plotGS {mogsa} | R Documentation

## 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

`x` | 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`

### 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`.

### Value

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

### Author(s)

Chen Meng

### Examples

      # 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

[Package mogsa version 1.18.1 Index]