plots hic normalized map with annotations — shaman_plot_map_score_with

shaman_plot_map_score_with_annotations

shaman_plot_map_score_with_annotations(
  genome,
  points_score,
  interval_range,
  point_size = 0.1,
  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,
  fig_fn = "",
  fig_width = 900,
  fig_height = 5/6 * 900
)

Arguments

genome: Name of reference genome (e.g. "hg19", "mm10")
points_score: A dataframe containing the points (start1, start2) and their normalized score.
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.
fig_fn: Name of png file to output to. Empty string will cause the figure to be plotted to the current device.
fig_width: Width in pixels of output png figure.
fig_height: Height in pixels of output png figure.
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 observerved hic contact matrix color-coded by normalized scores, aligned with linear data such as gene annotations, rna, chromatin, transcription factor binding, etc').

Examples


gsetroot(shaman_get_test_track_db())
#> Error in setwd(groot): cannot change working directory
points <- gextract("hic_score", gintervals.2d(2, 175e06, 178e06, 2, 175e06, 178e06), colnames = "score")
#> Error: Invalid interval (chr2, 1.75e+08, 1.78e+08): end coordinate exceeds chromosome boundaries
shaman_plot_map_score_with_annotations("hg19", points, gintervals(2, 175e06, 178e06))
#> Error in shaman_plot_map_score_with_annotations("hg19", points, gintervals(2,     175000000, 178000000)): points_score data frame must contain the following columns: start1, start2, score