Description Usage Arguments Value Author(s) Examples
View source: R/BinFeaturesPlot.R
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.
1 2 3 |
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. |
A plot indicating the values of the features of the LeadCpds in green and those of the others in blue.
Marijke Van Moerbeke
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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)
## End(Not run)
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