Plot allelic ratio heatmap

Plot allelic ratio heatmap over features and samples using the pheatmap package. The a1/(a2 + a1) ratio is displayed.

plotAllelicHeatmap(
  y,
  idx,
  breaks = NULL,
  cluster_cols = FALSE,
  main = "Allelic ratio",
  stripAfterChar = "-",
  ...
)

Arguments

y

a SummarizedExperiment (see swish)

idx

a numeric or logical vector of which features to plot

breaks

breaks passed along to pheatmap

cluster_cols

logical, passed to pheatmap

main

title of the plot

stripAfterChar

for the column names, if specified will strip allelic identifiers after this character, default is hyphen. set to NULL to avoid this action

...

other arguments passed to pheatmap

Value

nothing, a plot is displayed

References

The methods for allelic expression analysis are described in:

Euphy Wu, Noor P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro, Michael I. Love. "Detecting isoform-level allelic imbalance accounting for inferential uncertainty" bioRxiv (2022) https://doi.org/10.1101/2022.08.12.503785

This function makes use of the pheatmap package:

Kolde, Raivo. "Pheatmap: pretty heatmaps." R package version 1.2 (2012): 726.