gpatterns.spatial_meth_trend: Plot spatial trend of methylation around intervals
In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

gpatterns.spatial_meth_trend

R Documentation

Plot spatial trend of methylation around intervals

Description

calculates the distance of tracks values from intervals bins the distances based on dist_breaks, and then calculates the average methylation m / (m + um) in each bin and plots the results.

Usage

gpatterns.spatial_meth_trend(
  tracks,
  intervals,
  method = "extract",
  dist_breaks = c(-4000000, -1000000, seq(-1000, 1000, 50), 1000000, 4000000),
  iterator = .gpatterns.genome_cpgs_intervals,
  min_cov = NULL,
  min_cgs = NULL,
  names = NULL,
  include.lowest = TRUE,
  groups = NULL,
  group_name = NULL,
  add_vline = TRUE,
  ncol = 2,
  nrow = 2,
  width = 5,
  height = 4,
  units = "in",
  pointsize = 12,
  res = 150,
  fig_fn = NULL,
  xlab = "Distance (bp)",
  ylim = c(0, 1),
  linewidth = 0.8,
  title = "",
  legend = TRUE,
  colors = NULL,
  parallel = getOption("gpatterns.parallel")
)

Arguments

`tracks`	tracks to plot
`intervals`	intervals to plot spatial methylation around. Can be any intervals set, or one of the following 'special' intervals: 'tss', 'exon', 'utr3', 'intron', 'cgi'
`dist_breaks`	breaks to determine the distances from intervals
`iterator`	track expression iterator (of both tracks and strat_track)
`min_cov`	minimal coverage of each track
`min_cgs`	minimal number of CpGs per bin.
`names`	alternative names for the track
`include.lowest`	if 'TRUE', the lowest value of the range determined by breaks is included
`groups`	a vector the same length of `tracks` with group for each track. Each group will on a different facet.
`group_name`	name of the grouping variable (e.g. tumor, sample, patient, experiment)
`add_vline`	add vertical line at 0 coordinate
`ncol`	number of columns
`nrow`	number of rows
`width`	plot width (if fig_fn is not NULL)
`height`	plot height (if fig_fn is not NULL)
`units`	see `png`
`pointsize`	see `png`
`res`	see `png`
`fig_fn`	output filename for the figure (if NULL, figure would be returned)
`xlab`	label for the x axis'
`ylim`	ylim of the plot
`title`	title for the plot
`legend`	add legend
`colors`	custom colors
`parallel`	get trends parallely