smcPlot {PGSEA} | R Documentation |
This basic function will plot results from PGSEA with easy altering of margins, colors, and text.
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, ...)
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 alternatvie column names |
rnames |
boolean or character - vector of alternative row names |
... |
additional graphical parameters passed along to the plotting function |
Karl Dykema <karl.dykema@vai.org>
library(PGSEA) datadir <- system.file("data", 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))