msc.similarity: Minicircle Sequence Cluster similarity

In rKOMICS: Minicircle Sequence Cluster (MSC) Analyses

Description

The msc.similarity function allows you to check the absolute and relative frequency of shared and unique MSC between different groups across different percent identities.

Usage

msc.similarity(clustmatrices, samples, groups)

Arguments

clustmatrices	a list of cluster matrices.
samples	a vector containing the names of the samples. This can include all samples or it can be a subset.
groups	a vector, of equal length as samples, specifying to which group (e.g. species) the samples belong to.

Value

absfreq	a list per percent identity containing absolute frequency values of shared and unique MSCs.
absfreq.plot	a list of barplots visualizing previous results.
relfreq	a list per percent identity containing relative frequency values of shared and unique MSCs.
relfreq.plot	one barplot visualizing previous results.

Examples

require(viridis)
data(matrices)
data(exData)

### run function
sim <- msc.similarity(matrices, samples = exData$samples, 
                      groups = exData$species)

### visualize results (absolute frequencies)
barplot(sim$absfreq$id93)

### adjust plot (relative frequencies)
sim$relfreq.plot + scale_fill_viridis(discrete = TRUE)

sim$relfreq$id97["2"]*100 
sim$relfreq$id97["3"]*100 

### reduce number of groups 
groups <- exData$species
levels(groups)[levels(groups)!='hybrid'] <- "non-hybrid"
sim.red <- msc.similarity(matrices, samples = exData$samples, groups = groups)
sim.red$relfreq.plot + scale_fill_viridis(discrete = TRUE)

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