Plot relative CN diversity heatmap

Function to plot the copy number profile from relative copy numbers

Usage

RCNDiversityPlot(
  qdnaseq_obj,
  order_by = NULL,
  cluster = TRUE,
  subset = NULL,
  Xchr = FALSE,
  rmblacklist = NULL,
  limits = c(-1.5, 1.5),
  breaks = c(2.5, 1, 0.5, 0, -0.5, -1, -2.5),
  genome = "hg19"
)

Arguments

order_by

optional character vector containing the order the samples in the heatmap should be in

cluster

optional logical Do a row-wise sort of the heatmap (sort the samples)

subset

optional character vector A subset of samples that you'd like to plot.

rmblacklist

optional NULL or character vector. Filter the plot of blacklist regions from this genome. ex. 'hg19'

limits

vector containing the limits of your colour gradient. Passed to scale_fill_gradientn

breaks

vector containing the limits of your colour gradient. Passed to scale_fill_gradientn

genome

reference genome build

x

dataframe containing the copy number segments in long format: columns should be start, sample id (named sample) and segmented

Value

Heatmap of relative copy number calls

Details

Visualizing relative copy number calls from WiseCondorX and QDNASeq as heatmaps