getSoftThreshold: Analysis of scale free topology for soft-threshold

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Analysis of scale free topology for soft-threshold

Description

Analysis of scale free topology for multiple soft thresholding powers. The aim is to help the user pick an appropriate soft-thresholding power for network construction. This is an adaptation of the WGCNA::pickSoftThreshold function which has been customized for scRNAseq applications.

Usage

getSoftThreshold(
  s.mat,
  dataIsExpr = F,
  weights = NULL,
  RsquaredCut = 0.85,
  powerVector = c(seq(1, 10, by = 1), seq(12, 20, by = 2)),
  removeFirst = FALSE,
  nBreaks = 10,
  blockSize = 1000,
  corFnc = cor,
  corOptions = list(use = "p"),
  networkType = "signed",
  moreNetworkConcepts = FALSE,
  gcInterval = NULL,
  verbose = 0,
  indent = 0
)

Arguments

s.mat	similarity matrix
RsquaredCut	Rsq cutoff. Default is 0.85.
networkType	Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See WGCNA::adjacency.
...	Additional arguments passessed to pickSoftThreshold pickSoftThreshold

Value

list of soft threshold picks

Examples

# determine optimal soft threshold
sft <- getSoftThreshold(s.mat)

# Plot the results
sizeGrWindow(9, 5)
par(mfrow = c(1,2));
cex1 = 0.9;

# Scale-free topology fit index as a function of the soft-thresholding power
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit, signed R^2",type="n", main = paste("Scale independence"));
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],labels=powers,cex=cex1,col="red");

# Red line corresponds to using an R^2 cut-off
abline(h=0.80,col="red")

# Mean connectivity as a function of the soft-thresholding power
plot(sft$fitIndices[,1], sft$fitIndices[,5],xlab="Soft Threshold (power)",ylab="Mean Connectivity", type="n",main = paste("Mean connectivity"))
text(sft$fitIndices[,1], sft$fitIndices[,5], labels=powers, cex=cex1,col="red")

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.