box.gs.feature {mogsa} | R Documentation

## boxplot of gene set variables across all samples.

### Description

boxplot to show the variables (e.g. gene expression) of a gene set across all samples.

### Usage

      box.gs.feature(x, gs, moa = NULL, col = 1, layout = NULL, plot = TRUE, obs.order = NULL, ...)

### Arguments

`x` | An object of calss `mgsa-class` or `moa.sup-class`
`gs` | Gene set want to be explored
`moa` | An obejct of class `moa`. It is required if x is an object of class `moa.sup-class`
`col` | The coler code for samples
`layout` | The layout control, see examples.
`plot` | A logical indicates whether the result should be ploted. If FALSE, a list of expression matrix of the gene set genes is returned. Otherwise nothing returned.
`obs.order` | Can be used to reorder the martrix, could be used when clustering result is available.
`...` | The arguments passed to `boxplot`

### Details

This is a convenient function used to explore the expression of a set of features/genes

### Value

Do not return anything (plot=TRUE) or return a list of matrix (plot=FALSE) depends on plot arugment.

### 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)

      allgs <- colnames(NCI60_4array_supdata[[1]])
      colcode <- as.factor(sapply(strsplit(colnames(NCI60_4arrays$agilent), split="\\."), "[", 1))
      a <- box.gs.feature(x=mgsa, gs=allgs[5], type=3, col=colcode, plot=FALSE)
      box.gs.feature(x=mgsa, gs=allgs[5], type=3, col=colcode, plot=TRUE, layout=matrix(1:4, 2, 2))

[Package mogsa version 1.14.0 Index]