heatmapGenomewideClusters {AneuFinder} | R Documentation |
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.
heatmapGenomewideClusters(cl = NULL, cutree = NULL, file = NULL, ...)
cl |
The return value of |
cutree |
The return value of |
file |
A character specifying the output file. |
... |
Further parameters passed on to |
A cowplot
object or NULL
if a file was specified.
## 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)