Description Usage Arguments Value Examples
This function plots DNA bedgraph data
1 2 3 4 5 6 7 | 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)
|
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 |
ggplot object
1 | plot_bedgraph(bdg)
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