SpaCCI_local {SpaCCI} | R Documentation |
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.
SpaCCI_local(
gene_spot_df,
spot_cell_prop_df,
spatial_coord,
prop,
radius,
matching_L_R_pairs,
matching_L_R_pairs_info
)
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 |
matching_L_R_pairs_info |
A data frame providing additional information for each ligand-receptor pair, such as pathway information. |
A list containing:
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.
A list of matrices, each containing the IDs of the spots within the specified radius of each center spot.