mogsa (version 1.6.4)

box.gs.feature: 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

Value

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

Details

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

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))