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

In trichelab/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", "AA"),
  ...
)

genMTcircos(mvr)

initMTcircos(x)

genesMTcircos(x, anno, legends = F)

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 with annotations
how	optional specification for how to plot multiple samples
...	other arguments to pass on to called functions
x	something with a genome()
legends	plot legends? (FALSE)

Value

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

   annotations

Examples

library(MTseekerData)
BAMdir <- system.file("extdata", "BAMs", package="MTseekerData")
BAMs <- paste0(BAMdir, "/", list.files(BAMdir, pattern="^pt.*bam$"))
(mvr <- filterMTvars(pileupMT(BAMs[1], ref="rCRS")))
MTcircos(mvr)
title("Mitochondrial variants in a leukemia patient's blast cell")

trichelab/MTseeker documentation built on March 8, 2021, 6:20 p.m.