MetaChat analysis on spatial multi-omics data of human gastric cancer

In this tutorial, we use human gastric cancer dataset as an example to show the basic application of MetaChat to multi-omics data of transcriptomics and metabolomics [Sun et al., 2023].

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

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

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

Import dataset

Before running the code, you can download all sample data from Zenodo and save it to the datasets folder in your directory.

adata = sc.read('datasets/human_gastric_cancer/adata_combined.h5ad')

The spatial distribution of tissue types reveals well-defined anatomical layers and regions in the human gastric sample.

fig, ax = plt.subplots(figsize = (4,4))
sq.pl.spatial_scatter(adata = adata,
                      color = "tissue_type",
                      ax = ax)
ax.set_box_aspect(1)

MCC Inference

Import MetaChatDB

Load the curated MetaChat database containing metabolite–sensor interaction pairs for human (or mouse).

df_metasen = mc.pp.MetaChatDB(species='human') # If mouse, please input species='mouse'.

Identify long-range channels (LRCs)

In this example, we aim to identify blood vessels as potential LRC pathways. To achieve this, we use a gene-marker–based approach to locate candidate points, leveraging the expression of known vascular markers to guide the identification of regions likely involved in long-range metabolite transport.

LRC_name = "Blood"
LRC_marker_genes = ["MYH11", "CLDN5"]

mc.pl.plot_LRC_markers(adata = adata,
                       LRC_name = LRC_name,
                       LRC_marker_genes = LRC_marker_genes,
                       avg = False,
                       figsize = (10, 5))

<Axes: title={'center': 'CLDN5'}, xlabel='spatial1', ylabel='spatial2'>

We can observe that these blood vessel markers show localized enrichment around the peritumoral muscularis region, suggesting that blood vessels in this area may serve as potential LRC, facilitating metabolite transport or exchange between tissue compartments.

mc.pl.plot_LRC_markers(adata = adata,
                       LRC_name = LRC_name,
                       LRC_marker_genes = LRC_marker_genes,
                       avg = True,
                       figsize = (5, 5))

<Axes: title={'center': 'LRC_Blood_avg_markers'}, xlabel='spatial1', ylabel='spatial2'>

The mc.pl.plot_LRC_markers function can also visualize the average expression of multiple markers, providing a more robust signal for identifying potential LRC regions.

mc.pp.LRC_unfiltered(adata = adata,
                     LRC_name = LRC_name,
                     LRC_source = 'marker',
                     obs_name = 'LRC_' + LRC_name + '_avg_markers',
                     quantile = 80)

Cells above the 80% have been selected as candidates and stored in 'adata.obs['LRC_Blood_marker_unfiltered']'.

fig, ax = plt.subplots(figsize = (6,5))
sq.pl.spatial_scatter(adata,
                      color = 'LRC_Blood_marker_unfiltered',
                      ax = ax)
ax.set_box_aspect(1)

LRC_cluster_Blood = mc.pp.LRC_cluster(adata = adata,
                                      LRC_name = LRC_name,
                                      LRC_source = "marker",
                                      density_cutoff = 15,
                                      delta_cutoff = 500,
                                      outlier_cutoff = 8)

Then, the mc.pp.LRC_filtered() function was executed to remove outlier points from the clustered Blood LRC candidates, and the filtered LRCs were stored in adata.obs[‘LRC_Blood_marker_filtered’].

mc.pp.LRC_filtered(adata = adata,
                   LRC_name = LRC_name,
                   LRC_cluster = LRC_cluster_Blood,
                   LRC_source = "marker")

Candidate points for Blood LRC are clustered and outliers are removed. LRC points are stored in 'adata.obs['LRC_Blood_marker_filtered']'.

/home/project/metachat_packages/MetaChat-main/metachat_new/preprocessing/_identifyLRC.py:245: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  adata.obs[key_filtered][adata.obs[key_filtered] == 1] = newcluster

Then, we can visualize the determined LRC.

adata

AnnData object with n_obs × n_vars = 2694 × 42069
    obs: 'in_tissue', 'array_row', 'array_col', 'cluster_miso', 'highlight', 'tissue_type', 'LRC_Blood_marker_MYH11', 'LRC_Blood_marker_CLDN5', 'LRC_Blood_avg_markers', 'LRC_Blood_marker_unfiltered', 'LRC_Blood_marker_filtered'
    uns: 'highlight_colors', 'spatial', 'tissue_type_colors', 'LRC_Blood_marker_unfiltered_colors'
    obsm: 'spatial'

# Set color for LRCs
adata.obs['LRC_Blood_marker_filtered'] = adata.obs['LRC_Blood_marker_filtered'].astype('category')
adata.uns['LRC_Blood_marker_filtered' + '_colors'] = ['gray', 'orange']

fig, ax = plt.subplots(figsize = (6,5))
sq.pl.spatial_scatter(adata,
                      color = 'LRC_Blood_marker_filtered',
                      alpha = 1,
                      ax = ax)
ax.set_box_aspect(1)

Compute cost distance

Determined dis_thr

After identifying the LRCs, we compute the cost between any pair of points. In general, the cost is determined by the Euclidean distance; however, when LRCs and anatomical barriers are considered, the cost is redefined based on these additional constraints.

The parameter dis_thr is critical for defining how far a metabolite signal is assumed to propagate. Since the spatial scale of coordinates varies across datasets, it is important to visually inspect and adjust dis_thr. The function mc.pl.plot_dis_thr allows users to visualize this threshold by specifying the distance (dis_thr) and the central spot (spot_index), enabling intuitive calibration of the propagation range. Here we use dis_thr=200.

dis_thr = 200
mc.pl.plot_dis_thr(adata = adata, dis_thr = dis_thr, spot_index = 1000)

<Axes: title={'center': 'Spots within dis_thr=200 of spot 1000'}, xlabel='spatial1', ylabel='spatial2'>

The function mc.pp.compute_costDistance() calculates the spatial cost distance matrix between all spots, integrating both Euclidean proximity and long-range channel (LRC) effects. Specifically, it adjusts the pairwise distances according to the defined LRC_type and their corresponding LRC_strength, allowing metabolite diffusion or communication along designated LRC paths to be modeled more realistically.

The parameters LRC_type and LRC_source should correspond to the names used in adata.obs[‘LRC_<LRC_type>_<LRC_source>_filtered’]. A higher value of LRC_strength indicates a stronger influence of long-range communication, effectively expanding the propagation range through LRCs. The parameter dis_thr should match the distance threshold defined in the previous step. We support and recommend setting use_parallel = True and increasing n_jobs within the limits of your system performance, as this can significantly accelerate the computation of the cost distance matrix. The resulting distance matrix is stored in adata.obsp (e.g., adata.obsp[‘spatial_distance_LRC_Blood’]) and can be used in downstream analyses of metabolic cell communication.

mc.pp.compute_costDistance(
    adata = adata,
    LRC_type = ['Blood'],
    LRC_strength = [5],
    LRC_source = "marker",
    dis_thr = dis_thr,
    k_neighb = 5,
    use_parallel = True,
    n_jobs = 64
)

Computing baseline spatial distance without LRC.
  Barrier condition is not considered
Computing spatial distance with LRCs.
  Processing LRC type: Blood
    Constructing graph for each LRC subcluster.
    Computing shortest path between two points in Blood.
      For the cluster 1 in Blood.

100%|██████████| 345/345 [00:00<00:00, 680.99it/s]

    Incorporating LRC strength of 'Blood' into cost distance matrix (strength = 5).
adata.obsp['spatial_distance_LRC_Blood'] has been saved.
Finished!

adata

AnnData object with n_obs × n_vars = 2694 × 42069
    obs: 'in_tissue', 'array_row', 'array_col', 'cluster_miso', 'highlight', 'tissue_type', 'LRC_Blood_marker_MYH11', 'LRC_Blood_marker_CLDN5', 'LRC_Blood_avg_markers', 'LRC_Blood_marker_unfiltered', 'LRC_Blood_marker_filtered', 'LRC_Blood_closepoint_cluster1'
    uns: 'highlight_colors', 'spatial', 'tissue_type_colors', 'LRC_Blood_marker_unfiltered_colors', 'LRC_Blood_marker_filtered_colors'
    obsm: 'spatial'
    obsp: 'spatial_distance_LRC_base', 'LRC_shortest_Blood_dist200_cluster1', 'spatial_distance_LRC_Blood'

As shown, the distances from the central spot (spot_index) to the surrounding spots are markedly reduced near the LRC, since these locations lie along or close to the LRC and are therefore more likely to participate in long-range communication.

mc.pl.plot_spot_distance(adata = adata,
                         dist_matrix_key = 'spatial_distance_LRC_Blood',
                         spot_index = 1000)

<Axes: title={'center': 'Distance to spot index 1000'}, xlabel='X coordinate', ylabel='Y coordinate'>

We can visualize which spatial spots are influenced by the LRC.

fig, ax = plt.subplots(figsize = (6,5))
sq.pl.spatial_scatter(adata,
                      color = 'LRC_Blood_closepoint_cluster1',
                      alpha = 1,
                      ax = ax)
ax.set_box_aspect(1)
ax.set_title('LRC_Blood_closepoint_cluster1')
plt.tight_layout()
plt.show()

The function mc.tl.metabolic_communication performs the inference of MCC based on spatial proximity and the selected metabolite–sensor interaction database. Using the cost distance matrix and LRC information, it identifies potential sender–receiver pairs where metabolites can feasibly diffuse or be transported between spots within the defined distance threshold (dis_thr). In this example, 609 metabolite–sensor pairs were detected from the spatial data using the MetaChatDB reference and the Blood-related LRC configuration.

mc.tl.metabolic_communication(adata = adata,
                              database_name = 'MetaChatDB',
                              df_metasen = df_metasen,
                              LRC_type = ["Blood"],
                              dis_thr = dis_thr)

There are 609 pairs were found from the spatial data.

For each metabolite–sensor pair, the inferred signaling strength between all spatial spots is stored as an n_obs × n_obs sparse matrix in adata.obsp['MetaChat-MetaChatDB-sender-<metabolite>-<sensor>'] and adata.obsp['MetaChat-MetaChatDB-receiver-<metabolite>-<sensor>'], where each entry represents the potential communication intensity from a sender spot to a receiver spot. Because transcriptomic (sensor) and metabolomic (metabolite) data are measured in different units, MetaChat provides two corresponding matrices — one for the sender (metabolite abundance) and one for the receiver (sensor expression). Their relative values are consistent, but they differ in scale to reflect the distinct quantitative units of each modality.

adata

AnnData object with n_obs × n_vars = 2694 × 42069
    obs: 'in_tissue', 'array_row', 'array_col', 'cluster_miso', 'highlight', 'tissue_type', 'LRC_Blood_marker_MYH11', 'LRC_Blood_marker_CLDN5', 'LRC_Blood_avg_markers', 'LRC_Blood_marker_unfiltered', 'LRC_Blood_marker_filtered', 'LRC_Blood_closepoint_cluster1'
    uns: 'highlight_colors', 'spatial', 'tissue_type_colors', 'LRC_Blood_marker_unfiltered_colors', 'LRC_Blood_marker_filtered_colors', 'df_metasen_filtered', 'MetaChat-MetaChatDB-info'
    obsm: 'spatial', 'MetaChat-MetaChatDB-sum-sender', 'MetaChat-MetaChatDB-sum-receiver'
    obsp: 'spatial_distance_LRC_base', 'LRC_shortest_Blood_dist200_cluster1', 'spatial_distance_LRC_Blood', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRM8', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRM8', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIN2A', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIN2A', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRM1', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRM1', 'MetaChat-MetaChatDB-sender-HMDB0000148-BEST2', 'MetaChat-MetaChatDB-receiver-HMDB0000148-BEST2', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC1A1', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC1A1', 'MetaChat-MetaChatDB-sender-HMDB0000148-LRRC8D', 'MetaChat-MetaChatDB-receiver-HMDB0000148-LRRC8D', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC25A13', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC25A13', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIN3A', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIN3A', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC1A6', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC1A6', 'MetaChat-MetaChatDB-sender-HMDB0000148-TRPV1', 'MetaChat-MetaChatDB-receiver-HMDB0000148-TRPV1', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC1A5', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC1A5', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRM5', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRM5', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRID1', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRID1', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRM7', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRM7', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIK2', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIK2', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRM4', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRM4', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIK1', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIK1', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIN2D', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIN2D', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRM2', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRM2', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC1A7', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC1A7', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIN1', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIN1', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRM6', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRM6', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIA3', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIA3', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC38A10', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC38A10', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRID2', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRID2', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIA1', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIA1', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRM3', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRM3', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIA2', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIA2', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC7A11', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC7A11', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC7A13', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC7A13', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIK5', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIK5', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC38A6', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC38A6', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIA4', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIA4', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC1A2', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC1A2', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIN2B', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIN2B', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIK3', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIK3', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC25A22', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC25A22', 'MetaChat-MetaChatDB-sender-HMDB0000148-GRIK4', 'MetaChat-MetaChatDB-receiver-HMDB0000148-GRIK4', 'MetaChat-MetaChatDB-sender-HMDB0000148-SLC1A3', 'MetaChat-MetaChatDB-receiver-HMDB0000148-SLC1A3', 'MetaChat-MetaChatDB-sender-HMDB0010382-GPR4', 'MetaChat-MetaChatDB-receiver-HMDB0010382-GPR4', 'MetaChat-MetaChatDB-sender-HMDB0003229-FZD2', 'MetaChat-MetaChatDB-receiver-HMDB0003229-FZD2', 'MetaChat-MetaChatDB-sender-HMDB0003229-CD36', 'MetaChat-MetaChatDB-receiver-HMDB0003229-CD36', 'MetaChat-MetaChatDB-sender-HMDB0003229-UCP1', 'MetaChat-MetaChatDB-receiver-HMDB0003229-UCP1', 'MetaChat-MetaChatDB-sender-HMDB0003229-FFAR4', 'MetaChat-MetaChatDB-receiver-HMDB0003229-FFAR4', 'MetaChat-MetaChatDB-sender-HMDB0003229-SLC27A2', 'MetaChat-MetaChatDB-receiver-HMDB0003229-SLC27A2', 'MetaChat-MetaChatDB-sender-HMDB0000064-SLC6A8', 'MetaChat-MetaChatDB-receiver-HMDB0000064-SLC6A8', 'MetaChat-MetaChatDB-sender-HMDB0000064-SLC25A32', 'MetaChat-MetaChatDB-receiver-HMDB0000064-SLC25A32', 'MetaChat-MetaChatDB-sender-HMDB0000064-SLC16A12', 'MetaChat-MetaChatDB-receiver-HMDB0000064-SLC16A12', 'MetaChat-MetaChatDB-sender-HMDB0001067-GRM3', 'MetaChat-MetaChatDB-receiver-HMDB0001067-GRM3', 'MetaChat-MetaChatDB-sender-HMDB0000132-SLC29A2', 'MetaChat-MetaChatDB-receiver-HMDB0000132-SLC29A2', 'MetaChat-MetaChatDB-sender-HMDB0002100-PPARA', 'MetaChat-MetaChatDB-receiver-HMDB0002100-PPARA', 'MetaChat-MetaChatDB-sender-HMDB0003252-SLCO2A1', 'MetaChat-MetaChatDB-receiver-HMDB0003252-SLCO2A1', 'MetaChat-MetaChatDB-sender-HMDB0001220-SLC22A1', 'MetaChat-MetaChatDB-receiver-HMDB0001220-SLC22A1', 'MetaChat-MetaChatDB-sender-HMDB0001220-SLCO2A1', 'MetaChat-MetaChatDB-receiver-HMDB0001220-SLCO2A1', 'MetaChat-MetaChatDB-sender-HMDB0001220-PTGER1', 'MetaChat-MetaChatDB-receiver-HMDB0001220-PTGER1', 'MetaChat-MetaChatDB-sender-HMDB0001220-ABCC4', 'MetaChat-MetaChatDB-receiver-HMDB0001220-ABCC4', 'MetaChat-MetaChatDB-sender-HMDB0001220-SLC22A6', 'MetaChat-MetaChatDB-receiver-HMDB0001220-SLC22A6', 'MetaChat-MetaChatDB-sender-HMDB0001220-PTGER3', 'MetaChat-MetaChatDB-receiver-HMDB0001220-PTGER3', 'MetaChat-MetaChatDB-sender-HMDB0001220-PTGER4', 'MetaChat-MetaChatDB-receiver-HMDB0001220-PTGER4', 'MetaChat-MetaChatDB-sender-HMDB0001220-PTGER2', 'MetaChat-MetaChatDB-receiver-HMDB0001220-PTGER2', 'MetaChat-MetaChatDB-sender-HMDB0001220-OR52N2', 'MetaChat-MetaChatDB-receiver-HMDB0001220-OR52N2', 'MetaChat-MetaChatDB-sender-HMDB0001220-SLC22A8', 'MetaChat-MetaChatDB-receiver-HMDB0001220-SLC22A8', 'MetaChat-MetaChatDB-sender-HMDB0001220-SLC22A2', 'MetaChat-MetaChatDB-receiver-HMDB0001220-SLC22A2', 'MetaChat-MetaChatDB-sender-HMDB0001389-MTNR1B', 'MetaChat-MetaChatDB-receiver-HMDB0001389-MTNR1B', 'MetaChat-MetaChatDB-sender-HMDB0001389-MTNR1A', 'MetaChat-MetaChatDB-receiver-HMDB0001389-MTNR1A', 'MetaChat-MetaChatDB-sender-HMDB0002088-PPARA', 'MetaChat-MetaChatDB-receiver-HMDB0002088-PPARA', 'MetaChat-MetaChatDB-sender-HMDB0002088-GPR119', 'MetaChat-MetaChatDB-receiver-HMDB0002088-GPR119', 'MetaChat-MetaChatDB-sender-HMDB0008138-ABCB4', 'MetaChat-MetaChatDB-receiver-HMDB0008138-ABCB4', 'MetaChat-MetaChatDB-sender-HMDB0000294-SLC14A1', 'MetaChat-MetaChatDB-receiver-HMDB0000294-SLC14A1', 'MetaChat-MetaChatDB-sender-HMDB0000294-SLC5A1', 'MetaChat-MetaChatDB-receiver-HMDB0000294-SLC5A1', 'MetaChat-MetaChatDB-sender-HMDB0000294-SLC14A2', 'MetaChat-MetaChatDB-receiver-HMDB0000294-SLC14A2', 'MetaChat-MetaChatDB-sender-HMDB0000294-SLC5A5', 'MetaChat-MetaChatDB-receiver-HMDB0000294-SLC5A5', 'MetaChat-MetaChatDB-sender-HMDB0000056-SLC36A1', 'MetaChat-MetaChatDB-receiver-HMDB0000056-SLC36A1', 'MetaChat-MetaChatDB-sender-HMDB0000056-MRGPRD', 'MetaChat-MetaChatDB-receiver-HMDB0000056-MRGPRD', 'MetaChat-MetaChatDB-sender-HMDB0000056-SLC6A6', 'MetaChat-MetaChatDB-receiver-HMDB0000056-SLC6A6', 'MetaChat-MetaChatDB-sender-HMDB0000073-SLC18A1', 'MetaChat-MetaChatDB-receiver-HMDB0000073-SLC18A1', 'MetaChat-MetaChatDB-sender-HMDB0000073-SLC29A4', 'MetaChat-MetaChatDB-receiver-HMDB0000073-SLC29A4', 'MetaChat-MetaChatDB-sender-HMDB0000073-SLC6A3', 'MetaChat-MetaChatDB-receiver-HMDB0000073-SLC6A3', 'MetaChat-MetaChatDB-sender-HMDB0000073-SLC18A2', 'MetaChat-MetaChatDB-receiver-HMDB0000073-SLC18A2', 'MetaChat-MetaChatDB-sender-HMDB0000073-TRPV1', 'MetaChat-MetaChatDB-receiver-HMDB0000073-TRPV1', 'MetaChat-MetaChatDB-sender-HMDB0000073-SLC6A2', 'MetaChat-MetaChatDB-receiver-HMDB0000073-SLC6A2', 'MetaChat-MetaChatDB-sender-HMDB0000073-CCR9', 'MetaChat-MetaChatDB-receiver-HMDB0000073-CCR9', 'MetaChat-MetaChatDB-sender-HMDB0000073-SLC22A5', 'MetaChat-MetaChatDB-receiver-HMDB0000073-SLC22A5', 'MetaChat-MetaChatDB-sender-HMDB0000073-SLC22A3', 'MetaChat-MetaChatDB-receiver-HMDB0000073-SLC22A3', 'MetaChat-MetaChatDB-sender-HMDB0000073-DRD4', 'MetaChat-MetaChatDB-receiver-HMDB0000073-DRD4', 'MetaChat-MetaChatDB-sender-HMDB0000073-DRD2', 'MetaChat-MetaChatDB-receiver-HMDB0000073-DRD2', 'MetaChat-MetaChatDB-sender-HMDB0000073-ADRA2C', 'MetaChat-MetaChatDB-receiver-HMDB0000073-ADRA2C', 'MetaChat-MetaChatDB-sender-HMDB0000073-DRD3', 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'MetaChat-MetaChatDB-receiver-HMDB0000022-TAAR1', 'MetaChat-MetaChatDB-sender-HMDB0000300-SLC29A2', 'MetaChat-MetaChatDB-receiver-HMDB0000300-SLC29A2', 'MetaChat-MetaChatDB-sender-HMDB0000673-FABP1', 'MetaChat-MetaChatDB-receiver-HMDB0000673-FABP1', 'MetaChat-MetaChatDB-sender-HMDB0000673-CD36', 'MetaChat-MetaChatDB-receiver-HMDB0000673-CD36', 'MetaChat-MetaChatDB-sender-HMDB0000673-FFAR1', 'MetaChat-MetaChatDB-receiver-HMDB0000673-FFAR1', 'MetaChat-MetaChatDB-sender-HMDB0000673-FABP7', 'MetaChat-MetaChatDB-receiver-HMDB0000673-FABP7', 'MetaChat-MetaChatDB-sender-HMDB0000673-TRPV4', 'MetaChat-MetaChatDB-receiver-HMDB0000673-TRPV4', 'MetaChat-MetaChatDB-sender-HMDB0000673-SLC27A5', 'MetaChat-MetaChatDB-receiver-HMDB0000673-SLC27A5', 'MetaChat-MetaChatDB-sender-HMDB0000673-SLC27A6', 'MetaChat-MetaChatDB-receiver-HMDB0000673-SLC27A6', 'MetaChat-MetaChatDB-sender-HMDB0000673-FABP5', 'MetaChat-MetaChatDB-receiver-HMDB0000673-FABP5', 'MetaChat-MetaChatDB-sender-HMDB0003550-CUBN', 'MetaChat-MetaChatDB-receiver-HMDB0003550-CUBN', 'MetaChat-MetaChatDB-sender-HMDB0003550-LRP2', 'MetaChat-MetaChatDB-receiver-HMDB0003550-LRP2', 'MetaChat-MetaChatDB-sender-HMDB0003550-GC', 'MetaChat-MetaChatDB-receiver-HMDB0003550-GC', 'MetaChat-MetaChatDB-sender-HMDB0003550-VDR', 'MetaChat-MetaChatDB-receiver-HMDB0003550-VDR', 'MetaChat-MetaChatDB-sender-HMDB0001085-PPARA', 'MetaChat-MetaChatDB-receiver-HMDB0001085-PPARA', 'MetaChat-MetaChatDB-sender-HMDB0001085-LTB4R2', 'MetaChat-MetaChatDB-receiver-HMDB0001085-LTB4R2', 'MetaChat-MetaChatDB-sender-HMDB0001085-LTB4R', 'MetaChat-MetaChatDB-receiver-HMDB0001085-LTB4R', 'MetaChat-MetaChatDB-sender-HMDB0000014-SLC29A2', 'MetaChat-MetaChatDB-receiver-HMDB0000014-SLC29A2', 'MetaChat-MetaChatDB-sender-HMDB0001934-CHRNA5', 'MetaChat-MetaChatDB-receiver-HMDB0001934-CHRNA5', 'MetaChat-MetaChatDB-sender-HMDB0001934-CHRNA4', 'MetaChat-MetaChatDB-receiver-HMDB0001934-CHRNA4', 'MetaChat-MetaChatDB-sender-HMDB0001488-SLC5A8', 'MetaChat-MetaChatDB-receiver-HMDB0001488-SLC5A8', 'MetaChat-MetaChatDB-sender-HMDB0001488-HCAR2', 'MetaChat-MetaChatDB-receiver-HMDB0001488-HCAR2', 'MetaChat-MetaChatDB-sender-HMDB0000684-AHR', 'MetaChat-MetaChatDB-receiver-HMDB0000684-AHR', 'MetaChat-MetaChatDB-sender-HMDB0000691-UCP3', 'MetaChat-MetaChatDB-receiver-HMDB0000691-UCP3', 'MetaChat-MetaChatDB-sender-total-total', 'MetaChat-MetaChatDB-receiver-total-total'

The matrices adata.obsm['MetaChat–MetaChatDB–sum–sender'] and adata.obsm['MetaChat–MetaChatDB–sum–receiver'] represent the total communication strength of each spot acting as a sender or receiver, respectively. Technically, these values are obtained by summing the corresponding rows (for senders) and columns (for receivers) of each metabolite–sensor communication matrix, providing a global measure of how actively each spot participates in metabolite-mediated signaling.

adata.write('datasets/human_gastric_cancer/metachat_result.h5ad')