subsetCommunication | R Documentation |
NB: If all arguments are NULL, it returns a data frame consisting of all the inferred cell-cell communications
subsetCommunication(
object = NULL,
net = NULL,
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
)
object |
CellChat object |
net |
Alternative input is a data frame with at least with three columns defining the cell-cell communication network ("source","target","interaction_name") |
slot.name |
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 |
sources.use |
a vector giving the index or the name of source cell groups |
targets.use |
a vector giving the index or the name of target cell groups. |
signaling |
a character vector giving the name of signaling pathways of interest |
pairLR.use |
a data frame consisting of one column named either "interaction_name" or "pathway_name", defining the interactions of interest |
thresh |
threshold of the p-value for determining significant interaction |
datasets |
select the inferred cell-cell communications from a particular 'datasets' when inputing a data frame 'net' |
ligand.pvalues, ligand.logFC, ligand.pct.1, ligand.pct.2 |
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 |
receptor.pvalues, receptor.logFC, receptor.pct.1, receptor.pct.2 |
set threshold for receptor genes |
If input object is created from a single dataset, a data frame of the inferred cell-cell communications of interest, consisting of source, target, interaction_name, pathway_name, prob and other information
If input object is a merged object from multiple datasets, it will return a list and each element is a data frame for one dataset
## Not run:
# access all the inferred cell-cell communications
df.net <- subsetCommunication(cellchat)
# access all the inferred cell-cell communications at the level of signaling pathways
df.net <- subsetCommunication(cellchat, slot.name = "netP")
# Subset to certain cells with sources.use and targets.use
df.net <- subsetCommunication(cellchat, sources.use = c(1,2), targets.use = c(4,5))
# Subset to certain signaling, e.g., WNT and TGFb
df.net <- subsetCommunication(cellchat, signaling = c("WNT", "TGFb"))
## End(Not run)
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