pcaColored: PCA with samples coloured by group properties

In shraddhapai/dataExplore: Stats and Viz for Data Exploration

Description

PCA with samples coloured by group properties

Usage

pcaColored(m, mdata, groupToPlot, cex = 0.5, plotType = "full",
  bufSpace = 0.01, legendCex = 0.8, center = TRUE, scale = TRUE,
  pal = "Dark2", ...)

Arguments

m	(matrix)
mdata	(data.frame) metadata. rownames(mdata)=colnames(m)
groupToPlot	(char) vector of metadata variables using which to colour-code samples
plotType	(char, full or point) if "full" plots sample name. If "point", simply plots a dot
legendCex	(numeric) cex for legend
center, scale	(logical) options to center/scale matrix before PCA See prcomp()
pal	(char) RColorBrewer2 palette name
bufType	(numeric) buffer around the points, by which to extend x/y lim. Increase this value to allow space to see the full sample name.

Value

No value. side effect of plotting pca graph

shraddhapai/dataExplore documentation built on March 9, 2020, 9:17 a.m.