sigPlot: Signature PCA plot

In sidiropoulos/PSigA: A gene-signature ranking method based on sample density in PCA space

Description

Plot of the selected signature's PCA using ggplot2.

Usage

sigPlot(data, signature, groups = NULL, text = FALSE, pcs = c(1, 2),
  main = "", palette = "Paired", ...)

Arguments

data	gene expression matrix where rownames correspond to unique gene identifiers in signature format, and columns correspond to samples.
signature	character vector containing the signature's gene identifiers.
groups	optional factor variable indicating the groups that the observations belong to.
text	when TRUE it plots textual annotations instead of points based on groups parameter.
pcs	which PCs to plot. default: 1,2
main	plot title
palette	colorbrewer palette scheme to be used.
...	methods passed to ggplot

Value

A ggplot2 plot

Examples

dummyData <- do.call(rbind, lapply(seq(0.1, 0.9, by = 0.1),
                     rnorm, n = 100, m = 6))

#add a row with bimodal gene expression
dummyData <- rbind(dummyData, c(rnorm(70, 6, 0.1), rnorm(30, 9, 0.1)))

rownames(dummyData) <- paste(rep("gene", nrow(dummyData)),
                             seq(1, nrow(dummyData)), sep = "")

dummySig <- c("gene1", "gene8", "gene9", "gene10")

sigPlot(dummyData, dummySig)

groups <- factor(c(rep("GroupA", 70), rep("GroupB", 30)))
sigPlot(dummyData, dummySig, groups, main = "dummySig")

sidiropoulos/PSigA documentation built on May 29, 2019, 9:58 p.m.