track_bedgraph_matrix {rGenomeTracks}R Documentation

Generate bedgraph matrix track

Description

A track for file like bedgraph but with more than 4 columns, like the insulation score from hicPlotTADs

Usage

track_bedgraph_matrix(
  file,
  title = NULL,
  height = 2,
  overlay_previous = "no",
  orientation = NULL,
  max_value = NULL,
  min_value = NULL,
  show_data_range = FALSE,
  type = "matrix",
  rasterize = TRUE,
  pos_score_in_bin = "center",
  plot_horizontal_lines = FALSE,
  colormap = "virdis"
)

Arguments

file

String. The location of the track file

title

String. If specificed, the title of the track to be displayed.

height

Numeric. The height of the plotted track in cm.

overlay_previous

String. Options are "no" (default) or "yes" or

orientation

String. Set to "inverted" to make the track upside down. Default is NULL.

max_value

Numeric. Default is NULL. The max value cut-off for the numeric column.

min_value

Numeric. Default is NULL. The min value cut-off for the numeric column.

show_data_range

Boolean. Default is FALSE.

type

"matrix" (default) or "lines".

rasterize

Boolean. Default is TRUE

pos_score_in_bin

String value to indicate the position of score with respect to bin start and end. Possible values are either "center" (default) or "block".

plot_horizontal_lines

Boolean. Can be used only if type parameter is set to "lines".

colormap

String with matplotlib-compatible colormap. Default is set to "viridis".

Details

The different options for color maps can be found here: https://matplotlib.org/users/colormaps.html.

Value

genome_track

Note

fontsize argument can be overriden by the same argument in plot_gtracks()

Author(s)

Omar Elashkar

Examples

IS_dir <- system.file("extdata", package = "rGenomeTracks", "tad_separation_score.bm.gz")
IS <- track_bedgraph_matrix(IS_dir)
## Not run: 
plot_gtracks(IS, chr = "X", start = 2000000, end = 3500000)

## End(Not run)

[Package rGenomeTracks version 0.99.8 Index]