SpaCCI_local {SpaCCI}R Documentation

Infer Cell-Cell Interactions on a Local Scale

Description

This function infers cell-cell interactions on a local scale using spatial transcriptomics data. It utilizes permutation testing to identify significant ligand-receptor interactions within specified neighborhoods around randomly selected center spots.

Usage

SpaCCI_local(
  gene_spot_df,
  spot_cell_prop_df,
  spatial_coord,
  prop,
  radius,
  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.

prop

A numeric value representing the proportion of spots to randomly sample as center spots for local neighborhood analysis.

radius

A numeric value specifying the radius of the spatial neighborhood around each center spot.

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:

dataframelist

A list of data frames, each representing the inferred interactions for a specific center spot. Each data frame includes information on ligand and receptor cell types, P-values, and adjusted P-values.

RegionIDs_matrix

A list of matrices, each containing the IDs of the spots within the specified radius of each center spot.


[Package SpaCCI version 1.0.4 Index]