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Last data update: 2014.03.03

R: Plot PGSEA results

smcPlot

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))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PGSEA)
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Loading required package: annaffy
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PGSEA/smcPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: smcPlot
> ### Title: Plot PGSEA results
> ### Aliases: smcPlot
> ### Keywords: hplot
> 
> ### ** 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))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>