Plot the raw counts for primer pairs matched in different sample files as a heatmap
plotAmpliconNumbers(MA, transf = function(x) log10(x + 1), ...) # S4 method for matrix plotAmpliconNumbers(MA, transf = function(x) log10(x + 1), ...) # S4 method for MultiAmplicon plotAmpliconNumbers(MA, transf = function(x) log10(x + 1), ...) # S4 method for MultiAmplicon plotPipelineSummary(MA) # S4 method for data.frame plotPipelineSummary(MA)
| 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 |
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.
The function uses pheatmap to plot the primer matching statistics stored in the rawCounts slot of a MultiAmplicons-class object
Emanuel Heitlinger