IntClust (version 0.0.2)

FeaturesOfCluster: Lists all features present in a selected cluster of compounds

Description

The function FeaturesOfCluster lists the number of features compounds of the cluster have in common. A threshold can be set selecting among how many compounds of the cluster the features should be shared. An optional plot of the features is available.

Usage

FeaturesOfCluster(LeadCpds,Data,Threshold=1,Plot=TRUE,plottype="new",location=NULL)

Arguments

LeadCpds

A character vector containing the compounds one wants to investigate in terms of features.

Data

The data matrix the features are derived from.

Threshold

The number of compounds the features at least should be shared amongst. Default is set to 1 implying that the features should be present in at least one of the compounds specified in leadCpds.

Plot

Logical. Indicates whether or not a BinFeaturesPlot should be set up for the selectcion of compounds and discovered features.

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. It list all features which are present in at least the threshold number of compounds. By including all other compounds as well, one can see whether features are common in the compounds or rather specific for the cluster.

Further, it returns a list with 2 items. The first indicates the number of shared features among the compounds. This provides an overview of which compounds are more similar than others. The second item is a character vector of the plotted features such that these can be retrieved for further investigation.

Examples

# NOT RUN {
data(fingerprintMat)

Lead=rownames(fingerprintMat)[1:5]

FeaturesOfCluster(LeadCpds=Lead,Data=fingerprintMat,
Threshold=1,Plot=TRUE,plottype="new",location=NULL)
# }