PAA (version 1.7.1)

plotFeaturesHeatmap: Plot feature intensities as a heatmap.

Description

Plots intensities of given features as a heatmap.

Usage

plotFeaturesHeatmap(features = NULL, elist = NULL, n1 = NULL, n2 = NULL,  output.path = NULL, description=FALSE)

Arguments

features

vector containing "BRC"-IDs (mandatory).

elist

EListRaw or EList object containing all intensity data in log2 scale (mandatory).

n1

integer indicating the sample size of group 1 (mandatory).

n2

integer indicating the sample size of group 2 (mandatory).

output.path

path for saving the heatmap as a tiff file (default: NULL).

description

if TRUE, features will be described via protein names instead of UniProtKB accessions (default: FALSE).

Value

No value is returned.

Details

Plots intensities of all features given in the vector features via their corresponding "BRC"-IDs as a heatmap. If description is TRUE (default: FALSE), features will be described via protein names instead of UniProtKB accessions. Furthermore, if output.path is not NULL, the heatmap will be saved as a tiff file in output.path. This function can be used to check whether the selected features are differential.

Examples

cwd <- system.file(package="PAA")
load(paste(cwd, "/extdata/Alzheimer.RData", sep=""))
#elist <- elist[elist$genes$Block < 10,]

#c1 <- paste(rep("AD",20), 1:20, sep="")
#c2 <- paste(rep("NDC",20), 1:20, sep="")

#pre.sel.results <- preselect(elist=elist, columns1=c1, columns2=c2, label1="AD",
# label2="NDC", discard.threshold=0.1, fold.thresh=1.9, discard.features=TRUE,
# method="tTest")
#elist <- elist[-pre.sel.results$discard,]

#selectFeatures.results <- selectFeatures(elist,n1=20,n2=20,label1="AD",
# label2="NDC",selection.method="rf.rfe",preselection.method="none",subruns=2,
# k=2,candidate.number=20,method="frequency")
 
load(paste(cwd, "/extdata/selectFeaturesResultsFreq.RData", sep="")) 
plotFeaturesHeatmap(features=selectFeatures.results$features, elist=elist,
 n1=20, n2=20, description=TRUE)