	0	0	0	3339841	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8147411
skin-celldive-ge	0	0	0	0	0	0	22427	0	0	0	0	0	0	0	0	0	0	0	0	0	12407	0	0	0	1133	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12356	0	0	0	0	0	0
skin-confocal-sorgerlab	23908	0	257	0	6736	0	2042	0	0	0	0	0	0	0	0	0	0	0	0	0	948	13	390	0	2154	0	0	0	0	0	0	0	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11021	0	0	0	0	0	7768
spleen-codex-ufl	0	0	154676	0	0	0	0	0	0	11069	191107	48199	0	0	0	0	0	0	0	0	0	0	0	0	103112	0	0	0	0	0	0	0	72380	0	0	0	0	0	0	0	159397	0	0	0	0	0	0	0	0	0	145931	0	0	0	0	0	106527
tonsil-codex-stanford	0	0	34110	0	0	0	3295	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61932	0	0	0	0	0	0	0	152	0	0	0	0	0	0	0	281	0	0	0	0	0	0	0	5013	0	20507	48678	0	0	0	0	0	0

heatmap_df_l1 = df_all_data.groupby(['Tissue Type', 'Level One Cell Type']).size().unstack(fill_value=0)
# Create a heatmap of the summary DataFrame
create_heatmap(heatmap_df_l1, normalize_method='percent', cell_type_level='Level One Cell Type')
heatmap_df_l1

Level One Cell Type	endothelial cell	epithelial cell	hematopoietic precursor cell	immune cell	mesenchymal cell	mixed immune/epithelial cell population	neural cell	unknown cell
Tissue Type
bonemarrow-codex-chop	31767	0	531962	528183	38730	0	52	83394
colon-cycif-sorgerlab	870316	4970579	0	4755298	1517623	0	0	644325
colon-xenium-stanford	102137	1383531	0	556535	485675	0	24761	86576
esophagus-codex-stanford	6181	16700	0	6875	14155	0	2047	0
intestine-codex-stanford	245260	893692	0	674418	621912	0	76903	0
lung-codex-urmc	268507	294110	5595	443414	84712	36072	0	76899
lymphnode-codex-yale	303403	0	0	8556416	59026	0	0	0
maternalfetalinterface-mibitof-stanford	19045	63109	0	140244	218760	0	0	36589
oralcavity-codex-czi	79789	537875	0	187796	307818	0	2525	296386
pancreas-geomx-ufl	3280557	3463907	0	0	0	0	0	8147411
skin-celldive-ge	22427	12407	0	13489	0	0	0	0
skin-confocal-sorgerlab	2042	948	0	20589	0	0	0	31676
spleen-codex-ufl	250375	0	0	635496	0	0	0	106527
tonsil-codex-stanford	3295	5013	0	144720	20659	0	281	0

Bar Distribution of cell types across datasets

def create_bar_distribution_plot (df, cell_type_level='Original Cell Type', log_scale=True):
    # Count the occurrences of each cell type
    cell_type_counts = df[cell_type_level].value_counts()
    plt.rcParams["svg.fonttype"] = 'none'  # to store text as text, not as path

    # Create a bar plot using plotly
    fig = px.bar(x=cell_type_counts.index, 
                y=cell_type_counts.values,
                log_y=log_scale,  # Use log scale for y-axis
                # color=cell_type_counts.values,
                color_continuous_scale='golden',
                color_discrete_sequence=['#D5A023'], 
                title='Distribution of Cell Types Across All Datasets',
                labels={'x': 'Cell Type', 'y': 'Count'},
                template='plotly_white')

    y_axis_title = 'Count (log scale)' if log_scale else 'Count'

    # Update layout
    fig.update_layout(
        showlegend=False,
        xaxis_tickangle=270,
        height=600,
        width=1200,
        margin=dict(b=150),  # Increase bottom margin for long labels
        xaxis_title=cell_type_level,
        yaxis_title=y_axis_title,
        title_x=0.5,  # Center the title
        # yaxis=dict(type='log')  # Use log scale for better visualization
    )
    
    # Adjust layout with specific margins
    plt.tight_layout(pad=1.5)

    
    # Save figure with high quality
    plt.savefig(f'{os.path.join(basepath, figures_output_dir)}/cell_type_distribution_bar_plot_{cell_type_level}.png',
                dpi=300,
                bbox_inches='tight',
                pad_inches=0.5,
                # facecolor=bg_color
                )
    
    # Save fig as svg
    plt.savefig(f'{os.path.join(basepath, figures_output_dir)}/cell_type_distribution_bar_plot_{cell_type_level}.svg',
                dpi=600,
                bbox_inches='tight',
                pad_inches=0.5,
                # facecolor=bg_color
                )

    fig.show()

create_bar_distribution_plot(df_all_data, cell_type_level='Original Cell Type', log_scale=True)

<Figure size 640x480 with 0 Axes>

create_bar_distribution_plot(df_all_data, cell_type_level='Level Three Cell Type', log_scale=True)

<Figure size 640x480 with 0 Axes>

create_bar_distribution_plot(df_all_data, cell_type_level='Level Two Cell Type', log_scale=True)

<Figure size 640x480 with 0 Axes>

create_bar_distribution_plot(df_all_data, cell_type_level='Level One Cell Type', log_scale=True)

<Figure size 640x480 with 0 Axes>

create_bar_distribution_plot(df_all_data, cell_type_level='Level One Cell Type', log_scale=False)

<Figure size 640x480 with 0 Axes>

Donut Chart of Cell Type Distribution

def create_donut_chart_datasets_per_tissue(df):
    """
    Create a donut chart showing the distribution of unique datasets per tissue type.
    """
    # Get the data for the chart
    datasets_per_tissue = df.groupby('Tissue Type')['Dataset'].nunique().sort_values(ascending=False)
    
    # Create the donut chart using plotly
    fig = px.pie(
        values=datasets_per_tissue.values,
        names=datasets_per_tissue.index,
        title='Distribution of Unique Datasets per Tissue Type',
        hole=0.4,  # Creates the donut hole
        color_discrete_sequence=px.colors.qualitative.Set3
    )
    
    # Update layout for better appearance
    fig.update_layout(
        title_x=0.5,  # Center the title
        font=dict(size=12),
        showlegend=True,
        legend=dict(
            orientation="v",
            yanchor="middle",
            y=0.5,
            xanchor="left",
            x=1.05
        ),
        width=800,
        height=600,
        template='plotly_white'
    )
    
    # Update traces to show both percentage and count
    fig.update_traces(
        textposition='inside',
        textinfo='label+percent+value',  # Show label, percentage, and count
        textfont_size=9,  # Slightly smaller font to fit more text
        texttemplate='%{label}<br>%{percent}<br>(%{value})',  # Custom format with count
        marker=dict(line=dict(color='white', width=2))
    )
    
    # Add annotation in the center of the donut
    total_datasets = datasets_per_tissue.sum()
    fig.add_annotation(
        text=f"Total<br>{total_datasets}<br>Datasets",
        x=0.5, y=0.5,
        font_size=16,
        font_color="black",
        showarrow=False
    )
    
    # Save the figure
    fig.write_image(f'{os.path.join(basepath, figures_output_dir)}/datasets_per_tissue_donut_chart.png',
                    width=800, height=600, scale=2)
    fig.write_image(f'{os.path.join(basepath, figures_output_dir)}/datasets_per_tissue_donut_chart.svg',
                    width=800, height=600)
    
    # Show the chart
    fig.show()
    
    # Also print the underlying data
    print("Total number of unique datasets per each tissue type:")
    for tissue, count in datasets_per_tissue.items():
        print(f"{tissue}: {count}")
    print(f"\nTotal datasets across all tissues: {total_datasets}")

# Call the function
create_donut_chart_datasets_per_tissue(df_all_data)

Total number of unique datasets per each tissue type:
maternalfetalinterface-mibitof-stanford: 209
intestine-codex-stanford: 64
colon-xenium-stanford: 29
colon-cycif-sorgerlab: 25
bonemarrow-codex-chop: 20
oralcavity-codex-czi: 13
pancreas-geomx-ufl: 12
skin-celldive-ge: 10
spleen-codex-ufl: 6
lymphnode-codex-yale: 5
skin-confocal-sorgerlab: 2
lung-codex-urmc: 2
esophagus-codex-stanford: 1
tonsil-codex-stanford: 1

Total datasets across all tissues: 399

def create_donut_chart_cells_per_tissue(df):
    """
    Create a donut chart showing the distribution of total cells per tissue type.
    """
    # Get the data for the chart
    cells_per_tissue = df.groupby('Tissue Type')['Original Cell Type'].count().sort_values(ascending=False)
    
    # Create the donut chart using plotly
    fig = px.pie(
        values=cells_per_tissue.values,
        names=cells_per_tissue.index,
        title='Distribution of Total Cells per Tissue Type',
        hole=0.4,  # Creates the donut hole
        color_discrete_sequence=px.colors.qualitative.Set3
    )
    
    # Update layout for better appearance
    fig.update_layout(
        title_x=0.5,  # Center the title
        font=dict(size=12),
        showlegend=True,
        legend=dict(
            orientation="v",
            yanchor="middle",
            y=0.5,
            xanchor="left",
            x=1.05
        ),
        width=800,
        height=600,
        template='plotly_white'
    )
    
    # Update traces to show both percentage and count
    fig.update_traces(
        textposition='inside',
        textinfo='label+percent+value',  # Show label, percentage, and count
        textfont_size=9,  # Slightly smaller font to fit more text
        texttemplate='%{label}<br>%{percent}<br>(%{value:,})',  # Custom format with count
        marker=dict(line=dict(color='white', width=2))
    )
    
    # Add annotation in the center of the donut
    total_cells = cells_per_tissue.sum()
    fig.add_annotation(
        text=f"Total<br>{total_cells:,}<br>Cells",
        x=0.5, y=0.5,
        font_size=16,
        font_color="black",
        showarrow=False
    )
    
    # Save the figure
    fig.write_image(f'{os.path.join(basepath, figures_output_dir)}/cells_per_tissue_donut_chart.png',
                    width=800, height=600, scale=2)
    fig.write_image(f'{os.path.join(basepath, figures_output_dir)}/cells_per_tissue_donut_chart.svg',
                    width=800, height=600)
    
    # Show the chart
    fig.show()
    
    # Also print the underlying data
    print("Total number of cells per tissue type:")
    for tissue, count in cells_per_tissue.items():
        print(f"{tissue}: {count:,}")
    print(f"\nTotal cells across all tissues: {total_cells:,}")

# Call the function
create_donut_chart_cells_per_tissue(df_all_data)

Total number of cells per tissue type:
pancreas-geomx-ufl: 14,891,875
colon-cycif-sorgerlab: 12,758,141
lymphnode-codex-yale: 8,918,845
colon-xenium-stanford: 2,639,215
intestine-codex-stanford: 2,512,185
oralcavity-codex-czi: 1,412,189
bonemarrow-codex-chop: 1,214,088
lung-codex-urmc: 1,209,309
spleen-codex-ufl: 992,398
maternalfetalinterface-mibitof-stanford: 477,747
tonsil-codex-stanford: 173,968
skin-confocal-sorgerlab: 55,255
skin-celldive-ge: 48,323
esophagus-codex-stanford: 45,958

Total cells across all tissues: 47,349,496