possible_L_R_pairs_cellchat {SpaCCI} | R Documentation |
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
)
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. |
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.
Examples
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)