shaman_plot_tracks_and_annotations: plots misha 1D tracks and annotations

In tanaylab/shaman: shaman - Sampling HiC contAct Matrices for Aparametric Normalization

plots misha 1D tracks and annotations

Description

shaman_gplot_tracks_and_annotations

Usage

shaman_plot_tracks_and_annotations(
  genome,
  interval_range,
  misha_tracks = list(),
  mt_colors = getOption("shaman.track_colors"),
  mt_ylims = NULL,
  annotations = list(),
  a_colors = getOption("shaman.annotation_colors"),
  add_genes = T,
  add_ideogram = T,
  add_axis = T,
  gene_stacking = "squish",
  gene_size = 0.7,
  track_size = 0.8,
  annotation_size = 0.7
)

Arguments

genome	Name of reference genome (e.g. "hg19", "mm10")
interval_range	1D interval (chrom, start, end) specifying the region to plot
misha_tracks	List of 1D track expressions (virtual tracks also supported) which can be extracted from.
mt_colors	Array of colors, one for each misha_track, which will be used to plot each 1d track.
annotations	List of gintervals highlighting annotated regions.
a_colors	Array of colors, one for each annotation set.
add_genes	Boolean flag indicating whether to show gene annotations.
add_ideogram	Boolean flag indicating whether to add an chromosomal ideogram.
add_axis	Boolean flag indicating whether to show chromosmal axis.
gene_stacking	Describes the viewing option of the genes track. Can be either "squish", or "dense"
gene_size	Size of gene annotation view
track_size	Size of track view
my_ylims	Y-axis limits for each misha track. If not provided, generated automatically based on the data to be displayed in the region.
annot_size	Size of annotation view

Details

Plots 1D tracks in UCSC format. Along with gene annotations and chromosomal axis, this function plots one dimensional misha tracks (e.g. rna-seq, chip-seq data) and marks annotated intervals in the plotting region.

Examples

gsetroot(shaman_get_test_track_db())
shaman_plot_tracks_and_annotations("hg19", gintervals(2, 175.5e06, 177.5e06))

tanaylab/shaman documentation built on April 2, 2022, 1:32 a.m.