MTcircos: plot a canonical human (or, in principle, any) mitochondrial...

In MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

The default font sizes, orientations, etc. are optimized for a "cold" start; if you want to fiddle with the details, crack open the code and modify it... or alternatively, add sectors/dendrograms inside of this "framed" version.

Usage

MTcircos(variants = NULL, outside = NULL, inside = NULL,
  outcol = NULL, incol = NULL, anno = NULL, how = c("matrix",
  "VAF"), ...)

Arguments

variants	optional MVRanges or MVRangesList to split by strand & plot
outside	optional MVRanges or MVRangesList to plot outside the circle
inside	optional MVRanges or MVRangesList to plot inside the circle
outcol	optional color assignment function or matrix for outside
incol	optional color assignment function or matrix for inside
anno	a GRanges (optional, defaults to mtAnno.rCRS if none given)
how	optional specification for how to plot multiple samples
...	other arguments to pass on to called functions

Details

FIXME: add variant type coloration (del=blue, SNV=black, ins=red)

Value

invisibly, a list: 'anno' (data.frame) + 'pfun' (panel.fun)

Examples

library(MTseekerData)
data(RONKSvariants) 
MTcircos(RONKSvariants)
# same as plot(RONKSvariants)
title("Renal oncocytomas and normal kidney samples")

MTseeker documentation built on Oct. 31, 2019, 3:20 a.m.