msc.heatmap: Visualization of cluster matrices

Description Usage Arguments Value Examples

View source: R/msc.heatmap.R

Description

The msc.heatmap function generates a heatmap of the input cluster matrix that summarizes the presence or absence of Minicircle Cluster Sequences (MCSs) between groups of samples.

Usage

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msc.heatmap(clustmatrix, samples, groups)

Arguments

clustmatrix

one cluster matrix generated with the msc.matrix function.

samples

a vector containing the sample names. This can include all samples or it can be a subset.

groups

a vector specifying to which groups (e.g. species) the samples belong to.

Value

a heatmap

Examples

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data(exData)
data(matrices)

### run function 
msc.heatmap(matrices[["id80"]], groups = exData$species,
            samples = exData$samples )
   
### run function on every cluster matrix with subset of samples
### you will be asked to confirm
table(exData$species)
hybrid <- which(exData$species=="hybrid")
# msc.heatmap(matrices[["id97"]], groups = exData$species[hybrid], 
#             samples = exData$samples[hybrid])

rKOMICS documentation built on July 21, 2021, 5:07 p.m.