支持中心

简体中文

English

简体中文

English

Appearance

COMMOT 空间细胞通讯：基于最优传输算法的信号推断 ​

作者: SeekGene
时长: 25 分钟
字数: 5.2k 字
更新: 2026-03-02
阅读: 0 次
空间转录组 分析指南 Notebooks 细胞通讯分析

背景介绍 ​

（1）首先，使用非概率质量分布来控制运输计划的边缘，以保持物种之间的可比性；
（2）第二，对 CCC 实施空间距离约束，以避免连接空间上相距较远的部分；
（3）最后，将多物种分布（配体）传输到多物种分布（受体）以解释多物种相互作用。

COMMOT 的计算结果 ​

python
%%capture
import os
import gc
import ot
import pickle
import anndata
import scanpy as sc
import pandas as pd
import numpy as np
from scipy import sparse
from scipy.stats import spearmanr, pearsonr
from scipy.spatial import distance_matrix
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.colors import Normalize

import commot as ct
import stlearn as st
from PIL import Image
import plotly
import sys
import logging
import re
import warnings
output
2025-09-02 09:50:32.611263: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2025-09-02 09:50:38.107938: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2025-09-02 09:50:38.107975: I tensorflow/compiler/xla/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
2025-09-02 09:51:03.232851: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory
2025-09-02 09:51:03.234823: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory
2025-09-02 09:51:03.234839: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.

COMMOT 细胞通讯模块输入参数介绍

  • SAMple_name：样本名
  • meta_path：注释的细胞类型文件路径，文件中需要以 barcode 为行名，列名为“celltype”（细胞类型）为列
  • species：物种，与下面参数 lr_database_bool 有关，若 lr_database_bool 为 True，则该处只能填"human"或者"mouse"；若为 False，则不需要填写
  • lr_database：填写 COMMOT 自带的数据库名称，可选"CellChat"或者"CellPhoneDB_v4.0"；若参数 provide_lr_database 是 True，则设置名称
  • signaling_type：若 lr_database 填 CellChat，可选'Secreted Signaling'，'Cell-Cell Contact'，'ECM-Receptor'；若 lr_database 填 CellPhoneDB_v4.0，可选'Secreted Signaling'，'Cell-Cell Contact';若填 None，则用选择的 lr_database 所有信号。
  • col_SAM：metadata 的样本列名称
  • col_celltype：metadata 的细胞类型列名称
python
sample_name = "N1"
meta_path = "../../data/AY1748480899609/meta.tsv"
species = "human"
lr_database = "CellChat"
signaling_type = None
col_sam="Sample"
col_celltype="CellAnnotation"
python

def get_cmap_qualitative(cmap_name):
    if cmap_name == "Plotly":
        cmap = plotly.colors.qualitative.Plotly
    elif cmap_name == "Alphabet":
        cmap = plotly.colors.qualitative.Alphabet
    elif cmap_name == "Light24":
        cmap = plotly.colors.qualitative.Light24
    elif cmap_name == "Dark24":
        cmap = plotly.colors.qualitative.Dark24
    # Safe and Vivid are strings of form "rbg(...)"
    # Handle this later.
    elif cmap_name == "Safe":
        cmap = plotly.colors.qualitative.Safe
    elif cmap_name == "Vivid":
        cmap = plotly.colors.qualitative.Vivid
    return cmap
  • 读取 SeekSpace 数据并进行标准化、降维、聚类
python

adata = sc.read_10x_mtx("filtered_feature_bc_matrix/")
spatial = pd.read_csv('filtered_feature_bc_matrix/cell_locations.tsv',sep="\t",index_col=0)
spatial = spatial.loc[:,("x","y")]
selected_rows = spatial.loc[spatial.index.isin(adata.obs_names)]
selected_rows.columns = ["imagecol","imagerow"]
selected_rows = selected_rows.reindex(adata.obs_names)
selected_rows = selected_rows*0.265385
a = st.create_stlearn(count=adata.to_df(),spatial=selected_rows,library_id=sample_name, scale=1)
a.raw = a
#a.layers["raw_count"] = a.X
# Preprocessing
#st.pp.filter_genes(a,min_cells=3)
st.pp.normalize_total(a)
st.pp.log1p(a)
a_dis500 = a.copy()
# Keep raw data
#a.raw = a
st.pp.scale(a)
st.em.run_pca(a,n_comps=50,random_state=0)
st.pp.neighbors(a,n_neighbors=25,use_rep='X_pca',random_state=0)
st.tl.clustering.louvain(a,random_state=0)
sc.tl.umap(a)
output
Normalization step is finished in adata.X
Log transformation step is finished in adata.X
Scale step is finished in adata.X
PCA is done! Generated in adata.obsm['X_pca'], adata.uns['pca'] and adata.varm['PCs']
Created k-Nearest-Neighbor graph in adata.uns['neighbors']
Applying Louvain cluster ...n Louvain cluster is done! The labels are stored in adata.obs['louvain']
  • 将注释好的细胞类型添加到 adata 对象中
python

cluster_name = "celltype"
celltype = pd.read_csv(meta_path,index_col=0,sep = "\t")
celltype = celltype.loc[a.obs.index]
a.obs[cluster_name] = celltype[col_celltype]
a.obs[cluster_name] = a.obs[cluster_name].astype('category')
a_dis500 = a_dis500[a.obs.index,:]
  • 选择需要的受配体库，根据受配体的表达进行过滤
python

df_ligrec = ct.pp.ligand_receptor_database(species=species, signaling_type=signaling_type, database=lr_database)
df_ligrec_filtered = ct.pp.filter_lr_database(df_ligrec, a_dis500, min_cell_pct=0.05)
df_ligrec_filtered
0123
0TGFB1TGFBR1_TGFBR2TGFbSecreted Signaling
1TGFB2TGFBR1_TGFBR2TGFbSecreted Signaling
2TGFB3TGFBR1_TGFBR2TGFbSecreted Signaling
3TGFB1ACVR1B_TGFBR2TGFbSecreted Signaling
4TGFB2ACVR1B_TGFBR2TGFbSecreted Signaling
...............
252SEMA4GPLXNB2SEMA4Cell-Cell Contact
253SEMA5APLXNA1SEMA5Cell-Cell Contact
254SEMA5APLXNA3SEMA5Cell-Cell Contact
255SEMA6APLXNA2SEMA6Cell-Cell Contact
256SEMA6APLXNA4SEMA6Cell-Cell Contact

257 rows × 4 columns

  • 针对过滤后的受配体进行细胞通讯推断，距离范围在 500um。
python

ct.tl.spatial_communication(a_dis500,
    database_name=lr_database, df_ligrec=df_ligrec_filtered, dis_thr=500, heteromeric=True, pathway_sum=True)
python
a_dis500.write("./adata_dis500.h5ad")

受配体对发送和接收信号的数量 ​

python
pts = a_dis500.obsm['spatial']
sender = a_dis500.obsm['commot-' + lr_database + '-sum-sender'][a_dis500.obsm['commot-' + lr_database + '-sum-sender'].columns[1]]
receiver = a_dis500.obsm['commot-' + lr_database + '-sum-receiver'][a_dis500.obsm['commot-' + lr_database + '-sum-receiver'].columns[1]]
fig, ax = plt.subplots(1,2, figsize=(20,8))
ax[0].scatter(pts[:,0], pts[:,1], c=sender, s=5, cmap='Blues')
ax[0].set_title(a_dis500.obsm['commot-' + lr_database + '-sum-sender'].columns[1]+'_Sender')
norm_sender = Normalize(vmin=min(sender), vmax=max(sender))
plt.colorbar(cm.ScalarMappable(norm=norm_sender, cmap='Blues'), ax=ax[0])
ax[0].set_aspect("equal")

ax[1].scatter(pts[:,0], pts[:,1], c=receiver, s=5, cmap='Reds')
ax[1].set_title(a_dis500.obsm['commot-' + lr_database + '-sum-receiver'].columns[1]+'_Receiver')
norm_receiver = Normalize(vmin=min(receiver), vmax=max(receiver))
plt.colorbar(cm.ScalarMappable(norm=norm_receiver, cmap='Reds'), ax=ax[1])
ax[1].set_aspect("equal")
受配体共表达情况。左图代表着配体的表达情况；右图代表着受体的表达情况；颜色越深表达越高。若配受体表达在同一区域，从而推断出表达该受配体细胞之间会发生互作。（这里以一种受配体对展示）
python
#ct.tl.communication_direction(a_dis500, database_name=lr_database, pathway_name='PSAP', k=5)
#ct.pl.plot_cell_communication(a_dis500, database_name=lr_database, pathway_name='PSAP', plot_method='grid', background_legend=True,
#    scale=0.00003, ndsize=8, grid_density=0.4, summary='sender', background='image', clustering=cluster_name, cmap='Alphabet',
#    normalize_v = True, normalize_v_quantile=0.995)

细胞通讯信号流可视化 ​

COMMOT 认为细胞通讯是某个细胞会与邻近细胞互作，邻近细胞与下一个邻近细胞互作，依次进行就会形成“信号流”，图中展示了通路的信号流方向。

python
#print("total_signature_stream")
ct.tl.communication_direction(a_dis500, database_name=lr_database, k=5)
ct.pl.plot_cell_communication(a_dis500, database_name=lr_database, lr_pair=('total','total'), plot_method='stream', background_legend=True,
    scale=0.00003, ndsize=8, grid_density=0.4, summary='sender', background='summary', clustering=cluster_name, cmap='Reds',
    normalize_v = True, normalize_v_quantile=0.995)
output
AxesSubplot:
每个细胞之间通讯的方向性。箭头代表着通讯的方向，底色代表着细胞发送信号的强度。
  • 计算不同细胞类型之间通讯交流强度
python
a_dis500.obs[cluster_name] = a.obs[cluster_name]
#计算每个受配体对的结果
for i,j in enumerate(df_ligrec_filtered.values):
    ct.tl.cluster_communication(a_dis500, database_name=lr_database, clustering=cluster_name,n_permutations=100,lr_pair=(j[0],j[1]))


ct.tl.cluster_communication(a_dis500, database_name=lr_database, clustering=cluster_name,n_permutations=100)

细胞通讯网络 ​

python
a_dis500
output
AnnData object with n_obs × n_vars = 20820 × 34506
obs: 'imagecol', 'imagerow', 'celltype'
uns: 'spatial', 'log1p', 'commot-CellChat-info', 'commot_cluster-celltype-CellChat-TGFB1-TGFBR1_TGFBR2', 'commot_cluster-celltype-CellChat-TGFB2-TGFBR1_TGFBR2', 'commot_cluster-celltype-CellChat-TGFB3-TGFBR1_TGFBR2', 'commot_cluster-celltype-CellChat-TGFB1-ACVR1B_TGFBR2', 'commot_cluster-celltype-CellChat-TGFB2-ACVR1B_TGFBR2', 'commot_cluster-celltype-CellChat-TGFB3-ACVR1B_TGFBR2', 'commot_cluster-celltype-CellChat-TGFB1-ACVR1_TGFBR1_TGFBR2', 'commot_cluster-celltype-CellChat-TGFB2-ACVR1_TGFBR1_TGFBR2', 'commot_cluster-celltype-CellChat-TGFB3-ACVR1_TGFBR1_TGFBR2', 'commot_cluster-celltype-CellChat-WNT5B-FZD6', 'commot_cluster-celltype-CellChat-NRG1-ERBB3', 'commot_cluster-celltype-CellChat-NRG1-ERBB2_ERBB3', 'commot_cluster-celltype-CellChat-NRG1-ERBB4', 'commot_cluster-celltype-CellChat-NRG1-ERBB2_ERBB4', 'commot_cluster-celltype-CellChat-NRG2-ERBB3', 'commot_cluster-celltype-CellChat-NRG2-ERBB2_ERBB3', 'commot_cluster-celltype-CellChat-NRG2-ERBB4', 'commot_cluster-celltype-CellChat-NRG2-ERBB2_ERBB4', 'commot_cluster-celltype-CellChat-PDGFA-PDGFRA', 'commot_cluster-celltype-CellChat-PDGFA-PDGFRB', 'commot_cluster-celltype-CellChat-PDGFC-PDGFRA', 'commot_cluster-celltype-CellChat-IGF1-IGF1R', 'commot_cluster-celltype-CellChat-IGF1-ITGA6_ITGB4', 'commot_cluster-celltype-CellChat-MIF-CD74_CXCR4', 'commot_cluster-celltype-CellChat-MIF-CD74_CD44', 'commot_cluster-celltype-CellChat-CSF1-CSF1R', 'commot_cluster-celltype-CellChat-NAMPT-INSR', 'commot_cluster-celltype-CellChat-NAMPT-ITGA5_ITGB1', 'commot_cluster-celltype-CellChat-MDK-SDC2', 'commot_cluster-celltype-CellChat-MDK-SDC4', 'commot_cluster-celltype-CellChat-MDK-ITGA4_ITGB1', 'commot_cluster-celltype-CellChat-MDK-ITGA6_ITGB1', 'commot_cluster-celltype-CellChat-MDK-LRP1', 'commot_cluster-celltype-CellChat-MDK-NCL', 'commot_cluster-celltype-CellChat-PTN-SDC2', 'commot_cluster-celltype-CellChat-PTN-SDC3', 'commot_cluster-celltype-CellChat-PTN-SDC4', 'commot_cluster-celltype-CellChat-PTN-NCL', 'commot_cluster-celltype-CellChat-C3-ITGAX_ITGB2', 'commot_cluster-celltype-CellChat-SEMA3C-NRP1_PLXNA1', 'commot_cluster-celltype-CellChat-SEMA3C-NRP1_PLXNA2', 'commot_cluster-celltype-CellChat-SEMA3C-NRP1_PLXNA3', 'commot_cluster-celltype-CellChat-SEMA3C-NRP1_PLXNA4', 'commot_cluster-celltype-CellChat-SEMA3C-PLXND1', 'commot_cluster-celltype-CellChat-GAS6-AXL', 'commot_cluster-celltype-CellChat-GAS6-MERTK', 'commot_cluster-celltype-CellChat-GRN-SORT1', 'commot_cluster-celltype-CellChat-LGALS9-PTPRC', 'commot_cluster-celltype-CellChat-LGALS9-CD44', 'commot_cluster-celltype-CellChat-COL1A1-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL1A2-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL4A1-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL4A2-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL4A3-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL4A4-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL4A5-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL4A6-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL6A1-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL6A2-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL6A3-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-COL1A1-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL1A2-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL4A1-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL4A2-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL4A3-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL4A4-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL4A5-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL4A6-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL6A1-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL6A2-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-COL6A3-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-FN1-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-FN1-ITGA4_ITGB1', 'commot_cluster-celltype-CellChat-FN1-ITGA5_ITGB1', 'commot_cluster-celltype-CellChat-LAMA2-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-LAMA3-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-LAMA4-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-LAMA5-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-LAMB1-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-LAMB2-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-LAMC1-ITGA1_ITGB1', 'commot_cluster-celltype-CellChat-LAMA2-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-LAMA3-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-LAMA4-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-LAMA5-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-LAMB1-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-LAMB2-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-LAMC1-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-LAMA2-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-LAMA3-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-LAMA4-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-LAMA5-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-LAMB1-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-LAMB2-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-LAMC1-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-THBS1-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-THBS3-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL1A1-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL1A2-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL4A1-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL4A2-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL4A3-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL4A4-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL4A5-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL4A6-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL6A1-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL6A2-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-COL6A3-ITGA3_ITGB1', 'commot_cluster-celltype-CellChat-LAMA2-ITGA6_ITGB1', 'commot_cluster-celltype-CellChat-LAMA3-ITGA6_ITGB1', 'commot_cluster-celltype-CellChat-LAMA4-ITGA6_ITGB1', 'commot_cluster-celltype-CellChat-LAMA5-ITGA6_ITGB1', 'commot_cluster-celltype-CellChat-LAMB1-ITGA6_ITGB1', 'commot_cluster-celltype-CellChat-LAMB2-ITGA6_ITGB1', 'commot_cluster-celltype-CellChat-LAMC1-ITGA6_ITGB1', 'commot_cluster-celltype-CellChat-TNC-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-TNXB-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL1A1-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL1A2-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL4A1-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL4A2-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL4A3-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL4A4-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL4A5-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL4A6-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL6A1-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL6A2-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-COL6A3-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-LAMA2-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-LAMA3-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-LAMA4-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-LAMA5-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-LAMB1-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-LAMB2-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-LAMC1-ITGA9_ITGB1', 'commot_cluster-celltype-CellChat-FN1-ITGAV_ITGB1', 'commot_cluster-celltype-CellChat-FN1-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-LAMA2-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-LAMA3-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-LAMA4-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-LAMA5-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-LAMB1-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-LAMB2-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-LAMC1-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL1A1-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL1A2-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL4A1-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL4A2-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL4A3-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL4A4-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL4A5-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL4A6-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL6A1-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL6A2-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-COL6A3-ITGAV_ITGB8', 'commot_cluster-celltype-CellChat-LAMA2-ITGA6_ITGB4', 'commot_cluster-celltype-CellChat-LAMA3-ITGA6_ITGB4', 'commot_cluster-celltype-CellChat-LAMA4-ITGA6_ITGB4', 'commot_cluster-celltype-CellChat-LAMA5-ITGA6_ITGB4', 'commot_cluster-celltype-CellChat-LAMB1-ITGA6_ITGB4', 'commot_cluster-celltype-CellChat-LAMB2-ITGA6_ITGB4', 'commot_cluster-celltype-CellChat-LAMC1-ITGA6_ITGB4', 'commot_cluster-celltype-CellChat-FN1-CD44', 'commot_cluster-celltype-CellChat-COL1A1-CD44', 'commot_cluster-celltype-CellChat-COL1A2-CD44', 'commot_cluster-celltype-CellChat-COL4A1-CD44', 'commot_cluster-celltype-CellChat-COL4A2-CD44', 'commot_cluster-celltype-CellChat-COL4A3-CD44', 'commot_cluster-celltype-CellChat-COL4A4-CD44', 'commot_cluster-celltype-CellChat-COL4A5-CD44', 'commot_cluster-celltype-CellChat-COL4A6-CD44', 'commot_cluster-celltype-CellChat-COL6A1-CD44', 'commot_cluster-celltype-CellChat-COL6A2-CD44', 'commot_cluster-celltype-CellChat-COL6A3-CD44', 'commot_cluster-celltype-CellChat-LAMA2-CD44', 'commot_cluster-celltype-CellChat-LAMA3-CD44', 'commot_cluster-celltype-CellChat-LAMA4-CD44', 'commot_cluster-celltype-CellChat-LAMA5-CD44', 'commot_cluster-celltype-CellChat-LAMB1-CD44', 'commot_cluster-celltype-CellChat-LAMB2-CD44', 'commot_cluster-celltype-CellChat-LAMC1-CD44', 'commot_cluster-celltype-CellChat-COL1A1-SDC4', 'commot_cluster-celltype-CellChat-COL1A2-SDC4', 'commot_cluster-celltype-CellChat-COL4A1-SDC4', 'commot_cluster-celltype-CellChat-COL4A2-SDC4', 'commot_cluster-celltype-CellChat-COL4A3-SDC4', 'commot_cluster-celltype-CellChat-COL4A4-SDC4', 'commot_cluster-celltype-CellChat-COL4A5-SDC4', 'commot_cluster-celltype-CellChat-COL4A6-SDC4', 'commot_cluster-celltype-CellChat-COL6A1-SDC4', 'commot_cluster-celltype-CellChat-COL6A2-SDC4', 'commot_cluster-celltype-CellChat-COL6A3-SDC4', 'commot_cluster-celltype-CellChat-FN1-SDC4', 'commot_cluster-celltype-CellChat-TNC-SDC4', 'commot_cluster-celltype-CellChat-TNXB-SDC4', 'commot_cluster-celltype-CellChat-THBS1-SDC4', 'commot_cluster-celltype-CellChat-THBS3-SDC4', 'commot_cluster-celltype-CellChat-THBS1-CD47', 'commot_cluster-celltype-CellChat-THBS3-CD47', 'commot_cluster-celltype-CellChat-AGRN-DAG1', 'commot_cluster-celltype-CellChat-HSPG2-DAG1', 'commot_cluster-celltype-CellChat-LAMA2-DAG1', 'commot_cluster-celltype-CellChat-LAMA3-DAG1', 'commot_cluster-celltype-CellChat-LAMA4-DAG1', 'commot_cluster-celltype-CellChat-LAMA5-DAG1', 'commot_cluster-celltype-CellChat-LAMB1-DAG1', 'commot_cluster-celltype-CellChat-LAMB2-DAG1', 'commot_cluster-celltype-CellChat-LAMC1-DAG1', 'commot_cluster-celltype-CellChat-APP-CD74', 'commot_cluster-celltype-CellChat-CADM1-CADM1', 'commot_cluster-celltype-CellChat-PTPRC-MRC1', 'commot_cluster-celltype-CellChat-CD46-JAG1', 'commot_cluster-celltype-CellChat-CD96-NECTIN1', 'commot_cluster-celltype-CellChat-CD96-PVR', 'commot_cluster-celltype-CellChat-CD99-CD99', 'commot_cluster-celltype-CellChat-CD99-CD99L2', 'commot_cluster-celltype-CellChat-CDH1-CDH1', 'commot_cluster-celltype-CellChat-CDH1-ITGA2_ITGB1', 'commot_cluster-celltype-CellChat-EFNA1-EPHA3', 'commot_cluster-celltype-CellChat-EFNA1-EPHA4', 'commot_cluster-celltype-CellChat-EFNA1-EPHA7', 'commot_cluster-celltype-CellChat-EFNA5-EPHA3', 'commot_cluster-celltype-CellChat-EFNA5-EPHA4', 'commot_cluster-celltype-CellChat-EFNA5-EPHA7', 'commot_cluster-celltype-CellChat-EFNB2-EPHA4', 'commot_cluster-celltype-CellChat-EFNB2-EPHB4', 'commot_cluster-celltype-CellChat-F11R-ITGAL_ITGB2', 'commot_cluster-celltype-CellChat-F11R-F11R', 'commot_cluster-celltype-CellChat-F11R-JAM3', 'commot_cluster-celltype-CellChat-JAM3-F11R', 'commot_cluster-celltype-CellChat-JAM3-JAM3', 'commot_cluster-celltype-CellChat-MPZL1-MPZL1', 'commot_cluster-celltype-CellChat-NECTIN1-CD96', 'commot_cluster-celltype-CellChat-NEGR1-NEGR1', 'commot_cluster-celltype-CellChat-DLL1-NOTCH1', 'commot_cluster-celltype-CellChat-DLL1-NOTCH3', 'commot_cluster-celltype-CellChat-JAG1-NOTCH1', 'commot_cluster-celltype-CellChat-JAG1-NOTCH2', 'commot_cluster-celltype-CellChat-JAG1-NOTCH3', 'commot_cluster-celltype-CellChat-DLL1-NOTCH2', 'commot_cluster-celltype-CellChat-NRXN3-NLGN1', 'commot_cluster-celltype-CellChat-NRXN3-NLGN2', 'commot_cluster-celltype-CellChat-PECAM1-PECAM1', 'commot_cluster-celltype-CellChat-PTPRM-PTPRM', 'commot_cluster-celltype-CellChat-SEMA4A-NRP1_PLXNA1', 'commot_cluster-celltype-CellChat-SEMA4A-NRP1_PLXNA2', 'commot_cluster-celltype-CellChat-SEMA4A-NRP1_PLXNA3', 'commot_cluster-celltype-CellChat-SEMA4A-NRP1_PLXNA4', 'commot_cluster-celltype-CellChat-SEMA4A-PLXNB1', 'commot_cluster-celltype-CellChat-SEMA4A-PLXNB2', 'commot_cluster-celltype-CellChat-SEMA4D-PLXNB1', 'commot_cluster-celltype-CellChat-SEMA4D-PLXNB2', 'commot_cluster-celltype-CellChat-SEMA4G-PLXNB2', 'commot_cluster-celltype-CellChat-SEMA5A-PLXNA1', 'commot_cluster-celltype-CellChat-SEMA5A-PLXNA3', 'commot_cluster-celltype-CellChat-SEMA6A-PLXNA2', 'commot_cluster-celltype-CellChat-SEMA6A-PLXNA4', 'commot_cluster-celltype-CellChat-total-total'
obsm: 'spatial', 'commot-CellChat-sum-sender', 'commot-CellChat-sum-receiver', 'commot_sender_vf-CellChat-total-total', 'commot_receiver_vf-CellChat-total-total'
obsp: 'commot-CellChat-LAMC1-ITGA6_ITGB4', 'commot-CellChat-LAMC1-ITGA6_ITGB1', 'commot-CellChat-LAMC1-ITGA2_ITGB1', 'commot-CellChat-LAMC1-ITGA3_ITGB1', 'commot-CellChat-LAMC1-ITGA9_ITGB1', 'commot-CellChat-LAMC1-DAG1', 'commot-CellChat-LAMC1-CD44', 'commot-CellChat-LAMC1-ITGAV_ITGB8', 'commot-CellChat-LAMC1-ITGA1_ITGB1', 'commot-CellChat-LAMB2-ITGA6_ITGB4', 'commot-CellChat-LAMB2-ITGA6_ITGB1', 'commot-CellChat-LAMB2-ITGA2_ITGB1', 'commot-CellChat-LAMB2-ITGA3_ITGB1', 'commot-CellChat-LAMB2-ITGA9_ITGB1', 'commot-CellChat-LAMB2-DAG1', 'commot-CellChat-LAMB2-CD44', 'commot-CellChat-LAMB2-ITGAV_ITGB8', 'commot-CellChat-LAMB2-ITGA1_ITGB1', 'commot-CellChat-NAMPT-INSR', 'commot-CellChat-NAMPT-ITGA5_ITGB1', 'commot-CellChat-COL6A1-SDC4', 'commot-CellChat-COL6A1-ITGA2_ITGB1', 'commot-CellChat-COL6A1-ITGA3_ITGB1', 'commot-CellChat-COL6A1-ITGA9_ITGB1', 'commot-CellChat-COL6A1-CD44', 'commot-CellChat-COL6A1-ITGAV_ITGB8', 'commot-CellChat-COL6A1-ITGA1_ITGB1', 'commot-CellChat-THBS1-CD47', 'commot-CellChat-THBS1-SDC4', 'commot-CellChat-THBS1-ITGA3_ITGB1', 'commot-CellChat-JAM3-JAM3', 'commot-CellChat-JAM3-F11R', 'commot-CellChat-SEMA4G-PLXNB2', 'commot-CellChat-NRXN3-NLGN2', 'commot-CellChat-NRXN3-NLGN1', 'commot-CellChat-COL4A4-SDC4', 'commot-CellChat-COL4A4-ITGA2_ITGB1', 'commot-CellChat-COL4A4-ITGA3_ITGB1', 'commot-CellChat-COL4A4-ITGA9_ITGB1', 'commot-CellChat-COL4A4-CD44', 'commot-CellChat-COL4A4-ITGAV_ITGB8', 'commot-CellChat-COL4A4-ITGA1_ITGB1', 'commot-CellChat-PTPRC-MRC1', 'commot-CellChat-CD99-CD99L2', 'commot-CellChat-CD99-CD99', 'commot-CellChat-TGFB1-ACVR1_TGFBR1_TGFBR2', 'commot-CellChat-TGFB1-TGFBR1_TGFBR2', 'commot-CellChat-TGFB1-ACVR1B_TGFBR2', 'commot-CellChat-COL4A2-SDC4', 'commot-CellChat-COL4A2-ITGA2_ITGB1', 'commot-CellChat-COL4A2-ITGA3_ITGB1', 'commot-CellChat-COL4A2-ITGA9_ITGB1', 'commot-CellChat-COL4A2-CD44', 'commot-CellChat-COL4A2-ITGAV_ITGB8', 'commot-CellChat-COL4A2-ITGA1_ITGB1', 'commot-CellChat-TGFB3-ACVR1_TGFBR1_TGFBR2', 'commot-CellChat-TGFB3-TGFBR1_TGFBR2', 'commot-CellChat-TGFB3-ACVR1B_TGFBR2', 'commot-CellChat-LAMA3-ITGA6_ITGB4', 'commot-CellChat-LAMA3-ITGA6_ITGB1', 'commot-CellChat-LAMA3-ITGA2_ITGB1', 'commot-CellChat-LAMA3-ITGA3_ITGB1', 'commot-CellChat-LAMA3-ITGA9_ITGB1', 'commot-CellChat-LAMA3-DAG1', 'commot-CellChat-LAMA3-CD44', 'commot-CellChat-LAMA3-ITGAV_ITGB8', 'commot-CellChat-LAMA3-ITGA1_ITGB1', 'commot-CellChat-CDH1-ITGA2_ITGB1', 'commot-CellChat-CDH1-CDH1', 'commot-CellChat-LAMA2-ITGA6_ITGB4', 'commot-CellChat-LAMA2-ITGA6_ITGB1', 'commot-CellChat-LAMA2-ITGA2_ITGB1', 'commot-CellChat-LAMA2-ITGA3_ITGB1', 'commot-CellChat-LAMA2-ITGA9_ITGB1', 'commot-CellChat-LAMA2-DAG1', 'commot-CellChat-LAMA2-CD44', 'commot-CellChat-LAMA2-ITGAV_ITGB8', 'commot-CellChat-LAMA2-ITGA1_ITGB1', 'commot-CellChat-EFNA1-EPHA4', 'commot-CellChat-EFNA1-EPHA3', 'commot-CellChat-EFNA1-EPHA7', 'commot-CellChat-CD46-JAG1', 'commot-CellChat-AGRN-DAG1', 'commot-CellChat-C3-ITGAX_ITGB2', 'commot-CellChat-NECTIN1-CD96', 'commot-CellChat-DLL1-NOTCH2', 'commot-CellChat-DLL1-NOTCH1', 'commot-CellChat-DLL1-NOTCH3', 'commot-CellChat-SEMA4D-PLXNB1', 'commot-CellChat-SEMA4D-PLXNB2', 'commot-CellChat-SEMA6A-PLXNA2', 'commot-CellChat-SEMA6A-PLXNA4', 'commot-CellChat-COL6A2-SDC4', 'commot-CellChat-COL6A2-ITGA2_ITGB1', 'commot-CellChat-COL6A2-ITGA3_ITGB1', 'commot-CellChat-COL6A2-ITGA9_ITGB1', 'commot-CellChat-COL6A2-CD44', 'commot-CellChat-COL6A2-ITGAV_ITGB8', 'commot-CellChat-COL6A2-ITGA1_ITGB1', 'commot-CellChat-FN1-ITGA4_ITGB1', 'commot-CellChat-FN1-SDC4', 'commot-CellChat-FN1-ITGA3_ITGB1', 'commot-CellChat-FN1-CD44', 'commot-CellChat-FN1-ITGAV_ITGB8', 'commot-CellChat-FN1-ITGA5_ITGB1', 'commot-CellChat-FN1-ITGAV_ITGB1', 'commot-CellChat-HSPG2-DAG1', 'commot-CellChat-PDGFA-PDGFRA', 'commot-CellChat-PDGFA-PDGFRB', 'commot-CellChat-EFNA5-EPHA4', 'commot-CellChat-EFNA5-EPHA3', 'commot-CellChat-EFNA5-EPHA7', 'commot-CellChat-MPZL1-MPZL1', 'commot-CellChat-COL1A2-SDC4', 'commot-CellChat-COL1A2-ITGA2_ITGB1', 'commot-CellChat-COL1A2-ITGA3_ITGB1', 'commot-CellChat-COL1A2-ITGA9_ITGB1', 'commot-CellChat-COL1A2-CD44', 'commot-CellChat-COL1A2-ITGAV_ITGB8', 'commot-CellChat-COL1A2-ITGA1_ITGB1', 'commot-CellChat-JAG1-NOTCH2', 'commot-CellChat-JAG1-NOTCH1', 'commot-CellChat-JAG1-NOTCH3', 'commot-CellChat-LAMB1-ITGA6_ITGB4', 'commot-CellChat-LAMB1-ITGA6_ITGB1', 'commot-CellChat-LAMB1-ITGA2_ITGB1', 'commot-CellChat-LAMB1-ITGA3_ITGB1', 'commot-CellChat-LAMB1-ITGA9_ITGB1', 'commot-CellChat-LAMB1-DAG1', 'commot-CellChat-LAMB1-CD44', 'commot-CellChat-LAMB1-ITGAV_ITGB8', 'commot-CellChat-LAMB1-ITGA1_ITGB1', 'commot-CellChat-LAMA5-ITGA6_ITGB4', 'commot-CellChat-LAMA5-ITGA6_ITGB1', 'commot-CellChat-LAMA5-ITGA2_ITGB1', 'commot-CellChat-LAMA5-ITGA3_ITGB1', 'commot-CellChat-LAMA5-ITGA9_ITGB1', 'commot-CellChat-LAMA5-DAG1', 'commot-CellChat-LAMA5-CD44', 'commot-CellChat-LAMA5-ITGAV_ITGB8', 'commot-CellChat-LAMA5-ITGA1_ITGB1', 'commot-CellChat-WNT5B-FZD6', 'commot-CellChat-GRN-SORT1', 'commot-CellChat-NRG2-ERBB2_ERBB4', 'commot-CellChat-NRG2-ERBB3', 'commot-CellChat-NRG2-ERBB4', 'commot-CellChat-NRG2-ERBB2_ERBB3', 'commot-CellChat-CSF1-CSF1R', 'commot-CellChat-F11R-JAM3', 'commot-CellChat-F11R-F11R', 'commot-CellChat-F11R-ITGAL_ITGB2', 'commot-CellChat-PECAM1-PECAM1', 'commot-CellChat-SEMA4A-NRP1_PLXNA3', 'commot-CellChat-SEMA4A-NRP1_PLXNA1', 'commot-CellChat-SEMA4A-NRP1_PLXNA2', 'commot-CellChat-SEMA4A-NRP1_PLXNA4', 'commot-CellChat-SEMA4A-PLXNB1', 'commot-CellChat-SEMA4A-PLXNB2', 'commot-CellChat-GAS6-MERTK', 'commot-CellChat-GAS6-AXL', 'commot-CellChat-PDGFC-PDGFRA', 'commot-CellChat-COL4A6-SDC4', 'commot-CellChat-COL4A6-ITGA2_ITGB1', 'commot-CellChat-COL4A6-ITGA3_ITGB1', 'commot-CellChat-COL4A6-ITGA9_ITGB1', 'commot-CellChat-COL4A6-CD44', 'commot-CellChat-COL4A6-ITGAV_ITGB8', 'commot-CellChat-COL4A6-ITGA1_ITGB1', 'commot-CellChat-LAMA4-ITGA6_ITGB4', 'commot-CellChat-LAMA4-ITGA6_ITGB1', 'commot-CellChat-LAMA4-ITGA2_ITGB1', 'commot-CellChat-LAMA4-ITGA3_ITGB1', 'commot-CellChat-LAMA4-ITGA9_ITGB1', 'commot-CellChat-LAMA4-DAG1', 'commot-CellChat-LAMA4-CD44', 'commot-CellChat-LAMA4-ITGAV_ITGB8', 'commot-CellChat-LAMA4-ITGA1_ITGB1', 'commot-CellChat-EFNB2-EPHB4', 'commot-CellChat-EFNB2-EPHA4', 'commot-CellChat-MDK-SDC2', 'commot-CellChat-MDK-ITGA4_ITGB1', 'commot-CellChat-MDK-SDC4', 'commot-CellChat-MDK-ITGA6_ITGB1', 'commot-CellChat-MDK-LRP1', 'commot-CellChat-MDK-NCL', 'commot-CellChat-COL4A3-SDC4', 'commot-CellChat-COL4A3-ITGA2_ITGB1', 'commot-CellChat-COL4A3-ITGA3_ITGB1', 'commot-CellChat-COL4A3-ITGA9_ITGB1', 'commot-CellChat-COL4A3-CD44', 'commot-CellChat-COL4A3-ITGAV_ITGB8', 'commot-CellChat-COL4A3-ITGA1_ITGB1', 'commot-CellChat-COL4A5-SDC4', 'commot-CellChat-COL4A5-ITGA2_ITGB1', 'commot-CellChat-COL4A5-ITGA3_ITGB1', 'commot-CellChat-COL4A5-ITGA9_ITGB1', 'commot-CellChat-COL4A5-CD44', 'commot-CellChat-COL4A5-ITGAV_ITGB8', 'commot-CellChat-COL4A5-ITGA1_ITGB1', 'commot-CellChat-COL6A3-SDC4', 'commot-CellChat-COL6A3-ITGA2_ITGB1', 'commot-CellChat-COL6A3-ITGA3_ITGB1', 'commot-CellChat-COL6A3-ITGA9_ITGB1', 'commot-CellChat-COL6A3-CD44', 'commot-CellChat-COL6A3-ITGAV_ITGB8', 'commot-CellChat-COL6A3-ITGA1_ITGB1', 'commot-CellChat-PTN-SDC2', 'commot-CellChat-PTN-SDC4', 'commot-CellChat-PTN-SDC3', 'commot-CellChat-PTN-NCL', 'commot-CellChat-CADM1-CADM1', 'commot-CellChat-NRG1-ERBB2_ERBB4', 'commot-CellChat-NRG1-ERBB3', 'commot-CellChat-NRG1-ERBB4', 'commot-CellChat-NRG1-ERBB2_ERBB3', 'commot-CellChat-TNC-SDC4', 'commot-CellChat-TNC-ITGA9_ITGB1', 'commot-CellChat-THBS3-CD47', 'commot-CellChat-THBS3-SDC4', 'commot-CellChat-THBS3-ITGA3_ITGB1', 'commot-CellChat-TGFB2-ACVR1_TGFBR1_TGFBR2', 'commot-CellChat-TGFB2-TGFBR1_TGFBR2', 'commot-CellChat-TGFB2-ACVR1B_TGFBR2', 'commot-CellChat-SEMA3C-NRP1_PLXNA3', 'commot-CellChat-SEMA3C-NRP1_PLXNA1', 'commot-CellChat-SEMA3C-NRP1_PLXNA2', 'commot-CellChat-SEMA3C-NRP1_PLXNA4', 'commot-CellChat-SEMA3C-PLXND1', 'commot-CellChat-TNXB-SDC4', 'commot-CellChat-TNXB-ITGA9_ITGB1', 'commot-CellChat-MIF-CD74_CXCR4', 'commot-CellChat-MIF-CD74_CD44', 'commot-CellChat-IGF1-ITGA6_ITGB4', 'commot-CellChat-IGF1-IGF1R', 'commot-CellChat-COL1A1-SDC4', 'commot-CellChat-COL1A1-ITGA2_ITGB1', 'commot-CellChat-COL1A1-ITGA3_ITGB1', 'commot-CellChat-COL1A1-ITGA9_ITGB1', 'commot-CellChat-COL1A1-CD44', 'commot-CellChat-COL1A1-ITGAV_ITGB8', 'commot-CellChat-COL1A1-ITGA1_ITGB1', 'commot-CellChat-COL4A1-SDC4', 'commot-CellChat-COL4A1-ITGA2_ITGB1', 'commot-CellChat-COL4A1-ITGA3_ITGB1', 'commot-CellChat-COL4A1-ITGA9_ITGB1', 'commot-CellChat-COL4A1-CD44', 'commot-CellChat-COL4A1-ITGAV_ITGB8', 'commot-CellChat-COL4A1-ITGA1_ITGB1', 'commot-CellChat-APP-CD74', 'commot-CellChat-CD96-NECTIN1', 'commot-CellChat-CD96-PVR', 'commot-CellChat-PTPRM-PTPRM', 'commot-CellChat-SEMA5A-PLXNA3', 'commot-CellChat-SEMA5A-PLXNA1', 'commot-CellChat-LGALS9-PTPRC', 'commot-CellChat-LGALS9-CD44', 'commot-CellChat-NEGR1-NEGR1', 'commot-CellChat-AGRN', 'commot-CellChat-APP', 'commot-CellChat-CADM', 'commot-CellChat-CD45', 'commot-CellChat-CD46', 'commot-CellChat-CD96', 'commot-CellChat-CD99', 'commot-CellChat-CDH', 'commot-CellChat-CDH1', 'commot-CellChat-COLLAGEN', 'commot-CellChat-COMPLEMENT', 'commot-CellChat-CSF', 'commot-CellChat-EPHA', 'commot-CellChat-EPHB', 'commot-CellChat-FN1', 'commot-CellChat-GALECTIN', 'commot-CellChat-GAS', 'commot-CellChat-GRN', 'commot-CellChat-HSPG', 'commot-CellChat-IGF', 'commot-CellChat-JAM', 'commot-CellChat-LAMININ', 'commot-CellChat-MIF', 'commot-CellChat-MK', 'commot-CellChat-MPZ', 'commot-CellChat-NECTIN', 'commot-CellChat-NEGR', 'commot-CellChat-NOTCH', 'commot-CellChat-NRG', 'commot-CellChat-NRXN', 'commot-CellChat-PDGF', 'commot-CellChat-PECAM1', 'commot-CellChat-PTN', 'commot-CellChat-PTPRM', 'commot-CellChat-SEMA3', 'commot-CellChat-SEMA4', 'commot-CellChat-SEMA5', 'commot-CellChat-SEMA6', 'commot-CellChat-TENASCIN', 'commot-CellChat-TGFb', 'commot-CellChat-THBS', 'commot-CellChat-VISFATIN', 'commot-CellChat-ncWNT', 'commot-CellChat-total-total'
python
os.environ["PATH"] += os.pathsep + '/PROJ2/FLOAT/jinwen/apps/miniconda3/envs/COMMOT/bin'
#print("total_network")
ct.pl.plot_cluster_communication_network(a_dis500, uns_names=['commot_cluster'+'-'+cluster_name+'-'+lr_database+'-total-total'],
    nx_node_pos=None, nx_bg_pos=False, p_value_cutoff = 5e-2, filename='total-total_cluster.png', nx_node_cmap='Light24')
display(Image.open("./total-total_cluster.png"))
细胞通讯网络图中展示细胞类型互作情况。每一种颜色代表着一种细胞类型；线条从一个细胞类型指向自己或者其他的细胞类型，代表着互作的情况。

结果文件 ​

  • sender_receiver_signature.png/pdf 受配体信号共表达图

  • *_signature_stream.png/pdf 细胞类型互作信号流图

  • *_cluster.png/pdf 细胞类型互作网络图

  • *_chord_plot.png/pdf 细胞类型互作和弦图 结果目录：目录下包括此项分析所涉及的所有图片以及表格等结果文件

文献案例解析 ​

  • 文献一： 文献《Single-cell and spatial transcriptome analyses reveal tertiary lymphoid structures linked to tumour progression and immunotherapy response in nasopharyngeal carcinoma》前文通过细胞通讯发现 CXCL13+ CAFs B cells

参考资料 ​

[1] Cang Z, Zhao Y, Almet A A et al. Screening cell–cell communication in spatial transcriptomics via collective optimal transport[J]. Nat Methods, 2023, 20: 218–228.

[2] Takano Y, Suzuki J, Nomura K et al. Spatially resolved gene expression profiling of tumor microenvironment reveals key steps of lung adenocarcinoma development[J]. Nat Commun, 2024, 15: 10637.

0 条评论·0 条回复