SpaCCI_local: Infer Cell-Cell Interactions on a Local Scale
In SpaCCI: Spatially Aware Cell-Cell Interaction Analysis

SpaCCI_local

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.