heatmapAneuploidies: Plot aneuploidy state

Description Usage Arguments Value Author(s) Examples

View source: R/plotting.R

Description

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

Usage

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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

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## 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)

ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.