heatmapAneuploidies {AneuFinder} | R Documentation

## Plot aneuploidy state

### Description

Plot a heatmap of aneuploidy state for multiple samples. Samples can be clustered and the output can be returned as data.frame.

### Usage

    heatmapAneuploidies(hmms, ylabels = NULL, cluster = TRUE,
      as.data.frame = FALSE)

### Arguments

`hmms` | A list of `aneuHMM` objects or a character vector with files that contain such objects.
`ylabels` | A vector with labels for the y-axis. The vector must have the same length as `hmms`. If `NULL` the IDs from the `aneuHMM` objects will be used.
`cluster` | If `TRUE`, the samples will be clustered by similarity in their CNV-state.
`as.data.frame` | If `TRUE`, instead of a plot, a data.frame with the aneuploidy state for each sample will be returned.

### Value

A `ggplot` object or a data.frame, depending on option `as.data.frame`.

### Author(s)

Aaron Taudt

### Examples

    ## Get results from a small-cell-lung-cancer
    folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData")
    files <- list.files(folder, full.names=TRUE)
    ## Plot the ploidy state per chromosome
    heatmapAneuploidies(files, cluster=FALSE)
    ## Return the ploidy state as data.frame
    df <- heatmapAneuploidies(files, cluster=FALSE, as.data.frame=TRUE)
    head(df)

[Package AneuFinder version 1.12.1 Index]