tSNEPlotter: Plot tSNE

In BaderLab/netDx: Network-based patient classifier

Description

Plot tSNE

Usage

tSNEPlotter(psn, pheno, ...)

Arguments

psn	(matrix) Patient similarity network represented as adjacency matrix (symmetric). Row and column names are patient IDs. Note that NA values will be replaced by very small number (effectively zero).
pheno	(data.frame) Patient labels. ID column is patient ID and STATUS is patient label of interest. tSNE will colour-code nodes by patient label.
...	Parameters for Rtsne() function.

Details

Plots tSNE of integrated patient similarity network using Rtsne

Value

(Rtsne) output of Rtsne call. Side effect of tSNE plot

Examples

pid <- paste("P",1:100,sep="")
psn <- matrix(rnorm(100*100),nrow=100,dimnames=list(pid,pid))
psn[lower.tri(psn)] <- NA; diag(psn) <- NA
psn2 <- reshape2::melt(psn); psn2 <- psn2[-which(is.na(psn2[,3])),]
colnames(psn2) <- c("SOURCE","TARGET","WEIGHT")
pheno <- data.frame(ID=pid,STATUS=c(rep("control",50),rep("case",50)))
tSNEPlotter(psn2,pheno)

BaderLab/netDx documentation built on Sept. 26, 2021, 9:13 a.m.