selectK: Select the number of the patterns for running...

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

Select the number of the patterns for running 'identifyCommunicationPatterns'

Description

We infer the number of patterns based on two metrics that have been implemented in the NMF R package, including Cophenetic and Silhouette. Both metrics measure the stability for a particular number of patterns based on a hierarchical clustering of the consensus matrix. For a range of the number of patterns, a suitable number of patterns is the one at which Cophenetic and Silhouette values begin to drop suddenly.

Usage

selectK(
  object,
  slot.name = "netP",
  pattern = c("outgoing", "incoming"),
  title.name = NULL,
  do.facet = TRUE,
  k.range = seq(2, 10),
  nrun = 30,
  seed.use = 10
)

Arguments

object	CellChat object
slot.name	the slot name of object that is used to compute centrality measures of signaling networks
pattern	"outgoing" or "incoming"
title.name	title of plot
do.facet	whether use facet plot showing the two measures
k.range	a range of the number of patterns
nrun	number of runs when performing NMF
seed.use	seed when performing NMF

Value

a ggplot object

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.