plotExpressionProfiles {geNetClassifier} | R Documentation |
Plots the expression profiles of the given genes.
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)
eset |
ExpressionSet or Matrix. Gene expression of the samples. |
genes |
Vector or Matrix. IDs of the genes to plot. |
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. |
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. |
The expression profiles plot, saved in the working directory as 'fileName.pdf'.
Bioinformatics and Functional Genomics Group. Centro de Investigacion del Cancer (CIC-IBMCC, USAL-CSIC). Salamanca. Spain
###### # 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")