plotAmpliconNumbers: plotAmpliconNumbers

In derele/MultiAmplicon: Metabarcoding and microbiome analysis using multiple amplicons

plotAmpliconNumbers

Description

Plot the raw counts for primer pairs matched in different sample files as a heatmap

Usage

plotAmpliconNumbers(MA, transf = function(x) log10(x + 1), ...)

## S4 method for signature 'matrix'
plotAmpliconNumbers(MA, transf = function(x) log10(x + 1), ...)

## S4 method for signature 'MultiAmplicon'
plotAmpliconNumbers(MA, transf = function(x) log10(x + 1), ...)

## S4 method for signature 'MultiAmplicon'
plotPipelineSummary(MA)

## S4 method for signature 'data.frame'
plotPipelineSummary(MA)

Arguments

MA	The primer matching (amplicon) matrix of a MultiAmplicon object or the object itself
transf	transformation to be applied, recommended default is log10(x+1)
...	additional parameter to be passed to pheatmap function

Details

The function uses pheatmap to plot the primer matching statistics stored in the rawCounts slot of a MultiAmplicons-class object

Value

just like the original pheatmap function, A heatmap is drawn to the graphics output device. Returned are (invisibly) a list of components: 1."tree_row" the clustering of rows as hclust object 2. "tree_col" the clustering of columns as hclust object 3. "kmeans" the kmeans clustering of rows if parameter kmeans_k was specified.

Author(s)

Emanuel Heitlinger

derele/MultiAmplicon documentation built on Oct. 14, 2023, 7:43 p.m.