plot_loops: loops or interactions plotter

In RubD/GeTrackViz2:

Description

This function plots data in bedpe format

Usage

plot_loops(bedpe, name_bedpe, color_column = NULL,
  color_bedpe = "black", mychr, start_loc, end_loc, breaks_wanted = 4,
  y_title = "prob", show_partial_overlap = T, anchor_width = 1.3,
  loop_width = 1, axis_line_size = 0.2, marginvec_mm = c(0, 0, 0, 0),
  reverse_strand = FALSE, show_labels = F, print_plot = F)

Arguments

bedpe	bedpe file for DNA loops or interaction data
name_bedpe	name of sample
color_bedpe	color of track
mychr	chromosome
start_loc	start location on chromomse
end_loc	end location on chromosome
breaks_wanted	number of breaks on x-axis
y_title	title for y-axis
show_partial_overlap	include loops that do not entirely overlap the coordinates
axis_line_size	line size of x-axis
marginvec_mm	margin around plot, default = c(0,0,0,0)
reverse_strand	reverse the x-axis, default = FALSE
show_labels	boolean: show x-axis lables
print_plot	boolean: print individual plot

Value

ggplot object

Examples

    plot_loops(bedpe)

RubD/GeTrackViz2 documentation built on May 31, 2019, 2:45 p.m.