smcPlot {PGSEA} | R Documentation

## 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

### Author(s)

Karl Dykema <karl.dykema@vai.org>

### 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))

[Package PGSEA version 1.56.0 Index]