heatmapGenomewideClusters {AneuFinder} | R Documentation

## 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)

[Package AneuFinder version 1.20.0 Index]