mbecSCOEFStatsPlot: Plot Silhouette Coefficient

In buschlab/MBECS: Evaluation and correction of batch effects in microbiome data-sets

Description

The goodness of clustering assessed by the silhouette coefficient. It works with the output of 'mbecVarianceStats()' for the method 's.coef'. Format of this output is a data.frame that contains a column for every model variable and as many rows as there are features (OTUs, Genes, ..). Multiple frames may be used as input by putting them into a list - IF the data.frames contain a column named 'type', this function will use 'facet_grid()' to display side-by-side panels to enable easy comparison.

Usage

mbecSCOEFStatsPlot(scoef.obj)

Arguments

scoef.obj,

output of 'mbecVarianceStats' with method s.coef

Value

A ggplot2 dot-plot object.

Examples

# This will return a paneled plot that shows results for the variance
# assessment.
df.var.scoef <- mbecModelVariance(input.obj=dummy.mbec,
model.vars=c('batch','group'), method='s.coef', type='clr')
plot.scoef <- mbecSCOEFStatsPlot(scoef.obj=df.var.scoef)

buschlab/MBECS documentation built on Jan. 21, 2022, 1:27 a.m.