plotHeterogeneity {AneuFinder} | R Documentation |
Make heterogeneity vs. aneuploidy plots using individual chromosomes as datapoints.
plotHeterogeneity(hmms, hmms.list = NULL, normalChromosomeNumbers = NULL, plot = TRUE, regions = NULL, exclude.regions = NULL)
hmms |
A list of |
hmms.list |
Alternative input for a faceted plot. A named list() of lists of |
normalChromosomeNumbers |
A named integer vector or matrix with physiological copy numbers, where each element (vector) or column (matrix) corresponds to a chromosome. This is useful to specify male or female samples, e.g. |
plot |
A logical indicating whether to plot or to return the underlying data.frame. |
regions |
A |
exclude.regions |
A |
A ggplot
object or a data.frame if plot=FALSE
.
### Example 1: A faceted plot of lung and liver cells ### ## Get results from a small-cell-lung-cancer lung.folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData") lung.files <- list.files(lung.folder, full.names=TRUE) ## Get results from the liver metastasis of the same patient liver.folder <- system.file("extdata", "metastasis-liver", "hmms", package="AneuFinderData") liver.files <- list.files(liver.folder, full.names=TRUE) ## Make heterogeneity plots plotHeterogeneity(hmms.list = list(lung=lung.files, liver=liver.files)) ### Example 2: Plot a mixture sample of male and female cells ### ## Get results from a small-cell-lung-cancer folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData") files <- list.files(lung.folder, full.names=TRUE) ## Construct a matrix with physiological copy numbers for a mix of 48 male and 48 female samples normal.chrom.numbers <- matrix(2, nrow=96, ncol=24, dimnames=list(sample=c(paste('male', 1:48), paste('female', 49:96)), chromosome=c(1:22,'X','Y'))) normal.chrom.numbers[1:48,c('X','Y')] <- 1 normal.chrom.numbers[49:96,c('Y')] <- 0 head(normal.chrom.numbers) ## Make heterogeneity plots plotHeterogeneity(hmms = files, normalChromosomeNumbers = normal.chrom.numbers) ### Example 3: A faceted plot of male lung and female liver cells ### ## Get results from a small-cell-lung-cancer lung.folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData") lung.files <- list.files(lung.folder, full.names=TRUE) ## Specify the physiological copy numbers chrom.numbers.lung <- c(rep(2, 22), 1, 1) names(chrom.numbers.lung) <- c(1:22, 'X', 'Y') print(chrom.numbers.lung) ## Get results from the liver metastasis of the same patient liver.folder <- system.file("extdata", "metastasis-liver", "hmms", package="AneuFinderData") liver.files <- list.files(liver.folder, full.names=TRUE) ## Specify the physiological copy numbers chrom.numbers.liver <- c(rep(2, 22), 2, 0) names(chrom.numbers.liver) <- c(1:22, 'X', 'Y') print(chrom.numbers.liver) ## Make heterogeneity plots plotHeterogeneity(hmms.list = list(lung=lung.files, liver=liver.files), normalChromosomeNumbers = list(chrom.numbers.lung, chrom.numbers.liver)) ### Example 4 ### ## Exclude artifact regions with high variance consensus <- consensusSegments(c(lung.files, liver.files)) variance <- apply(consensus$copy.number, 1, var) exclude.regions <- consensus[variance > quantile(variance, 0.999)] ## Make heterogeneity plots plotHeterogeneity(hmms.list = list(lung=lung.files, liver=liver.files), exclude.regions=exclude.regions)