IntClust (version 0.0.2)

BinFeaturesPlot: Plot of a selection of features

Description

The function BinFeaturesPlot plots the binary data matrix for a selection of features. It is possible to separate between compounds of interest and the other compounds. This is a visualization to see which characteristics are (not) expressed in a specific cluster.

Usage

BinFeaturesPlot(LeadCpds, OrderLab, Features, Data, ColorLab, nrclusters = NULL, 
cols = NULL, name = c("FP"),colors1 = c("gray90", "blue"), colors2 = c("gray90",
"green"),margins=c(5.5,3.5,0.5,5.5),plottype="new",location=NULL)

Arguments

LeadCpds

A character vector containing the compounds one wants to separate from the others.

Features

A character vector containing the selection of features to be plotted.

Data

The data matrix the features are derived from.

OrderLab

Optional. If the compounds are to set in a specific order of a specific clustering.

ColorLab

Optional. The clustering result that determines the clusters of the labels of the objects in the plot.

nrclusters

Optional. The number of clusters to consider if ColorLab is specified.

cols

The colors for the clusters of the labels of the objects as determined by ColorLab.

name

The overall name to give the features.

colors1

Colors to indicate the present and abscence of features of the compounds not in LeadComps.

colors2

Colors to indicate the present and abscence of features of the LeadComps.

margins

Optional. Margins to be used for the plot.

plottype

Should be one of "pdf","new" or "sweave". If "pdf", a location should be provided in "location" and the figure is saved there. If "new" a new graphic device is opened and if "sweave", the figure is made compatible to appear in a sweave or knitr document, i.e. no new device is opened and the plot appears in the current device or document.

location

If plottype is "pdf", a location should be provided in "location" and the figure is saved there.

Value

A plot indicating the values of the features of the LeadCpds in green and those of the others in blue.

Examples

# NOT RUN {
data(fingerprintMat)
data(targetMat)
data(geneMat)

MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55)
# }
# NOT RUN {
MCF7_Interactive=ChooseFeatures(Interactive=TRUE,LeadCpds=NULL,ClusterResult=MCF7_T,
ClusterColors=MCF7_F,BinData=list(fingerprintMat),Datanames=c("FP"),geneMat,
topChar = 20, topG = 20,nrclusters=7,N=1)

Lead=MCF7_Interactive$"Choice 1"$Compounds$LeadCpds
Feat=MCF7_Interactive$"Choice 1"$Characteristic$FP

BinFeaturesPlot(LeadCpds=Lead,Features=Feat,Data=fingerprintMat,OrderLab=MCF7_F,ColorLab=MCF7_F,
nrclusters=7,cols=Colors1,name=c("FP"),margins=c(5.5,3.5,0.5,5.5),plottype="new",location=NULL)
# }