plot_bedgraph: DNA bedgraph plotter

Description Usage Arguments Value Examples

Description

This function plots DNA bedgraph data

Usage

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plot_bedgraph(bdg, name_bdg, color_bdg, mychr, start_loc, end_loc,
  binsize = 100, breaks_wanted = 4, y_title = "RPM/bp",
  chrom_col = "chr", start_col = "start", end_col = "end",
  counts_col = "RPKM", forced_y_min = NULL, forced_y_max = NULL,
  axis_line_size = 0.2, marginvec_mm = c(0, 0, 0, 0),
  use_barplot = F, alpha_fill = 1, reverse_strand = FALSE,
  show_labels = F, print_plot = F)

Arguments

bdg

bedgraph file for DNA coverage data

name_bdg

name of sample

color_bdg

color of track

mychr

chromosome

start_loc

start location on chromomse

end_loc

end location on chromosome

binsize

size of bin

breaks_wanted

number of breaks on x-axis

y_title

title for y-axis

chrom_col

column name for chromosomes

start_col

column name for start

end_col

column name for end

counts_col

column name with counts

forced_y_min

hard minimum y-axis value

forced_y_max

hard maximum y-axis value

axis_line_size

line size of x-axis

marginvec_mm

margin around plot, default = c(0,0,0,0)

use_barplot

plot track as barplot, default = F

alpha_fill

alpha for lineplot, default = 1

reverse_strand

boolean: flip strand x-axis direction

show_labels

boolean: show x-axis lables

print_plot

boolean: print individual plot

Value

ggplot object

Examples

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