plot.cluster.flow: Plot the mean/median of the clusters of variants across...

In hdng/clonevol: Clonal ordering and visualization

Description

Plot the mean or median of the clusters VAF across samples in a single plot

Usage

plot.cluster.flow(variants, cluster.col.name, vaf.col.names, ...)

Arguments

variants	Variant data frame
cluster.col.name	Name of cluster column (default='cluster')
sample.names	Names of samples, corresponding to vaf.col.names (default=NULL)
vaf.in.percent	VAF is in percent (default=TRUE)
center.measure	Method used to determine the center of VAFs of variants within a cluster (default='median', can also be 'mean')
line.size	Size of lines (default=1)
colors	Colors of the clusters' variant data points
shapes	Shapes of the clusters' variant data points
x.title	Title of x axis (default="Variant Allele Frequency (%)")
y.title	Title of y axis
out.file	Output file (can be pdf, png, etc.) (default=NULL). If equal NULL, this function return the plot that can be print
width	Width of the output file
height	Height of the output file

Examples

data(aml1)
plot.cluster.flow(aml1$variants,
                  vaf.col.names = aml1$params$vaf.col.names,
                  sample.names = c('Primary', 'Relapse'),
                  out.file = paste0(tempfile(), '.pdf'),
                  colors = c('#999793', '#8d4891', '#f8e356',
                     '#fe9536', '#d7352e'))

hdng/clonevol documentation built on May 17, 2019, 3:19 p.m.