locus_plot: locus_plot

In lutsik/MeDeCom: Decomposition of heterogeneous methylomes

locus_plot

Description

Plot results for a selected locus

Usage

locus_plot(
  That,
  ann,
  cgs,
  locus.chr,
  locus.start,
  locus.end,
  locus.name = sprintf("%s:%d-%d", locus.chr, locus.start, locus.end),
  locus.forward = FALSE,
  flank.start = 1000,
  flank.end = 1000,
  comp.cols = rainbow(ncol(That)),
  legend.pos = "topleft",
  Tstar = NULL,
  D = NULL,
  plot.genes = FALSE,
  ann.genes = NULL
)

Arguments

That	a matrix of LMCs
ann	CpG annotation
cgs	indices of CpGs data for which are present in That with respect to ann
locus.chr	chromosome
locus.start	start coordinate
locus.end	end coordinate
flank.start	number of basepairs to extend the locus upstream
flank.end	number of basepairs to extend the locus downstream
comp.cols	color code for LMCs
legend.pos	location of the legend, in accordance with legend
Tstar	matrix of reference profiles
D	matrix of input methylation data used to produce That
plot.genes	if TRUE a track with gene locations will be plotted
ann.genes	gene annotation necessary for the gene plotting @author Pavlo Lutsik, with modifications by Michael Scherer @export

lutsik/MeDeCom documentation built on July 15, 2024, 4:51 a.m.