smcPlot: Plot PGSEA results

In PGSEA: Parametric Gene Set Enrichment Analysis

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

Author(s)

Karl Dykema <[e-mail]>

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))

PGSEA documentation built on April 28, 2020, 8:28 p.m.