plotFeaturesHeatmap {PAA} | R Documentation |
Plots intensities of given features as a heatmap.
plotFeaturesHeatmap(features = NULL, elist = NULL, n1 = NULL, n2 = NULL, output.path = NULL, description=FALSE)
features |
vector containing |
elist |
|
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). |
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.
No value is returned.
Michael Turewicz, michael.turewicz@rub.de
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)