SpaCCI_global {SpaCCI}R Documentation

Infer Cell-Cell Interactions on a Global Scale

Description

This function infers cell-cell interactions on a global scale using spatial transcriptomics data. It applies permutation testing to identify significant ligand-receptor interactions across all spots.

Usage

SpaCCI_global(
  gene_spot_df,
  spot_cell_prop_df,
  spatial_coord,
  matching_L_R_pairs,
  matching_L_R_pairs_info
)

Arguments

gene_spot_df

A data frame where the rows are genes and the columns are spots (Spot_IDs), representing gene expression levels across spatial spots.

spot_cell_prop_df

A data frame of cell type proportions for each spot. The rows represent spots (Spot_IDs), and the columns represent different cell types.

spatial_coord

A data frame of the spatial coordinates. The column names should include 'c("Spot_ID", "imagerow", "imagecol")', and the row names must be the Spot_IDs, which is the same as the row names in the cell type proportion data frame or the column names of the gene*spot expression data frame.

matching_L_R_pairs

A data frame containing matching ligand-receptor pairs. Each row corresponds to a ligand-receptor pair, with columns for ligand_vector and receptor_vector.

matching_L_R_pairs_info

A data frame providing additional information for each ligand-receptor pair, such as pathway information.

Value

A list containing:

pvalue_df

A data frame of inferred interactions across the global scale, including information on ligand and receptor cell types, interaction strength, P-values, and adjusted P-values.


[Package SpaCCI version 1.0.4 Index]