plot_consensus: Create plot of shared variants among samples

In brucemoran/somenone: R functions required by the somenone NextFlow nf-core pipeline

Create plot of shared variants among samples

Description

Create plot of shared variants among samples

Usage

plot_consensus(
  master_gr,
  tag,
  included_order,
  sample_map = NULL,
  colours = NULL,
  plot_label_pattern = "patho"
)

Arguments

master_gr	is a named list of GRanges object [[samples1..n]]
tag	is a string to tag output files
included_order	ordering of samples for plotting
sample_map	map included_order to new names, must be name vector where names equate to included_order elements
colours	to use for colouring/shading, made into a rampPalette, order according to low to high allele frequency
plot_label_pattern	match this to print label of variant (NB too vague and you will have a huge amount of labels which looks shit; currently set to show 'patho'genic)

Value

none, plots PDF and writes out tsv files

brucemoran/somenone documentation built on Nov. 1, 2022, 3:56 p.m.