For review post-doublet filtering, we'll partition cell types based on their CellTypist L3 label designations. Later, we'll perform clustering within each group for inspection.
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
warnings.simplefilter(action='ignore', category=RuntimeWarning)
from datetime import date
import hisepy
import os
import pandas as pd
import re
import scanpy as sc
out_dir = 'output/l3_types'
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
def cache_uuid_path(uuid):
cache_path = '/home/jupyter/cache/{u}'.format(u = uuid)
if not os.path.isdir(cache_path):
hise_res = hisepy.reader.cache_files([uuid])
filename = os.listdir(cache_path)[0]
cache_file = '{p}/{f}'.format(p = cache_path, f = filename)
return cache_file
def read_parquet_uuid(uuid):
cache_file = cache_uuid_path(uuid)
res = pd.read_parquet(cache_file)
return res
def read_adata_uuid(uuid):
cache_file = cache_uuid_path(uuid)
res = sc.read_h5ad(cache_file)
return res
def rm_cache_uuid(uuid):
cache_path = '/home/jupyter/cache/{u}'.format(u = uuid)
rm_call = 'rm -r {d}'.format(d = cache_path)
os.system(rm_call)
def format_cell_type(cell_type):
cell_type = re.sub('\\+', 'pos', cell_type)
cell_type = re.sub('-', 'neg', cell_type)
cell_type = re.sub(' ', '_', cell_type)
return cell_type
def element_id(n = 3):
import periodictable
from random import randrange
rand_el = []
for i in range(n):
el = randrange(0,118)
rand_el.append(periodictable.elements[el].name)
rand_str = '-'.join(rand_el)
return rand_str
l3_uuids = ['20e97e8f-2cb9-4fa6-bd84-ddcaf6a2c28b',
'd595ab6f-d1ad-4c7c-a8f6-395642927262',
'56e0840c-d432-45e3-ac57-4302b0e350a4',
'8bfe1a92-35c9-433a-9640-4d7cdd7cbad6']
l3_list = []
for l3_uuid in l3_uuids:
l3_list.append(read_parquet_uuid(l3_uuid))
l3_labels = pd.concat(l3_list)
l3_labels = l3_labels[['barcodes', 'AIFI_L3', 'AIFI_L3_score']]
Cells that were filtered in a previous notebook to remove most doublets and low-quality cells
search_id = 'lawrencium-chromium-vanadium'
Retrieve files stored in our HISE project store
ps_df = hisepy.list_files_in_project_store('cohorts')
ps_df = ps_df[['id', 'name']]
Filter for files from the previous notebook using our search_id
search_df = ps_df[ps_df['name'].str.contains(search_id)]
search_df = search_df.sort_values('name')
search_df.shape
(65, 2)
h5ad_uuids = {}
for i in range(search_df.shape[0]):
name = search_df['name'].tolist()[i]
if '.h5ad' in name:
group_name = re.sub('.+diha_','',name)
group_name = re.sub('_filtered.+','',group_name)
h5ad_uuids[group_name] = search_df['id'].tolist()[i]
h5ad_uuids
{'ASDC': '559cbab1-e3cd-438b-b951-ff7874555625', 'BR1_Female_Negative_CD14_monocyte': '40dfd96a-5795-479e-8ae7-5608f91db36d', 'BR1_Female_Negative_CD56dim_NK_cell': 'ceca06b2-f11c-40bf-988c-62ff51063c61', 'BR1_Female_Negative_Memory_CD4_T_cell': '5cd5c776-e44a-4b84-8869-48abce644ed7', 'BR1_Female_Negative_Memory_CD8_T_cell': 'c5d24858-9703-42ae-97cd-6834290b18a4', 'BR1_Female_Negative_Naive_CD4_T_cell': '50fe1d88-49a4-4eb0-bcc8-4ce983646163', 'BR1_Female_Positive_CD14_monocyte': 'e0270c3a-b428-4dd7-8c8e-f965814776c2', 'BR1_Female_Positive_CD56dim_NK_cell': '11b3c89c-8157-4b0e-bab3-e3198e8b1544', 'BR1_Female_Positive_Memory_CD4_T_cell': 'ac35ceb8-1272-477a-8e6b-ed33538ea4cc', 'BR1_Female_Positive_Memory_CD8_T_cell': '4a44b740-b280-4f5b-9aad-d0521fbb6fe2', 'BR1_Female_Positive_Naive_CD4_T_cell': '14dd7450-8773-4256-92b6-0b1084d187cb', 'BR1_Male_Negative_CD14_monocyte': '0fee75d4-6a98-47ec-b1f2-23ff7ad1c18e', 'BR1_Male_Negative_CD56dim_NK_cell': 'cb6f833b-f286-478f-acd2-989ea4a4c7b8', 'BR1_Male_Negative_Memory_CD4_T_cell': '8d566aba-47de-452c-b9f1-bad3d5713135', 'BR1_Male_Negative_Memory_CD8_T_cell': 'b2ef0d39-8861-406b-936a-bb242e6809b7', 'BR1_Male_Negative_Naive_CD4_T_cell': '943f09d1-3190-4422-b050-b355daa29360', 'BR1_Male_Positive_CD14_monocyte': 'af58fd39-0156-450f-a38c-3213c3cffc66', 'BR1_Male_Positive_CD56dim_NK_cell': 'aeb088bf-bcef-4170-b07c-0e3282615066', 'BR1_Male_Positive_Memory_CD4_T_cell': 'f1c45e38-12d6-4b77-89eb-51bb46de485b', 'BR1_Male_Positive_Memory_CD8_T_cell': '982f64fc-bfb0-476a-808a-77df2828091d', 'BR1_Male_Positive_Naive_CD4_T_cell': '10e95fd0-85e2-40b5-a0f1-3bb1f885ab15', 'BR2_Female_Negative_CD14_monocyte': '6621dac9-f9b9-422b-90f9-3ea31c6f9545', 'BR2_Female_Negative_CD56dim_NK_cell': 'f01ebaa1-aaab-44b0-83b9-4ce40b89acb4', 'BR2_Female_Negative_Memory_CD4_T_cell': '18661b9d-7973-46ba-a0c7-22d21cd1a70a', 'BR2_Female_Negative_Memory_CD8_T_cell': '461db2c7-2f5a-4fe1-b7ea-56f4fc7ffd05', 'BR2_Female_Negative_Naive_CD4_T_cell': '6a865cec-fe93-4414-803f-01594f48a454', 'BR2_Female_Positive_CD14_monocyte': 'ecf2cc80-4081-4e53-b596-5e17810acf5b', 'BR2_Female_Positive_CD56dim_NK_cell': '27a4a7fd-e7d2-4216-9983-96ab6a60502a', 'BR2_Female_Positive_Memory_CD4_T_cell': '6a7bd1f6-36b5-4fa4-8f4d-2b0445d60956', 'BR2_Female_Positive_Memory_CD8_T_cell': '236d2541-d4f0-41f8-aca8-ead6742e9e9b', 'BR2_Female_Positive_Naive_CD4_T_cell': '545e74ea-811d-4fdc-848c-8689028f13b2', 'BR2_Male_Negative_CD14_monocyte': '7831f065-3437-4f43-96ca-64a614d7a45d', 'BR2_Male_Negative_CD56dim_NK_cell': 'e5de95ea-39da-4baf-8d32-9be31c35c9f0', 'BR2_Male_Negative_Memory_CD4_T_cell': 'dcd691fd-ee28-49a9-884f-7e3fe3e7c674', 'BR2_Male_Negative_Memory_CD8_T_cell': 'dc9c5c66-84dd-410c-96d1-be3b11d1f14f', 'BR2_Male_Negative_Naive_CD4_T_cell': '444c3f91-1513-49e1-8e73-fa167be2d073', 'BR2_Male_Positive_CD14_monocyte': '5d21f345-d47e-44ef-ab52-548eacc37635', 'BR2_Male_Positive_CD56dim_NK_cell': '90871db8-4606-4328-b2f1-02704841737a', 'BR2_Male_Positive_Memory_CD4_T_cell': '90e7db23-9176-4b46-9787-18c7f14825f2', 'BR2_Male_Positive_Memory_CD8_T_cell': '1c0d54cc-ebf3-4958-afad-7ed5e30d80e1', 'BR2_Male_Positive_Naive_CD4_T_cell': '8a6935c5-9980-4b44-a94d-e3c345ca20fb', 'CD16_monocyte': '75d8c79f-198f-4dea-ba10-90d4a83962c4', 'CD56bright_NK_cell': '609bc7b2-b9aa-4177-b8cb-3db01b219f25', 'CD8aa': 'c0ba77d1-65c3-48f1-8067-54b2e56f66a9', 'DN_T_cell': 'baf3ba2a-aa51-4cda-852c-434294ceaa4d', 'Effector_B_cell': 'cfc14e28-42b4-4d9f-aba5-65e6dd5ca69d', 'Erythrocyte': 'ce5a821a-ba1e-41b6-ba85-529da3e3b760', 'ILC': 'bd1c814a-1884-4e1b-8ae7-c92aa12d1b6e', 'Intermediate_monocyte': '468f4eb1-0470-4f78-85b0-9b31ea5bd4eb', 'MAIT': '3fa3f9ff-5044-491a-95ed-83ee35e08d0f', 'Memory_B_cell': '7dd864d9-9fd2-417f-b543-10dba41e2880', 'Naive_B_cell': '0eba1f2d-fa88-4121-9737-d8ad62b71788', 'Naive_CD8_T_cell': '99c98fa1-22bc-413e-9fb1-f5ddfc6dc257', 'Plasma_cell': '8dc888f7-3a42-49f2-bac4-8a603e511d9d', 'Platelet': 'eae1ea00-ac3d-4855-805f-4309ac2342e1', 'Progenitor_cell': 'd1e805a0-a799-4f25-bf73-db23ac7fd5bb', 'Proliferating_NK_cell': '92e9c744-b3c0-4e7b-97b3-57fa36b30893', 'Proliferating_T_cell': 'f4aeef6a-27db-434c-949c-063488bec6d7', 'Transitional_B_cell': '8f04564a-7419-4f5b-b793-825a22972c0c', 'Treg': 'b11f8ab7-5964-4203-ab39-e3f3ebdba7dc', 'cDC1': 'd31cde8f-3c84-42be-8fe1-ac6e721f163f', 'cDC2': '1e0ce70c-ec16-47c2-ad8c-74fe7a2ecad8', 'gdT': '0712fee1-d229-49a9-8b93-596b3042a210', 'pDC': '9748801b-b24d-4527-b863-dac0c7899105'}
for group_name, uuid in h5ad_uuids.items():
adata = read_adata_uuid(uuid)
# Integrate L3 labels
obs = adata.obs
obs = obs.reset_index(drop = True)
obs = obs.merge(l3_labels, on = 'barcodes', how = 'left')
obs = obs.set_index('barcodes', drop = False)
adata.obs = obs
l3_types = adata.obs['AIFI_L3'].unique().tolist()
for l3_type in l3_types:
out_type = format_cell_type(l3_type)
type_dir = 'output/l3_types/{ct}'.format(ct = out_type)
if not os.path.isdir(type_dir):
os.makedirs(type_dir)
out_file = '{td}/diha_celltypist_L3_{g}_{ct}.h5ad'.format(td = type_dir, g = group_name, ct = out_type)
type_adata = adata[adata.obs['AIFI_L3'] == l3_type].copy()
type_adata.write_h5ad(out_file)
rm_cache_uuid(uuid)
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type_dirs = os.listdir('output/l3_types')
type_h5ads = []
for type_dir in type_dirs:
type_path = 'output/l3_types/{td}'.format(td = type_dir)
type_files = os.listdir(type_path)
adata_list = []
for type_file in type_files:
adata = sc.read_h5ad('{tp}/{tf}'.format(tp = type_path, tf = type_file))
adata_list.append(adata)
type_adata = sc.concat(adata_list)
cell_type = type_adata.obs['AIFI_L3'][0]
out_type = format_cell_type(cell_type)
out_file = 'output/diha_celltypist_L3_{ct}.h5ad'.format(ct = out_type)
type_adata.write_h5ad(out_file)
type_h5ads.append(out_file)
study_space_uuid = 'de025812-5e73-4b3c-9c3b-6d0eac412f2a'
title = 'DIHA CellTypist L3 .h5ads {d}'.format(d = date.today())
search_id = element_id()
search_id
'nitrogen-rhenium-hafnium'
in_files = []
for group_name, uuid in h5ad_uuids.items():
in_files.append(uuid)
in_files
['559cbab1-e3cd-438b-b951-ff7874555625', '40dfd96a-5795-479e-8ae7-5608f91db36d', 'ceca06b2-f11c-40bf-988c-62ff51063c61', '5cd5c776-e44a-4b84-8869-48abce644ed7', 'c5d24858-9703-42ae-97cd-6834290b18a4', '50fe1d88-49a4-4eb0-bcc8-4ce983646163', 'e0270c3a-b428-4dd7-8c8e-f965814776c2', '11b3c89c-8157-4b0e-bab3-e3198e8b1544', 'ac35ceb8-1272-477a-8e6b-ed33538ea4cc', '4a44b740-b280-4f5b-9aad-d0521fbb6fe2', '14dd7450-8773-4256-92b6-0b1084d187cb', '0fee75d4-6a98-47ec-b1f2-23ff7ad1c18e', 'cb6f833b-f286-478f-acd2-989ea4a4c7b8', '8d566aba-47de-452c-b9f1-bad3d5713135', 'b2ef0d39-8861-406b-936a-bb242e6809b7', '943f09d1-3190-4422-b050-b355daa29360', 'af58fd39-0156-450f-a38c-3213c3cffc66', 'aeb088bf-bcef-4170-b07c-0e3282615066', 'f1c45e38-12d6-4b77-89eb-51bb46de485b', '982f64fc-bfb0-476a-808a-77df2828091d', '10e95fd0-85e2-40b5-a0f1-3bb1f885ab15', '6621dac9-f9b9-422b-90f9-3ea31c6f9545', 'f01ebaa1-aaab-44b0-83b9-4ce40b89acb4', '18661b9d-7973-46ba-a0c7-22d21cd1a70a', '461db2c7-2f5a-4fe1-b7ea-56f4fc7ffd05', '6a865cec-fe93-4414-803f-01594f48a454', 'ecf2cc80-4081-4e53-b596-5e17810acf5b', '27a4a7fd-e7d2-4216-9983-96ab6a60502a', '6a7bd1f6-36b5-4fa4-8f4d-2b0445d60956', '236d2541-d4f0-41f8-aca8-ead6742e9e9b', '545e74ea-811d-4fdc-848c-8689028f13b2', '7831f065-3437-4f43-96ca-64a614d7a45d', 'e5de95ea-39da-4baf-8d32-9be31c35c9f0', 'dcd691fd-ee28-49a9-884f-7e3fe3e7c674', 'dc9c5c66-84dd-410c-96d1-be3b11d1f14f', '444c3f91-1513-49e1-8e73-fa167be2d073', '5d21f345-d47e-44ef-ab52-548eacc37635', '90871db8-4606-4328-b2f1-02704841737a', '90e7db23-9176-4b46-9787-18c7f14825f2', '1c0d54cc-ebf3-4958-afad-7ed5e30d80e1', '8a6935c5-9980-4b44-a94d-e3c345ca20fb', '75d8c79f-198f-4dea-ba10-90d4a83962c4', '609bc7b2-b9aa-4177-b8cb-3db01b219f25', 'c0ba77d1-65c3-48f1-8067-54b2e56f66a9', 'baf3ba2a-aa51-4cda-852c-434294ceaa4d', 'cfc14e28-42b4-4d9f-aba5-65e6dd5ca69d', 'ce5a821a-ba1e-41b6-ba85-529da3e3b760', 'bd1c814a-1884-4e1b-8ae7-c92aa12d1b6e', '468f4eb1-0470-4f78-85b0-9b31ea5bd4eb', '3fa3f9ff-5044-491a-95ed-83ee35e08d0f', '7dd864d9-9fd2-417f-b543-10dba41e2880', '0eba1f2d-fa88-4121-9737-d8ad62b71788', '99c98fa1-22bc-413e-9fb1-f5ddfc6dc257', '8dc888f7-3a42-49f2-bac4-8a603e511d9d', 'eae1ea00-ac3d-4855-805f-4309ac2342e1', 'd1e805a0-a799-4f25-bf73-db23ac7fd5bb', '92e9c744-b3c0-4e7b-97b3-57fa36b30893', 'f4aeef6a-27db-434c-949c-063488bec6d7', '8f04564a-7419-4f5b-b793-825a22972c0c', 'b11f8ab7-5964-4203-ab39-e3f3ebdba7dc', 'd31cde8f-3c84-42be-8fe1-ac6e721f163f', '1e0ce70c-ec16-47c2-ad8c-74fe7a2ecad8', '0712fee1-d229-49a9-8b93-596b3042a210', '9748801b-b24d-4527-b863-dac0c7899105']
out_files = type_h5ads
out_files
['output/diha_celltypist_L3_GZMKpos_Vd2_gdT.h5ad', 'output/diha_celltypist_L3_GZMKneg_CD27pos_EM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Intermediate_monocyte.h5ad', 'output/diha_celltypist_L3_ILC.h5ad', 'output/diha_celltypist_L3_HLAnegDRhi_cDC2.h5ad', 'output/diha_celltypist_L3_Naive_CD4_Treg.h5ad', 'output/diha_celltypist_L3_KLRF1pos_effector_Vd1_gdT.h5ad', 'output/diha_celltypist_L3_GZMKpos_CD27pos_EM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Platelet.h5ad', 'output/diha_celltypist_L3_ISGpos_CD14_monocyte.h5ad', 'output/diha_celltypist_L3_Early_memory_B_cell.h5ad', 'output/diha_celltypist_L3_Memory_CD8_Treg.h5ad', 'output/diha_celltypist_L3_Core_CD14_monocyte.h5ad', 'output/diha_celltypist_L3_ISGpos_CD16_monocyte.h5ad', 'output/diha_celltypist_L3_cDC1.h5ad', 'output/diha_celltypist_L3_CD8_MAIT.h5ad', 'output/diha_celltypist_L3_Transitional_B_cell.h5ad', 'output/diha_celltypist_L3_CLP_cell.h5ad', 'output/diha_celltypist_L3_SOX4pos_naive_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_KLRB1pos_memory_CD4_Treg.h5ad', 'output/diha_celltypist_L3_Activated_memory_B_cell.h5ad', 'output/diha_celltypist_L3_CD8aa.h5ad', 'output/diha_celltypist_L3_GZMBneg_CD27neg_EM_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_CD56bright_NK_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_MAIT.h5ad', 'output/diha_celltypist_L3_CD4_MAIT.h5ad', 'output/diha_celltypist_L3_Naive_Vd1_gdT.h5ad', 'output/diha_celltypist_L3_ISGpos_cDC2.h5ad', 'output/diha_celltypist_L3_Core_naive_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_KLRF1neg_GZMBpos_CD27neg_EM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Proliferating_T_cell.h5ad', 'output/diha_celltypist_L3_Type_2_polarized_memory_B_cell.h5ad', 'output/diha_celltypist_L3_Plasma_cell.h5ad', 'output/diha_celltypist_L3_CD27pos_effector_B_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_memory_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_KLRB1pos_memory_CD8_Treg.h5ad', 'output/diha_celltypist_L3_Core_naive_B_cell.h5ad', 'output/diha_celltypist_L3_KLRF1neg_effector_Vd1_gdT.h5ad', 'output/diha_celltypist_L3_BaEoMaP_cell.h5ad', 'output/diha_celltypist_L3_CMP_cell.h5ad', 'output/diha_celltypist_L3_pDC.h5ad', 'output/diha_celltypist_L3_Memory_CD4_Treg.h5ad', 'output/diha_celltypist_L3_Adaptive_NK_cell.h5ad', 'output/diha_celltypist_L3_C1Qpos_CD16_monocyte.h5ad', 'output/diha_celltypist_L3_GZMKpos_memory_CD4_Treg.h5ad', 'output/diha_celltypist_L3_Core_memory_B_cell.h5ad', 'output/diha_celltypist_L3_CM_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_GZMBneg_CD27pos_EM_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_naive_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_SOX4pos_naive_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Core_CD16_monocyte.h5ad', 'output/diha_celltypist_L3_ISGpos_CD56dim_NK_cell.h5ad', 'output/diha_celltypist_L3_IL1Bpos_CD14_monocyte.h5ad', 'output/diha_celltypist_L3_KLRF1neg_GZMBpos_CD27neg_memory_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_CD14pos_cDC2.h5ad', 'output/diha_celltypist_L3_Erythrocyte.h5ad', 'output/diha_celltypist_L3_GZMKpos_CD56dim_NK_cell.h5ad', 'output/diha_celltypist_L3_Core_naive_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_memory_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_naive_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_GZMKneg_CD56dim_NK_cell.h5ad', 'output/diha_celltypist_L3_CM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_ASDC.h5ad', 'output/diha_celltypist_L3_GZMBpos_Vd2_gdT.h5ad', 'output/diha_celltypist_L3_ISGpos_naive_B_cell.h5ad', 'output/diha_celltypist_L3_CD27neg_effector_B_cell.h5ad', 'output/diha_celltypist_L3_KLRF1pos_GZMBpos_CD27neg_EM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Proliferating_NK_cell.h5ad', 'output/diha_celltypist_L3_SOX4pos_Vd1_gdT.h5ad', 'output/diha_celltypist_L3_CD95_memory_B_cell.h5ad', 'output/diha_celltypist_L3_DN_T_cell.h5ad']
hisepy.upload.upload_files(
files = out_files,
study_space_id = study_space_uuid,
title = title,
input_file_ids = in_files,
destination = search_id
)
Cannot determine the current notebook. 1) /home/jupyter/IH-A-Aging-Analysis-Notebooks/scrna-seq_analysis/02-reference_labeling/09-Python_partition_L3_data.ipynb 2) /home/jupyter/IH-A-Aging-Analysis-Notebooks/scrna-seq_analysis/02-reference_labeling/07a-R_filter_review_plots.ipynb 3) /home/jupyter/IH-A-Aging-Analysis-Notebooks/scrna-seq_analysis/02-reference_labeling/07-Python_filter_cell_classes.ipynb Please select (1-3)
you are trying to upload file_ids... ['output/diha_celltypist_L3_GZMKpos_Vd2_gdT.h5ad', 'output/diha_celltypist_L3_GZMKneg_CD27pos_EM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Intermediate_monocyte.h5ad', 'output/diha_celltypist_L3_ILC.h5ad', 'output/diha_celltypist_L3_HLAnegDRhi_cDC2.h5ad', 'output/diha_celltypist_L3_Naive_CD4_Treg.h5ad', 'output/diha_celltypist_L3_KLRF1pos_effector_Vd1_gdT.h5ad', 'output/diha_celltypist_L3_GZMKpos_CD27pos_EM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Platelet.h5ad', 'output/diha_celltypist_L3_ISGpos_CD14_monocyte.h5ad', 'output/diha_celltypist_L3_Early_memory_B_cell.h5ad', 'output/diha_celltypist_L3_Memory_CD8_Treg.h5ad', 'output/diha_celltypist_L3_Core_CD14_monocyte.h5ad', 'output/diha_celltypist_L3_ISGpos_CD16_monocyte.h5ad', 'output/diha_celltypist_L3_cDC1.h5ad', 'output/diha_celltypist_L3_CD8_MAIT.h5ad', 'output/diha_celltypist_L3_Transitional_B_cell.h5ad', 'output/diha_celltypist_L3_CLP_cell.h5ad', 'output/diha_celltypist_L3_SOX4pos_naive_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_KLRB1pos_memory_CD4_Treg.h5ad', 'output/diha_celltypist_L3_Activated_memory_B_cell.h5ad', 'output/diha_celltypist_L3_CD8aa.h5ad', 'output/diha_celltypist_L3_GZMBneg_CD27neg_EM_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_CD56bright_NK_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_MAIT.h5ad', 'output/diha_celltypist_L3_CD4_MAIT.h5ad', 'output/diha_celltypist_L3_Naive_Vd1_gdT.h5ad', 'output/diha_celltypist_L3_ISGpos_cDC2.h5ad', 'output/diha_celltypist_L3_Core_naive_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_KLRF1neg_GZMBpos_CD27neg_EM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Proliferating_T_cell.h5ad', 'output/diha_celltypist_L3_Type_2_polarized_memory_B_cell.h5ad', 'output/diha_celltypist_L3_Plasma_cell.h5ad', 'output/diha_celltypist_L3_CD27pos_effector_B_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_memory_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_KLRB1pos_memory_CD8_Treg.h5ad', 'output/diha_celltypist_L3_Core_naive_B_cell.h5ad', 'output/diha_celltypist_L3_KLRF1neg_effector_Vd1_gdT.h5ad', 'output/diha_celltypist_L3_BaEoMaP_cell.h5ad', 'output/diha_celltypist_L3_CMP_cell.h5ad', 'output/diha_celltypist_L3_pDC.h5ad', 'output/diha_celltypist_L3_Memory_CD4_Treg.h5ad', 'output/diha_celltypist_L3_Adaptive_NK_cell.h5ad', 'output/diha_celltypist_L3_C1Qpos_CD16_monocyte.h5ad', 'output/diha_celltypist_L3_GZMKpos_memory_CD4_Treg.h5ad', 'output/diha_celltypist_L3_Core_memory_B_cell.h5ad', 'output/diha_celltypist_L3_CM_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_GZMBneg_CD27pos_EM_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_naive_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_SOX4pos_naive_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Core_CD16_monocyte.h5ad', 'output/diha_celltypist_L3_ISGpos_CD56dim_NK_cell.h5ad', 'output/diha_celltypist_L3_IL1Bpos_CD14_monocyte.h5ad', 'output/diha_celltypist_L3_KLRF1neg_GZMBpos_CD27neg_memory_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_CD14pos_cDC2.h5ad', 'output/diha_celltypist_L3_Erythrocyte.h5ad', 'output/diha_celltypist_L3_GZMKpos_CD56dim_NK_cell.h5ad', 'output/diha_celltypist_L3_Core_naive_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_memory_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_ISGpos_naive_CD4_T_cell.h5ad', 'output/diha_celltypist_L3_GZMKneg_CD56dim_NK_cell.h5ad', 'output/diha_celltypist_L3_CM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_ASDC.h5ad', 'output/diha_celltypist_L3_GZMBpos_Vd2_gdT.h5ad', 'output/diha_celltypist_L3_ISGpos_naive_B_cell.h5ad', 'output/diha_celltypist_L3_CD27neg_effector_B_cell.h5ad', 'output/diha_celltypist_L3_KLRF1pos_GZMBpos_CD27neg_EM_CD8_T_cell.h5ad', 'output/diha_celltypist_L3_Proliferating_NK_cell.h5ad', 'output/diha_celltypist_L3_SOX4pos_Vd1_gdT.h5ad', 'output/diha_celltypist_L3_CD95_memory_B_cell.h5ad', 'output/diha_celltypist_L3_DN_T_cell.h5ad']. Do you truly want to proceed?
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import session_info
session_info.show()
----- anndata 0.10.3 hisepy 0.3.0 pandas 2.1.4 scanpy 1.9.6 session_info 1.0.0 -----
PIL 10.0.1 anyio NA arrow 1.3.0 asttokens NA attr 23.2.0 attrs 23.2.0 babel 2.14.0 beatrix_jupyterlab NA brotli NA cachetools 5.3.1 certifi 2024.02.02 cffi 1.16.0 charset_normalizer 3.3.2 cloudpickle 2.2.1 colorama 0.4.6 comm 0.1.4 cryptography 41.0.7 cycler 0.10.0 cython_runtime NA dateutil 2.8.2 db_dtypes 1.1.1 debugpy 1.8.0 decorator 5.1.1 defusedxml 0.7.1 deprecated 1.2.14 exceptiongroup 1.2.0 executing 2.0.1 fastjsonschema NA fqdn NA google NA greenlet 2.0.2 grpc 1.58.0 grpc_status NA h5py 3.10.0 idna 3.6 igraph 0.10.8 importlib_metadata NA ipykernel 6.28.0 ipython_genutils 0.2.0 ipywidgets 8.1.1 isoduration NA jedi 0.19.1 jinja2 3.1.2 joblib 1.3.2 json5 NA jsonpointer 2.4 jsonschema 4.20.0 jsonschema_specifications NA jupyter_events 0.9.0 jupyter_server 2.12.1 jupyterlab_server 2.25.2 jwt 2.8.0 kiwisolver 1.4.5 leidenalg 0.10.1 llvmlite 0.41.0 lz4 4.3.2 markupsafe 2.1.3 matplotlib 3.8.0 matplotlib_inline 0.1.6 mpl_toolkits NA mpmath 1.3.0 natsort 8.4.0 nbformat 5.9.2 numba 0.58.0 numpy 1.24.0 opentelemetry NA overrides NA packaging 23.2 parso 0.8.3 periodictable 1.5.2 pexpect 4.8.0 pickleshare 0.7.5 pkg_resources NA platformdirs 4.1.0 plotly 5.18.0 prettytable 3.9.0 prometheus_client NA prompt_toolkit 3.0.42 proto NA psutil NA ptyprocess 0.7.0 pure_eval 0.2.2 pyarrow 13.0.0 pydev_ipython NA pydevconsole NA pydevd 2.9.5 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygments 2.17.2 pynvml NA pyparsing 3.1.1 pyreadr 0.5.0 pythonjsonlogger NA pytz 2023.3.post1 referencing NA requests 2.31.0 rfc3339_validator 0.1.4 rfc3986_validator 0.1.1 rpds NA scipy 1.11.4 send2trash NA shapely 1.8.5.post1 six 1.16.0 sklearn 1.3.2 sniffio 1.3.0 socks 1.7.1 sql NA sqlalchemy 2.0.21 sqlparse 0.4.4 stack_data 0.6.2 sympy 1.12 termcolor NA texttable 1.7.0 threadpoolctl 3.2.0 torch 2.1.2+cu121 torchgen NA tornado 6.3.3 tqdm 4.66.1 traitlets 5.9.0 typing_extensions NA uri_template NA urllib3 1.26.18 wcwidth 0.2.12 webcolors 1.13 websocket 1.7.0 wrapt 1.15.0 xarray 2023.12.0 yaml 6.0.1 zipp NA zmq 25.1.2 zoneinfo NA
----- IPython 8.19.0 jupyter_client 8.6.0 jupyter_core 5.6.1 jupyterlab 4.1.5 notebook 6.5.4 ----- Python 3.10.13 | packaged by conda-forge | (main, Dec 23 2023, 15:36:39) [GCC 12.3.0] Linux-5.15.0-1042-gcp-x86_64-with-glibc2.31 ----- Session information updated at 2024-04-21 15:07