Downstream analysis on Visium HD data of mouse small intestine

# Importing packages
import os
import metachat as mc
import scanpy as sc

import matplotlib.pyplot as plt
from matplotlib import rcParams
from sklearn.cluster import KMeans
rcParams['pdf.fonttype'] = 42
import warnings
warnings.filterwarnings("ignore", category=FutureWarning)

# Setting your work dictionary
os.chdir("/home/project/metachat_packages/")

Import MetaChat results

adata = sc.read('datasets/mouse_small_intestine/metachat_result.h5ad')
adata.obs['Cluster'] = adata.obs['Cluster'].astype(str).astype('category')

adata

AnnData object with n_obs × n_vars = 3264 × 19488
    obs: 'in_tissue', 'array_row', 'array_col', 'location_id', 'region', 'Cluster', 'barrier_shapes', 'barrier', 'LRC_Blood_avg_markers', 'LRC_Blood_marker_unfiltered', 'LRC_Blood_marker_filtered', 'visualize_LRC_marker', 'LRC_Blood_closepoint_cluster1'
    var: 'gene_ids', 'feature_types', 'genome'
    uns: 'Cluster_colors', 'LRC_Blood_marker_filtered_colors', 'LRC_Blood_marker_unfiltered_colors', 'MetaChat-MetaChatDB-info', 'barrier_shapes', 'df_metasen_filtered', 'log1p', 'non_visible_pair', 'spatial', 'spatialdata_attrs', 'visualize_LRC_marker_colors'
    obsm: 'MetaChat-MetaChatDB-sum-receiver', 'MetaChat-MetaChatDB-sum-sender', 'spatial'
    obsp: 'LRC_shortest_Blood_dist80_cluster1', 'MetaChat-MetaChatDB-receiver-HMDB0000011-Hcar2', 'MetaChat-MetaChatDB-receiver-HMDB0000011-Slc16a7', 'MetaChat-MetaChatDB-receiver-HMDB0000011-Slc5a8', 'MetaChat-MetaChatDB-receiver-HMDB0000012-Slc29a2', 'MetaChat-MetaChatDB-receiver-HMDB0000014-Slc29a2', 'MetaChat-MetaChatDB-receiver-HMDB0000031-Ar', 'MetaChat-MetaChatDB-receiver-HMDB0000033-Slc16a13', 'MetaChat-MetaChatDB-receiver-HMDB0000034-Hnrnpa2b1', 'MetaChat-MetaChatDB-receiver-HMDB0000034-Ryr1', 'MetaChat-MetaChatDB-receiver-HMDB0000034-Slc28a3', 'MetaChat-MetaChatDB-receiver-HMDB0000034-Slc29a2', 'MetaChat-MetaChatDB-receiver-HMDB0000034-Slc29a3', 'MetaChat-MetaChatDB-receiver-HMDB0000034-Slc35f5', 'MetaChat-MetaChatDB-receiver-HMDB0000034-Slc43a3', 'MetaChat-MetaChatDB-receiver-HMDB0000036-Slc10a1', 'MetaChat-MetaChatDB-receiver-HMDB0000036-Slc10a2', 'MetaChat-MetaChatDB-receiver-HMDB0000036-Slc51a', 'MetaChat-MetaChatDB-receiver-HMDB0000036-Slc51b', 'MetaChat-MetaChatDB-receiver-HMDB0000037-Nr3c2', 'MetaChat-MetaChatDB-receiver-HMDB0000039-Ffar2', 'MetaChat-MetaChatDB-receiver-HMDB0000039-Ffar3', 'MetaChat-MetaChatDB-receiver-HMDB0000039-Hcar2', 'MetaChat-MetaChatDB-receiver-HMDB0000039-Slc5a12', 'MetaChat-MetaChatDB-receiver-HMDB0000039-Slc5a8', 'MetaChat-MetaChatDB-receiver-HMDB0000042-Fabp4', 'MetaChat-MetaChatDB-receiver-HMDB0000042-Ffar2', 'MetaChat-MetaChatDB-receiver-HMDB0000042-Ffar3', 'MetaChat-MetaChatDB-receiver-HMDB0000043-Slc6a1', 'MetaChat-MetaChatDB-receiver-HMDB0000043-Slc6a12', 'MetaChat-MetaChatDB-receiver-HMDB0000045-Adora1', 'MetaChat-MetaChatDB-receiver-HMDB0000045-Adora2a', 'MetaChat-MetaChatDB-receiver-HMDB0000045-Slc25a17', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Adora1', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Adora2a', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Adora2b', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Adora3', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Cxcr4', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Drd2', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Ryr1', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Slc28a2', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Slc29a1', 'MetaChat-MetaChatDB-receiver-HMDB0000050-Slc29a2', 'MetaChat-MetaChatDB-receiver-HMDB0000051-Rhbg', 'MetaChat-MetaChatDB-receiver-HMDB0000056-Mrgprd', 'MetaChat-MetaChatDB-receiver-HMDB0000056-Slc36a1', 'MetaChat-MetaChatDB-receiver-HMDB0000056-Slc6a6', 'MetaChat-MetaChatDB-receiver-HMDB0000058-Abcc4', 'MetaChat-MetaChatDB-receiver-HMDB0000058-Abcc5', 'MetaChat-MetaChatDB-receiver-HMDB0000058-Abcc8', 'MetaChat-MetaChatDB-receiver-HMDB0000058-Cngb1', 'MetaChat-MetaChatDB-receiver-HMDB0000058-Hcn3', 'MetaChat-MetaChatDB-receiver-HMDB0000058-Hcn4', 'MetaChat-MetaChatDB-receiver-HMDB0000058-Ryr1', 'MetaChat-MetaChatDB-receiver-HMDB0000058-Slc22a7', 'MetaChat-MetaChatDB-receiver-HMDB0000062-Slc22a21', 'MetaChat-MetaChatDB-receiver-HMDB0000062-Slc22a4', 'MetaChat-MetaChatDB-receiver-HMDB0000063-Adgrg3', 'MetaChat-MetaChatDB-receiver-HMDB0000063-Catsper3', 'MetaChat-MetaChatDB-receiver-HMDB0000063-Nr3c1', 'MetaChat-MetaChatDB-receiver-HMDB0000063-Nr3c2', 'MetaChat-MetaChatDB-receiver-HMDB0000064-Slc16a12', 'MetaChat-MetaChatDB-receiver-HMDB0000064-Slc25a32', 'MetaChat-MetaChatDB-receiver-HMDB0000064-Slc6a8', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Abca1', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Abca13', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Abcg1', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Atp6v0a1', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Cd247', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Cd36', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Cd81', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Kcnma1', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Ldlr', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Lsr', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Npc1l1', 'MetaChat-MetaChatDB-receiver-HMDB0000067-Nr1h2', 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'MetaChat-MetaChatDB-sender-HMDB0000641-Slc6a15', 'MetaChat-MetaChatDB-sender-HMDB0000641-Slc6a17', 'MetaChat-MetaChatDB-sender-HMDB0000641-Slc6a19', 'MetaChat-MetaChatDB-sender-HMDB0000641-Slc7a5', 'MetaChat-MetaChatDB-sender-HMDB0000641-Slc7a6', 'MetaChat-MetaChatDB-sender-HMDB0000641-Slc7a7', 'MetaChat-MetaChatDB-sender-HMDB0000641-Slc7a8', 'MetaChat-MetaChatDB-sender-HMDB0000660-Slc2a2', 'MetaChat-MetaChatDB-sender-HMDB0000660-Slc2a5', 'MetaChat-MetaChatDB-sender-HMDB0000660-Slc2a7', 'MetaChat-MetaChatDB-sender-HMDB0000660-Slc2a8', 'MetaChat-MetaChatDB-sender-HMDB0000660-Tas1r3', 'MetaChat-MetaChatDB-sender-HMDB0000673-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0000673-Fabp1', 'MetaChat-MetaChatDB-sender-HMDB0000673-Fabp5', 'MetaChat-MetaChatDB-sender-HMDB0000673-Fabp7', 'MetaChat-MetaChatDB-sender-HMDB0000673-Ffar1', 'MetaChat-MetaChatDB-sender-HMDB0000673-Slc27a5', 'MetaChat-MetaChatDB-sender-HMDB0000673-Slc27a6', 'MetaChat-MetaChatDB-sender-HMDB0000673-Trpv4', 'MetaChat-MetaChatDB-sender-HMDB0000696-Slc38a5', 'MetaChat-MetaChatDB-sender-HMDB0000696-Slc43a1', 'MetaChat-MetaChatDB-sender-HMDB0000696-Slc43a2', 'MetaChat-MetaChatDB-sender-HMDB0000696-Slc6a19', 'MetaChat-MetaChatDB-sender-HMDB0000696-Slc7a5', 'MetaChat-MetaChatDB-sender-HMDB0000719-Slc43a1', 'MetaChat-MetaChatDB-sender-HMDB0000722-Gpbar1', 'MetaChat-MetaChatDB-sender-HMDB0000722-Slc10a2', 'MetaChat-MetaChatDB-sender-HMDB0000759-Slc15a1', 'MetaChat-MetaChatDB-sender-HMDB0000761-Gpbar1', 'MetaChat-MetaChatDB-sender-HMDB0000761-Nr1h4', 'MetaChat-MetaChatDB-sender-HMDB0000761-Nr1i2', 'MetaChat-MetaChatDB-sender-HMDB0000761-Pparg', 'MetaChat-MetaChatDB-sender-HMDB0000761-Rxra', 'MetaChat-MetaChatDB-sender-HMDB0000761-Vdr', 'MetaChat-MetaChatDB-sender-HMDB0000791-Slc25a20', 'MetaChat-MetaChatDB-sender-HMDB0000801-Ppara', 'MetaChat-MetaChatDB-sender-HMDB0000801-Pparg', 'MetaChat-MetaChatDB-sender-HMDB0000806-Slc27a2', 'MetaChat-MetaChatDB-sender-HMDB0000827-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0000827-Ffar4', 'MetaChat-MetaChatDB-sender-HMDB0000827-Ppara', 'MetaChat-MetaChatDB-sender-HMDB0000827-Slc27a2', 'MetaChat-MetaChatDB-sender-HMDB0000827-Slc27a5', 'MetaChat-MetaChatDB-sender-HMDB0000870-Cxcr4', 'MetaChat-MetaChatDB-sender-HMDB0000870-Hrh1', 'MetaChat-MetaChatDB-sender-HMDB0000870-Hrh2', 'MetaChat-MetaChatDB-sender-HMDB0000870-Hrh3', 'MetaChat-MetaChatDB-sender-HMDB0000870-Hrh4', 'MetaChat-MetaChatDB-sender-HMDB0000870-Rho', 'MetaChat-MetaChatDB-sender-HMDB0000870-Slc22a2', 'MetaChat-MetaChatDB-sender-HMDB0000870-Slc22a21', 'MetaChat-MetaChatDB-sender-HMDB0000870-Slc22a3', 'MetaChat-MetaChatDB-sender-HMDB0000876-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0000876-Got2', 'MetaChat-MetaChatDB-sender-HMDB0000876-Tlr2', 'MetaChat-MetaChatDB-sender-HMDB0000876-Vdr', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrm1', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrm2', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrm3', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrm5', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrna1', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrna2', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrna3', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrna4', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrna5', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrna6', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrna7', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrna9', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrnb1', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrnb2', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrnb3', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrnb4', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrnd', 'MetaChat-MetaChatDB-sender-HMDB0000895-Chrne', 'MetaChat-MetaChatDB-sender-HMDB0000895-Slc22a1', 'MetaChat-MetaChatDB-sender-HMDB0000895-Slc22a4', 'MetaChat-MetaChatDB-sender-HMDB0000896-Gpbar1', 'MetaChat-MetaChatDB-sender-HMDB0000902-Cd38', 'MetaChat-MetaChatDB-sender-HMDB0000902-P2rx7', 'MetaChat-MetaChatDB-sender-HMDB0000902-Slc25a47', 'MetaChat-MetaChatDB-sender-HMDB0000902-Slc25a51', 'MetaChat-MetaChatDB-sender-HMDB0000951-Nr1h4', 'MetaChat-MetaChatDB-sender-HMDB0000951-Slco1b2', 'MetaChat-MetaChatDB-sender-HMDB0001032-Abcc3', 'MetaChat-MetaChatDB-sender-HMDB0001032-Ppara', 'MetaChat-MetaChatDB-sender-HMDB0001032-Slc10a6', 'MetaChat-MetaChatDB-sender-HMDB0001032-Slco2b1', 'MetaChat-MetaChatDB-sender-HMDB0001043-Adipor2', 'MetaChat-MetaChatDB-sender-HMDB0001043-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0001043-Fabp3', 'MetaChat-MetaChatDB-sender-HMDB0001043-Fabp7', 'MetaChat-MetaChatDB-sender-HMDB0001043-Kcnk4', 'MetaChat-MetaChatDB-sender-HMDB0001043-Ppara', 'MetaChat-MetaChatDB-sender-HMDB0001043-Pparg', 'MetaChat-MetaChatDB-sender-HMDB0001043-Rxra', 'MetaChat-MetaChatDB-sender-HMDB0001043-Slc27a1', 'MetaChat-MetaChatDB-sender-HMDB0001043-Slc27a5', 'MetaChat-MetaChatDB-sender-HMDB0001043-Slc3a2', 'MetaChat-MetaChatDB-sender-HMDB0001043-Trpv3', 'MetaChat-MetaChatDB-sender-HMDB0001043-Trpv4', 'MetaChat-MetaChatDB-sender-HMDB0001085-Ltb4r2', 'MetaChat-MetaChatDB-sender-HMDB0001085-Ppara', 'MetaChat-MetaChatDB-sender-HMDB0001139-Ptgfr', 'MetaChat-MetaChatDB-sender-HMDB0001139-Slc22a1', 'MetaChat-MetaChatDB-sender-HMDB0001139-Slc22a2', 'MetaChat-MetaChatDB-sender-HMDB0001139-Slco2a1', 'MetaChat-MetaChatDB-sender-HMDB0001173-Adora2b', 'MetaChat-MetaChatDB-sender-HMDB0001178-Cd38', 'MetaChat-MetaChatDB-sender-HMDB0001198-Abcc6', 'MetaChat-MetaChatDB-sender-HMDB0001198-Cysltr1', 'MetaChat-MetaChatDB-sender-HMDB0001220-Abcc4', 'MetaChat-MetaChatDB-sender-HMDB0001220-Ptger1', 'MetaChat-MetaChatDB-sender-HMDB0001220-Ptger2', 'MetaChat-MetaChatDB-sender-HMDB0001220-Ptger3', 'MetaChat-MetaChatDB-sender-HMDB0001220-Ptger4', 'MetaChat-MetaChatDB-sender-HMDB0001220-Slc22a1', 'MetaChat-MetaChatDB-sender-HMDB0001220-Slc22a2', 'MetaChat-MetaChatDB-sender-HMDB0001220-Slc22a6', 'MetaChat-MetaChatDB-sender-HMDB0001220-Slc22a8', 'MetaChat-MetaChatDB-sender-HMDB0001220-Slco2a1', 'MetaChat-MetaChatDB-sender-HMDB0001248-Slc25a17', 'MetaChat-MetaChatDB-sender-HMDB0001256-Atp13a2', 'MetaChat-MetaChatDB-sender-HMDB0001256-Casr', 'MetaChat-MetaChatDB-sender-HMDB0001256-Grin2b', 'MetaChat-MetaChatDB-sender-HMDB0001256-Slc22a1', 'MetaChat-MetaChatDB-sender-HMDB0001256-Slc22a4', 'MetaChat-MetaChatDB-sender-HMDB0001257-Grin2b', 'MetaChat-MetaChatDB-sender-HMDB0001257-Slc18b1', 'MetaChat-MetaChatDB-sender-HMDB0001264-Slc2a1', 'MetaChat-MetaChatDB-sender-HMDB0001264-Slc2a10', 'MetaChat-MetaChatDB-sender-HMDB0001264-Slc2a2', 'MetaChat-MetaChatDB-sender-HMDB0001264-Slc2a4', 'MetaChat-MetaChatDB-sender-HMDB0001311-Hcar1', 'MetaChat-MetaChatDB-sender-HMDB0001311-Slc16a1', 'MetaChat-MetaChatDB-sender-HMDB0001314-Abcc4', 'MetaChat-MetaChatDB-sender-HMDB0001314-Cnga1', 'MetaChat-MetaChatDB-sender-HMDB0001314-Cnga2', 'MetaChat-MetaChatDB-sender-HMDB0001314-Cnga3', 'MetaChat-MetaChatDB-sender-HMDB0001314-Cngb1', 'MetaChat-MetaChatDB-sender-HMDB0001314-Cngb3', 'MetaChat-MetaChatDB-sender-HMDB0001314-Hcn4', 'MetaChat-MetaChatDB-sender-HMDB0001314-Slc22a7', 'MetaChat-MetaChatDB-sender-HMDB0001335-Ptgir', 'MetaChat-MetaChatDB-sender-HMDB0001341-P2ry1', 'MetaChat-MetaChatDB-sender-HMDB0001341-P2ry12', 'MetaChat-MetaChatDB-sender-HMDB0001341-P2ry13', 'MetaChat-MetaChatDB-sender-HMDB0001341-P2ry2', 'MetaChat-MetaChatDB-sender-HMDB0001341-Slc25a42', 'MetaChat-MetaChatDB-sender-HMDB0001341-Slc35b1', 'MetaChat-MetaChatDB-sender-HMDB0001362-Gpr4', 'MetaChat-MetaChatDB-sender-HMDB0001362-Gpr65', 'MetaChat-MetaChatDB-sender-HMDB0001362-Gpr68', 'MetaChat-MetaChatDB-sender-HMDB0001396-Folr1', 'MetaChat-MetaChatDB-sender-HMDB0001403-Ptgdr', 'MetaChat-MetaChatDB-sender-HMDB0001403-Ptgdr2', 'MetaChat-MetaChatDB-sender-HMDB0001403-Slco2a1', 'MetaChat-MetaChatDB-sender-HMDB0001406-Slc29a1', 'MetaChat-MetaChatDB-sender-HMDB0001414-Slc22a4', 'MetaChat-MetaChatDB-sender-HMDB0001425-Slc10a6', 'MetaChat-MetaChatDB-sender-HMDB0001425-Slc22a8', 'MetaChat-MetaChatDB-sender-HMDB0001425-Slc51b', 'MetaChat-MetaChatDB-sender-HMDB0001425-Slco2b1', 'MetaChat-MetaChatDB-sender-HMDB0001429-Slc20a2', 'MetaChat-MetaChatDB-sender-HMDB0001429-Slc25a30', 'MetaChat-MetaChatDB-sender-HMDB0001442-Abcc4', 'MetaChat-MetaChatDB-sender-HMDB0001442-Ptger1', 'MetaChat-MetaChatDB-sender-HMDB0001448-Fgfr3', 'MetaChat-MetaChatDB-sender-HMDB0001448-Slc25a30', 'MetaChat-MetaChatDB-sender-HMDB0001452-Tbxa2r', 'MetaChat-MetaChatDB-sender-HMDB0001488-Hcar2', 'MetaChat-MetaChatDB-sender-HMDB0001488-Slc5a8', 'MetaChat-MetaChatDB-sender-HMDB0001514-Slc2a1', 'MetaChat-MetaChatDB-sender-HMDB0001514-Slc2a2', 'MetaChat-MetaChatDB-sender-HMDB0001514-Slc2a4', 'MetaChat-MetaChatDB-sender-HMDB0001520-Slc25a17', 'MetaChat-MetaChatDB-sender-HMDB0001546-Slc25a33', 'MetaChat-MetaChatDB-sender-HMDB0001546-Slc25a36', 'MetaChat-MetaChatDB-sender-HMDB0001547-Nr3c1', 'MetaChat-MetaChatDB-sender-HMDB0001547-Nr3c2', 'MetaChat-MetaChatDB-sender-HMDB0001547-Slc22a3', 'MetaChat-MetaChatDB-sender-HMDB0001830-Abcg3', 'MetaChat-MetaChatDB-sender-HMDB0001830-Ar', 'MetaChat-MetaChatDB-sender-HMDB0001830-Catsper1', 'MetaChat-MetaChatDB-sender-HMDB0001830-Catsper2', 'MetaChat-MetaChatDB-sender-HMDB0001830-Catsper3', 'MetaChat-MetaChatDB-sender-HMDB0001830-Catsper4', 'MetaChat-MetaChatDB-sender-HMDB0001830-Pgr', 'MetaChat-MetaChatDB-sender-HMDB0001846-Slc25a32', 'MetaChat-MetaChatDB-sender-HMDB0001852-Crabp1', 'MetaChat-MetaChatDB-sender-HMDB0001852-Crabp2', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rara', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rarb', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rarg', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rxra', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rxrb', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rxrg', 'MetaChat-MetaChatDB-sender-HMDB0001999-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0001999-Fabp7', 'MetaChat-MetaChatDB-sender-HMDB0001999-Ffar4', 'MetaChat-MetaChatDB-sender-HMDB0001999-Ppara', 'MetaChat-MetaChatDB-sender-HMDB0001999-Pparg', 'MetaChat-MetaChatDB-sender-HMDB0002003-Slc27a2', 'MetaChat-MetaChatDB-sender-HMDB0002086-Amn', 'MetaChat-MetaChatDB-sender-HMDB0002086-Cubn', 'MetaChat-MetaChatDB-sender-HMDB0002183-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0002183-Fabp7', 'MetaChat-MetaChatDB-sender-HMDB0002183-Ffar1', 'MetaChat-MetaChatDB-sender-HMDB0002183-Ffar4', 'MetaChat-MetaChatDB-sender-HMDB0002183-Mfsd2a', 'MetaChat-MetaChatDB-sender-HMDB0002183-Pparg', 'MetaChat-MetaChatDB-sender-HMDB0002183-Rxra', 'MetaChat-MetaChatDB-sender-HMDB0002183-Slc27a1', 'MetaChat-MetaChatDB-sender-HMDB0002200-Oxgr1', 'MetaChat-MetaChatDB-sender-HMDB0002200-P2ry12', 'MetaChat-MetaChatDB-sender-HMDB0002925-Slc27a5', 'MetaChat-MetaChatDB-sender-HMDB0002961-Ar', 'MetaChat-MetaChatDB-sender-HMDB0002961-Glp1r', 'MetaChat-MetaChatDB-sender-HMDB0003125-Aqp3', 'MetaChat-MetaChatDB-sender-HMDB0003125-Aqp5', 'MetaChat-MetaChatDB-sender-HMDB0003125-Aqp8', 'MetaChat-MetaChatDB-sender-HMDB0003125-Trpa1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Fabp1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Flvcr2', 'MetaChat-MetaChatDB-sender-HMDB0003178-Lrp1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Nr1d1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Nr1d2', 'MetaChat-MetaChatDB-sender-HMDB0003178-Pgrmc2', 'MetaChat-MetaChatDB-sender-HMDB0003178-Slc46a1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Slc48a1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Tlr4', 'MetaChat-MetaChatDB-sender-HMDB0003178-Trpv6', 'MetaChat-MetaChatDB-sender-HMDB0003229-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0003229-Ffar4', 'MetaChat-MetaChatDB-sender-HMDB0003229-Fzd2', 'MetaChat-MetaChatDB-sender-HMDB0003229-Slc27a2', 'MetaChat-MetaChatDB-sender-HMDB0003229-Ucp1', 'MetaChat-MetaChatDB-sender-HMDB0003276-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0003378-Npr1', 'MetaChat-MetaChatDB-sender-HMDB0003378-Trpa1', 'MetaChat-MetaChatDB-sender-HMDB0003406-Grid1', 'MetaChat-MetaChatDB-sender-HMDB0003406-Grid2', 'MetaChat-MetaChatDB-sender-HMDB0003406-Grin1', 'MetaChat-MetaChatDB-sender-HMDB0003406-Grin2a', 'MetaChat-MetaChatDB-sender-HMDB0003406-Lrrc8d', 'MetaChat-MetaChatDB-sender-HMDB0003406-Slc7a10', 'MetaChat-MetaChatDB-sender-HMDB0003550-Cubn', 'MetaChat-MetaChatDB-sender-HMDB0003550-Gc', 'MetaChat-MetaChatDB-sender-HMDB0003550-Lrp2', 'MetaChat-MetaChatDB-sender-HMDB0003550-Vdr', 'MetaChat-MetaChatDB-sender-HMDB0004484-Slc22a27', 'MetaChat-MetaChatDB-sender-HMDB0004484-Slc22a8', 'MetaChat-MetaChatDB-sender-HMDB0006216-Nr2f2', 'MetaChat-MetaChatDB-sender-HMDB0006224-Abcc4', 'MetaChat-MetaChatDB-sender-HMDB0006483-Slc1a1', 'MetaChat-MetaChatDB-sender-HMDB0006483-Slc1a3', 'MetaChat-MetaChatDB-sender-HMDB0006543-Slc22a2', 'MetaChat-MetaChatDB-sender-HMDB0011733-Slc15a1', 'MetaChat-MetaChatDB-sender-HMDB0012238-Slc5a8', 'MetaChat-MetaChatDB-sender-HMDB0015531-Slc11a2', 'MetaChat-MetaChatDB-sender-HMDB0015531-Slc25a37', 'MetaChat-MetaChatDB-sender-HMDB0015531-Slc39a14', 'MetaChat-MetaChatDB-sender-HMDB0015531-Slc40a1', 'MetaChat-MetaChatDB-sender-HMDB0015531-Tfr2', 'MetaChat-MetaChatDB-sender-HMDB0015531-Tfrc', 'MetaChat-MetaChatDB-sender-total-total', 'graph_visible', 'graph_visible_kneighb_5', 'spatial_distance_LRC_Blood', 'spatial_distance_LRC_base'

Compute group-level MCC of all pairs

To cluster MCC flow among all pairs, we need to compute group-level MCCs across all metabolite–sensor pairs.

# extract all_ms_pairs
df_metasen_filtered = adata.uns['df_metasen_filtered']
all_ms_pairs = (df_metasen_filtered['HMDB.ID'] + '-' + df_metasen_filtered['Sensor.Gene']).tolist()

mc.tl.communication_flow(adata = adata,
                         database_name = 'MetaChatDB',
                         sum_ms_pairs = all_ms_pairs,
                         k = 10)

Similarly, since the small intestine tissue is rolled, we used Napari to manually select a representative subregion for MCC flow clustering. Here, we directly import the preprocessed results of this selected subregion for further analysis.

adata = sc.read_h5ad('datasets/mouse_small_intestine/metachat_result_flow_subset.h5ad')
adata_sub = adata[adata.obs['subset_direction_shapes'] == True]

adata

AnnData object with n_obs × n_vars = 3264 × 19488
    obs: 'in_tissue', 'array_row', 'array_col', 'location_id', 'region', 'Cluster', 'barrier_shapes', 'barrier', 'LRC_Blood_avg_markers', 'LRC_Blood_marker_unfiltered', 'LRC_Blood_marker_filtered', 'visualize_LRC_marker', 'LRC_Blood_closepoint_cluster1', 'subset_direction_shapes'
    var: 'gene_ids', 'feature_types', 'genome'
    uns: 'Cluster_colors', 'LRC_Blood_marker_filtered_colors', 'LRC_Blood_marker_unfiltered_colors', 'MetaChat-MetaChatDB-info', 'barrier_shapes', 'df_metasen_filtered', 'log1p', 'non_visible_pair', 'spatial', 'spatialdata_attrs', 'subset_direction_shapes', 'visualize_LRC_marker_colors'
    obsm: 'MetaChat-MetaChatDB-sum-receiver', 'MetaChat-MetaChatDB-sum-sender', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000011-Hcar2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000011-Slc16a7', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000011-Slc5a8', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000012-Slc29a2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000014-Slc29a2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000031-Ar', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000033-Slc16a13', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000034-Hnrnpa2b1', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000034-Ryr1', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000034-Slc28a3', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000034-Slc29a2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000034-Slc29a3', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000034-Slc35f5', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000034-Slc43a3', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000036-Slc10a1', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000036-Slc10a2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000036-Slc51a', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000036-Slc51b', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000037-Nr3c2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000039-Ffar2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000039-Ffar3', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000039-Hcar2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000039-Slc5a12', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000039-Slc5a8', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000042-Fabp4', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000042-Ffar2', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000042-Ffar3', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000043-Slc6a1', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000043-Slc6a12', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000045-Adora1', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000045-Adora2a', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000045-Slc25a17', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000050-Adora1', 'MetaChat-vf-MetaChatDB-receiver-HMDB0000050-Adora2a', 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'MetaChat-MetaChatDB-sender-HMDB0001547-Slc22a3', 'MetaChat-MetaChatDB-sender-HMDB0001830-Abcg3', 'MetaChat-MetaChatDB-sender-HMDB0001830-Ar', 'MetaChat-MetaChatDB-sender-HMDB0001830-Catsper1', 'MetaChat-MetaChatDB-sender-HMDB0001830-Catsper2', 'MetaChat-MetaChatDB-sender-HMDB0001830-Catsper3', 'MetaChat-MetaChatDB-sender-HMDB0001830-Catsper4', 'MetaChat-MetaChatDB-sender-HMDB0001830-Pgr', 'MetaChat-MetaChatDB-sender-HMDB0001846-Slc25a32', 'MetaChat-MetaChatDB-sender-HMDB0001852-Crabp1', 'MetaChat-MetaChatDB-sender-HMDB0001852-Crabp2', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rara', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rarb', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rarg', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rxra', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rxrb', 'MetaChat-MetaChatDB-sender-HMDB0001852-Rxrg', 'MetaChat-MetaChatDB-sender-HMDB0001999-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0001999-Fabp7', 'MetaChat-MetaChatDB-sender-HMDB0001999-Ffar4', 'MetaChat-MetaChatDB-sender-HMDB0001999-Ppara', 'MetaChat-MetaChatDB-sender-HMDB0001999-Pparg', 'MetaChat-MetaChatDB-sender-HMDB0002003-Slc27a2', 'MetaChat-MetaChatDB-sender-HMDB0002086-Amn', 'MetaChat-MetaChatDB-sender-HMDB0002086-Cubn', 'MetaChat-MetaChatDB-sender-HMDB0002183-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0002183-Fabp7', 'MetaChat-MetaChatDB-sender-HMDB0002183-Ffar1', 'MetaChat-MetaChatDB-sender-HMDB0002183-Ffar4', 'MetaChat-MetaChatDB-sender-HMDB0002183-Mfsd2a', 'MetaChat-MetaChatDB-sender-HMDB0002183-Pparg', 'MetaChat-MetaChatDB-sender-HMDB0002183-Rxra', 'MetaChat-MetaChatDB-sender-HMDB0002183-Slc27a1', 'MetaChat-MetaChatDB-sender-HMDB0002200-Oxgr1', 'MetaChat-MetaChatDB-sender-HMDB0002200-P2ry12', 'MetaChat-MetaChatDB-sender-HMDB0002925-Slc27a5', 'MetaChat-MetaChatDB-sender-HMDB0002961-Ar', 'MetaChat-MetaChatDB-sender-HMDB0002961-Glp1r', 'MetaChat-MetaChatDB-sender-HMDB0003125-Aqp3', 'MetaChat-MetaChatDB-sender-HMDB0003125-Aqp5', 'MetaChat-MetaChatDB-sender-HMDB0003125-Aqp8', 'MetaChat-MetaChatDB-sender-HMDB0003125-Trpa1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Fabp1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Flvcr2', 'MetaChat-MetaChatDB-sender-HMDB0003178-Lrp1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Nr1d1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Nr1d2', 'MetaChat-MetaChatDB-sender-HMDB0003178-Pgrmc2', 'MetaChat-MetaChatDB-sender-HMDB0003178-Slc46a1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Slc48a1', 'MetaChat-MetaChatDB-sender-HMDB0003178-Tlr4', 'MetaChat-MetaChatDB-sender-HMDB0003178-Trpv6', 'MetaChat-MetaChatDB-sender-HMDB0003229-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0003229-Ffar4', 'MetaChat-MetaChatDB-sender-HMDB0003229-Fzd2', 'MetaChat-MetaChatDB-sender-HMDB0003229-Slc27a2', 'MetaChat-MetaChatDB-sender-HMDB0003229-Ucp1', 'MetaChat-MetaChatDB-sender-HMDB0003276-Cd36', 'MetaChat-MetaChatDB-sender-HMDB0003378-Npr1', 'MetaChat-MetaChatDB-sender-HMDB0003378-Trpa1', 'MetaChat-MetaChatDB-sender-HMDB0003406-Grid1', 'MetaChat-MetaChatDB-sender-HMDB0003406-Grid2', 'MetaChat-MetaChatDB-sender-HMDB0003406-Grin1', 'MetaChat-MetaChatDB-sender-HMDB0003406-Grin2a', 'MetaChat-MetaChatDB-sender-HMDB0003406-Lrrc8d', 'MetaChat-MetaChatDB-sender-HMDB0003406-Slc7a10', 'MetaChat-MetaChatDB-sender-HMDB0003550-Cubn', 'MetaChat-MetaChatDB-sender-HMDB0003550-Gc', 'MetaChat-MetaChatDB-sender-HMDB0003550-Lrp2', 'MetaChat-MetaChatDB-sender-HMDB0003550-Vdr', 'MetaChat-MetaChatDB-sender-HMDB0004484-Slc22a27', 'MetaChat-MetaChatDB-sender-HMDB0004484-Slc22a8', 'MetaChat-MetaChatDB-sender-HMDB0006216-Nr2f2', 'MetaChat-MetaChatDB-sender-HMDB0006224-Abcc4', 'MetaChat-MetaChatDB-sender-HMDB0006483-Slc1a1', 'MetaChat-MetaChatDB-sender-HMDB0006483-Slc1a3', 'MetaChat-MetaChatDB-sender-HMDB0006543-Slc22a2', 'MetaChat-MetaChatDB-sender-HMDB0011733-Slc15a1', 'MetaChat-MetaChatDB-sender-HMDB0012238-Slc5a8', 'MetaChat-MetaChatDB-sender-HMDB0015531-Slc11a2', 'MetaChat-MetaChatDB-sender-HMDB0015531-Slc25a37', 'MetaChat-MetaChatDB-sender-HMDB0015531-Slc39a14', 'MetaChat-MetaChatDB-sender-HMDB0015531-Slc40a1', 'MetaChat-MetaChatDB-sender-HMDB0015531-Tfr2', 'MetaChat-MetaChatDB-sender-HMDB0015531-Tfrc', 'MetaChat-MetaChatDB-sender-total-total', 'graph_visible', 'graph_visible_kneighb_5', 'spatial_distance_LRC_Blood', 'spatial_distance_LRC_base'

As an example:

fig, ax = plt.subplots(1, 1, figsize=(4,4))
pl = mc.pl.plot_communication_flow(
    adata = adata_sub, 
    database_name = 'MetaChatDB',
    ms_pair_name = 'HMDB0000094-Slc25a1',
    plot_method = 'grid',
    background = 'group',
    group_name = 'Cluster',
    summary = 'receiver',
    ndsize = 10,
    largest_arrow = 0.05,
    normalize_v_quantile = 0.995,
    grid_density = 0.5,
    title = 'MCC flow',
    ax = ax)

In this step, we compute the directional histograms of MCC (metabolite–sensor) flow vectors for all selected pairs. For each pair, the communication flow field is first sampled on a regular spatial grid (controlled by grid_density), and grid points with zero vectors across all pairs are excluded. Then, the angle of each nonzero vector is calculated using atan2(Vy, Vx) and binned into 18 angular intervals, while an additional bin records the fraction of zero vectors. The resulting 19-dimensional histogram represents the directional pattern of each M–S pair, which can be used for downstream analyses such as flow clustering or pathway-level comparison.

df_hist, coords_ref = mc.tl.compute_direction_histogram_per_pair(
    adata = adata_sub,
    database_name = "MetaChatDB",
    all_ms_pairs = all_ms_pairs,
    summary = "receiver",
    grid_density = 0.5,
    n_bins = 18,
    eps = 1e-4
)

Filtered out 373 all-zero grids, kept 302.
Computed 802 flows × 19 bins (after filtering).

df_filt = df_hist[df_hist["dir_bin_zero"] <= 0.9].copy()
print(f"Kept {len(df_filt)} / {len(df_hist)} pairs (zero ≤ 0.9).")

Kept 333 / 802 pairs (zero ≤ 0.9).

The last column represents the proportion of zero vectors. Here, we cluster the directional histograms of the first 18 bins.

kmeans = KMeans(n_clusters=5, random_state=0, n_init=50)
X = df_filt[[f"dir_bin_{i}" for i in range(18)]]
labels = kmeans.fit_predict(X)

mc.pl.plot_direction_similarity(
    df_direction=df_filt[[f"dir_bin_{i}" for i in range(18)]],
    cluster_labels=labels,
    cmap="mako",
    title="MCC directions similarity of all metabolites"
)