plotCateComparisonSetAndRef: Plot barplots and pheatmaps for the scores or the distance of...

In lldelisle/analysePeaks: Compare, annotate your peaks

Description

Plot barplots and pheatmaps for the scores or the distance of features in the Set and in the Reference As well as when it is in Set and in the Set but not in the Reference and vice-versa

Usage

plotCateComparisonSetAndRef(
  myGRAndAttributes,
  fontsize = 10,
  plotBarPlots = TRUE,
  only5categoriesBP = FALSE,
  plotPheatmaps = TRUE,
  display_numbers = TRUE,
  whichPheatmaps = 1:5,
  allCates = NULL,
  plotProportion = FALSE
)

Arguments

myGRAndAttributes	Should be the output of annotateWithCate
fontsize	base fontsize for the heatmaps (default is 10)
plotBarPlots	logical whether to plot the barplots (default is TRUE)
only5categoriesBP	logical whether to plot only the barplots with 5 categories (default is FALSE).
plotPheatmaps	logical whether to plot the pheatmaps (default is TRUE)
display_numbers	logical whether to display the numbers in the pheatmaps (default is TRUE)
whichPheatmaps	a vector containing the pheatmaps to plot between 1 to 5 with: 1=shared by all Set and at least one Ref or shared by all Set and Ref 2=shared by all Set none of the Ref or shared by all Set no Ref 3=shared by all Set: all or all shared by all Set 4=shared by all Ref in not a single of the set or Ref in not a single of the set 5=shared by all Ref: all or all Ref (default is 1:5)
allCates	a vector of string with the categories to plot, if NULL all categories in 'myGRAndAttributes' are used (default is NULL)
plotProportion	logical whether to display the pheatmap 1, 2, and 4 should be plot as proportion of pheatmap 3 and 5 (default is FALSE)

Value

Plot barplots and pheatmaps but do not return anything

lldelisle/analysePeaks documentation built on July 10, 2021, 1:02 p.m.