plotAllelicHeatmap: Plot allelic ratio heatmap

In mikelove/fishpond: Fishpond: downstream methods and tools for expression data

Plot allelic ratio heatmap

Description

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

Usage

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.

mikelove/fishpond documentation built on Aug. 29, 2023, 2:45 p.m.