NB: If all arguments are NULL, it returns a data frame consisting of all the inferred cell-cell communications
subsetCommunication_internal(
net,
LR,
cells.level,
slot.name = "net",
sources.use = NULL,
targets.use = NULL,
signaling = NULL,
pairLR.use = NULL,
thresh = 0.05,
datasets = NULL,
ligand.pvalues = NULL,
ligand.logFC = NULL,
ligand.pct.1 = NULL,
ligand.pct.2 = NULL,
receptor.pvalues = NULL,
receptor.logFC = NULL,
receptor.pct.1 = NULL,
receptor.pct.2 = NULL
)net is object@net or a data frame; LR: object@LR$LRsig; cells.level: levels(object@idents)
the slot name of object: slot.name = "net" when extracting the inferred communications at the level of ligands/receptors; slot.name = "netP" when extracting the inferred communications at the level of signaling pathways
a vector giving the index or the name of source cell groups
a vector giving the index or the name of target cell groups.
a character vector giving the name of signaling pathways of interest
a data frame consisting of one column named either "interaction_name" or "pathway_name", defining the interactions of interest
threshold of the p-value for determining significant interaction
select the inferred cell-cell communications from a particular `datasets` when inputing a data frame `net`
set threshold for ligand genes
ligand.pvalues: threshold for pvalues in the differential expression gene analysis (DEG)
ligand.logFC: threshold for logFoldChange in the DEG analysis; When ligand.logFC > 0, keep upgulated genes; otherwise, kepp downregulated genes
ligand.pct.1: threshold for the percent of expressed genes in the defined 'positive' cell group. keep genes with percent greater than ligand.pct.1
ligand.pct.2: threshold for the percent of expressed genes in the cells except for the defined 'positive' cell group
set threshold for receptor genes
A data frame of the inferred cell-cell communications of interest, consisting of source, target, interaction_name, pathway_name, prob and other information