SpaCCI (version 1.0.4)

possible_L_R_pairs_cellchat: CellChat Database: Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication

Description

This function identifies possible ligand-receptor (L-R) pairs for cell-cell communication analysis using a subset of the CellChat database. It checks for the presence of all genes involved in each L-R pair within the provided gene expression matrix.

Usage

possible_L_R_pairs_cellchat(
  species,
  gene_spot_expression_dataframe,
  percentage
)

Value

A list containing:

possible_L_R_pairs

A data frame of L-R pairs where all genes are present in the 'gene_spot_expression_dataframe'. The data frame includes the ligand and receptor vectors, and the combined gene vectors.

possible_L_R_pairs_details

A data frame with detailed information about the L-R pairs, including the original annotations from the CellChatDB.

Arguments

species

A string specifying the species ("Human" or "Mouse"). The function selects the appropriate CellChatDB object, typically 'CellChatDB.human' or 'CellChatDB.mouse', which contains information on ligand-receptor interactions.

gene_spot_expression_dataframe

A gene expression data frame with genes as row names and Spot IDs as column names. This data frame is used to verify the presence of all genes involved in the L-R pairs.

percentage

A numeric value specifying the minimum percentage of spots in which a gene must be expressed to be considered. The default is 10.

Examples

# \donttest{
library(SpaCCI)
#Load the example data
load(system.file("extdata", "Tutorial_example_data.rda", package = "SpaCCI"))
Example_Seurat <- NormalizeData(Example_Seurat)
gene_spot_df <- as.data.frame(Example_Seurat@assays$Spatial@data)
result <- possible_L_R_pairs_cellchat(CellChatDB.human,
      gene_spot_expression_dataframe = gene_spot_df)
# }