plotGS: Plot the gene set space

Description

Plot the gene set space of objects of "moa" and "mgsa"

Usage

plotGS(x, axes=1:2, center.only=FALSE, topN=1, data.pch=20, data.col=1, highlight.col = 2, label=NULL, label.cex=1, layout=NULL, ...)

Arguments

An object of class mgsa-class or moa.sup-class

axes

An integer vector in the length 2 to indicate the axes to be drawn.

center.only

A logical to indicate whether the separate gene set spaces from each of the data set should be plotted. Default is FALSE.

topN

An integer specify N gene set from the most positive and negative end of axes to be labeled

data.pch

The shape for plotting each data set. This argument is passed to points function, so only used when separate gene set spaces are plotted (i.e. center.only = FALSE).

data.col

The col for plotting each data set. This argument is passed to points function, so only used when separate gene set spaces are plotted (i.e. center.only = FALSE).

highlight.col

The color used to highlight the selected gene sets

label

Either a character vector or NULL (default). The character vector should be the name of some gene sets want ot be labeled.

label.cex

Passed to text function to adjust the the labels

layout

A matrix passed to the layout function.

...

Other arguments passed to points

Value

If assign to variable, A list of selected/highlighted gene set at the (positve and negative) end of each axis will be returned.

Details

This is a convenience function to explore the gene set space so not very flexible. For customized plot, please use the object of data@coord.comb and data@coord.sep.

Examples

Run this code

  
  # library(mogsa)
  # loading gene expression data and supplementary data
  data(NCI60_4array_supdata)
  data(NCI60_4arrays)
  mgsa <- mogsa(x = NCI60_4arrays, sup=NCI60_4array_supdata, nf=9,
                proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)

  plotGS(mgsa, center.only = TRUE, topN=5)
  res <- plotGS(mgsa, center.only = FALSE, data.pch=1:4, data.col=1:4)
  res