box.gs.feature {mogsa} | R Documentation |
boxplot to show the variables (e.g. gene expression) of a gene set across all samples.
box.gs.feature(x, gs, moa = NULL, col = 1, layout = NULL, plot = TRUE, obs.order = NULL, ...)
x |
An object of calss |
gs |
Gene set want to be explored |
moa |
An obejct of 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 |
This is a convenient function used to explore the expression of a set of features/genes
Do not return anything (plot=TRUE) or return a list of matrix (plot=FALSE) depends on plot arugment.
Chen meng
# 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))