PGSEA (version 1.46.0)

smcPlot: Plot PGSEA results

Description

This basic function will plot results from PGSEA with easy altering of margins, colors, and text.

Usage

smcPlot(m, ff = NULL, skip = "NO", scale = c(-3, 3), na.color = par("bg"), margins = NULL, r.cex = NULL, c.cex = NULL, show.grid = F, cnames = TRUE, rnames = TRUE, grid.lty = 3, clust = FALSE, ...)

Arguments

m

matrix - your results from PGSEA (or any other numeric matrix of data)

ff

factor - this factor corresponds to the subtypes of your samples and will control the column names

skip

character - which subtype(s) to skip from "ff"

scale

vector, length 2 - this vector sets the minimum and maximum values for the graph scale (at bottom of plot)

na.color

character - color to display in the result of an NA

margins

vector, length 4 - this vector gives the expansion values for the margins

r.cex

numeric - number giving the amount by which row names should be scaled relative to the default

c.cex

numeric - number giving the amount by which column names should be scaled relative to the default

show.grid

boolean - show grid outlines within plot?

cnames

boolean or character - vector of alternative column names

rnames

boolean or character - vector of alternative row names

grid.lty

numeric - line type of the grid lines

clust

boolean - want to cluster?

...

additional graphical parameters passed along to the plotting function

Examples

library(PGSEA)
datadir <- system.file("extdata", package = "PGSEA")
sample <- readGmt(file.path(datadir, "sample.gmt"))
data(nbEset)

pg <- PGSEA(nbEset,cl=sample,ref=1:5)
sub <- factor(c(rep(NA,5),rep("NeuroB",5),rep("NeuroB_MYC+",5)))

smcPlot(pg,sub,scale=c(-10,10),col=.rwb,margins=c(1,1,8,13))