msc.heatmap: Visualization of cluster matrices

In rKOMICS: Minicircle Sequence Cluster (MSC) Analyses

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

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

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.