geNetClassifier (version 1.12.0)

plotExpressionProfiles: Expression profiles plot.

Description

Plots the expression profiles of the given genes.

Usage

plotExpressionProfiles(eset, genes=NULL, fileName=NULL, 
geneLabels=NULL, type="lines", sampleLabels=NULL, sampleColors=NULL, 
labelsOrder=NULL, classColors=NULL, sameScale=TRUE, 
showSampleNames=FALSE, showMean= FALSE, identify=TRUE, verbose=TRUE)

Arguments

eset

ExpressionSet or Matrix. Gene expression of the samples.

genes

Vector or Matrix. IDs of the genes to plot. If matrix: genes should be ordered by classes. Columns should be named after the classes. If not provided, all available genes will be plot. Warning: If a list of genes is not provided, it will plot all available genes.

fileName

Character. File name to save the plots. If not provided, up to 20 genes will be shown on screen.

geneLabels

Vector or Matrix. Gene name, ID or label which should be shown in the returned results and plots.

type

Character. Plot type: "lines" or "boxplot".

sampleLabels

Character. PhenoData variable (column name) containing the train samples class labels. Matrix or Factor. Class labels of the train samples.

sampleColors

Character. Colors for the lines of the samples.

labelsOrder

Vector or Factor. Order in which the labels should be shown in the returned results and plots.

classColors

Character. Colors for each of the classes or samples of the class. Provide either sampleColors or classColors, not both.

sameScale

Logical. If TRUE, plots all the genes in the same expression scale.

showSampleNames

Logical. If TRUE, the sample names are shown in the plot. Not recommended for big datasets.

showMean

Logical. If TRUE, plots the class expression mean.

identify

Logical. If TRUE and supported (X11 or quartz devices), the plot will be interactive and clicking on a point will identify the sample the point represents. Press ESC or right-click on the plot screen to exit.

verbose

Logical. If TRUE, a message indicating where the pdf is saved will be printed on screen.

Value

The expression profiles plot, saved in the working directory as 'fileName.pdf'.

Examples

######
# Load libraries and expression data
######

# Load an expressionSet:
library(leukemiasEset)
data(leukemiasEset)

######
# Generic expression profile plot
######
# Plot expression of specific genes:
selectedGenes <- c("ENSG00000169575","ENSG00000078399","ENSG00000005381","ENSG00000154511")
plotExpressionProfiles(leukemiasEset, genes=selectedGenes, sampleLabels="LeukemiaType", type="boxplot")

# Color samples:
plotExpressionProfiles(leukemiasEset, genes="ENSG00000078399", 
 sampleLabels="LeukemiaType", 
 showMean=TRUE, identify=FALSE,
 sampleColors=c("grey","red")
 [(sampleNames(leukemiasEset) %in% c("GSM331386.CEL","GSM331392.CEL"))+1])

# Color classes:
plotExpressionProfiles(leukemiasEset, genes="ENSG00000078399", 
 sampleLabels="LeukemiaType", 
 showMean=TRUE, identify=TRUE,
 classColors=c("red", "blue", "red", "red","red"))

######
# Expression profiles related to a classifier
######
# Train a classifier or load a trained one:
trainSamples<- c(1:10, 13:22, 25:34, 37:46, 49:58) 
# summary(leukemiasEset$LeukemiaType[trainSamples])
# leukemiasClassifier <- geNetClassifier(leukemiasEset[,trainSamples], 
#    sampleLabels="LeukemiaType", plotsName="leukemiasClassifier") 
data(leukemiasClassifier) # Sample trained classifier

# Plot expression of the selected genes in the train samples:
plotExpressionProfiles(leukemiasEset[,trainSamples], leukemiasClassifier, 
    sampleLabels="LeukemiaType", fileName="leukExprs.pdf")

# Plot expression of all the genes of specific classes:
classGenes <- getRanking(leukemiasClassifier@classificationGenes, 
    showGeneID=TRUE)$geneID[,c("CLL"), drop=FALSE] # Feel free to modify
plotExpressionProfiles(leukemiasEset, genes=classGenes, sampleLabels="LeukemiaType", 
    type="boxplot")

# Plot (on screen) the expression of the top ranked genes of each class
plotExpressionProfiles(leukemiasEset, leukemiasClassifier, sampleLabels="LeukemiaType")