heatmapGenomewideClusters: Plot heatmaps for quality control

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Plot heatmaps for quality control

Description

This function is a convenient wrapper to call heatmapGenomewide for all clusters after calling clusterByQuality and plot the heatmaps into one pdf for efficient comparison.

Usage

heatmapGenomewideClusters(cl = NULL, cutree = NULL, file = NULL, ...)

Arguments

cl	The return value of clusterByQuality.
cutree	The return value of cutree, where the names correspond to the filenames to be loaded.
file	A character specifying the output file.
...	Further parameters passed on to heatmapGenomewide.

Value

A cowplot object or NULL if a file was specified.

Examples

## Get a list of HMMs and cluster them
folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData")
files <- list.files(folder, full.names=TRUE)
cl <- clusterByQuality(files, G=5)
heatmapGenomewideClusters(cl=cl)

## Plot sub-clones of the largest cluster
largest.cluster <- which.max(sapply(cl$classification, length))
files <- cl$classification[[largest.cluster]]
clust <- clusterHMMs(files)
groups <- cutree(tree = clust$hclust, k = 5)
heatmapGenomewideClusters(cutree = groups, cluster = FALSE)

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.