plot.probeset-methods: description of function plot.probeset

In stela2502/StefansExpressionSet: StefansExpressionSet

description of function plot.probeset

Description

This function plots the expression data grouped by the GroupName using ggplot2.

Works only for one probeset.

Usage

plot.probeset(x, probeset, boxplot = F, pdf = F,
  geneNameCol = "mgi_symbol", sampleGroup = "GroupName")

Arguments

x	the StefansExpressionSet object
probeset	the probeset name (rownames(x@data))
boxplot	(F or T) create a a dots- or box-plot
pdf	save the file as pdf (default svg)
geneNameCol	the column name for the gene symbol to use in the plots
sampleGroup	the sample table column containing the grouping information
groupcol	the grouping column in the samples data
colCol	the coloring column in the sample data
probeNames	the column in the annotation datacontaining the gene symbol
x	the StefansExpressionSet object

Examples

p <- plot.probeset( red, rownames(red@data)[20], geneNameCol= 'GeneID', boxplot=T)
#produces the file '../../tmp/reducedSet_boxplot_Mybl1_expression.svg'
p <- plot.probeset( red, rownames(red@data)[20], geneNameCol= 'GeneID', boxplot=F)
#produces the file '../../tmp/reducedSet_points_Mybl1_expression.svg'

stela2502/StefansExpressionSet documentation built on April 24, 2023, 8:15 p.m.