plotFeatures {PAA} | R Documentation |
Plots intensities of all given features (one sub-plot per feature) in group- specific colors.
plotFeatures(features = NULL, elist = NULL, n1 = NULL, n2 = NULL, group1 = "group1", group2 = "group2", output.path = NULL)
features |
vector containing |
elist |
|
n1 |
integer indicating the sample size of group 1 (mandatory). |
n2 |
integer indicating the sample size of group 2 (mandatory). |
group1 |
class label of group 1. |
group2 |
class label of group 2. |
output.path |
string indicating the folder where the figure will be saved (optional). |
Plots intensities of given features (e.g., selected by the function
selectFeatures()
) in group-specific colors (one sub-plot per feature).
All sub-plots are aggregated to one figure. When the argument
output.path
is not NULL this figure will be saved in 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$discard,] #selectFeatures.results <- selectFeatures(elist,n1=20,n2=20,label1="AD", # label2="NDC",selection.method="rf.rfe",preselection.method="none",subruns=2, # k=2,candidate.number=20,method="frequency") load(paste(cwd, "/extdata/selectFeaturesResultsFreq.RData", sep="")) plotFeatures(features=selectFeatures.results$features, elist=elist, n1=20, n2=20, group1="AD", group2="NDC")