track_links {rGenomeTracks} | R Documentation |
Generate links track from arc file.
track_links( file, title = NULL, height = 2, overlay_previous = "no", orientation = NULL, links_type = "arcs", line_width = NULL, line_style = "solid", color = "blue", alpha = 0.8, max_value = NULL, min_value = NULL, ylim = NULL, show_data_range = FALSE, compact_arcs_level = 0, use_middle = FALSE )
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. Default is 2. See notes. |
overlay_previous |
String. Options are "no" (default) or "yes" or "share-y". |
orientation |
String. Default is NULL. Other option is "inverted". |
links_type |
String value with options "arcs" (default) or "triangles" or "loops". |
line_width |
Numeric value for line width. |
line_style |
String with options of either "solid", "dashed", "dotted", and "dashdot". |
color |
String. Hex color or string color. Default is "#1f78b4". |
alpha |
Numeric variable between 0 and 1 to indicate level of transparancy. Default is 1. |
max_value |
Numeric. Default is NULL. The max value cut-off for the numeric column. |
min_value |
Numeric. Default is NULL. The max value cut-off for the numeric column. |
ylim |
Numeric value above 0 to set arcs' height cutoff. Default is NULL |
show_data_range |
Boolean. Default is TRUE. |
compact_arcs_level |
Numeric value of either 0, 1 or 2 to indicate level of arcs' compactness by distance it travels. |
use_middle |
Boolean. Default is FALSE. |
Level of compactness relative to arcs' length can be manipulated using the argument compact_arcs_level where:
compact_arcs_level = 0, The default where the height is proportional to distance
compact_arcs_level = 1, the height is proportional to the square root of the distance
compact_arcs_level = 2, the height is the same for all distances
ylim argument sets the cutoff for arcs' height. This could be handy if you have small arc overridden by larger arc.
genome_track
ylim argument is incompatible with compact_arcs_level = 2
Omar Elashkar
tads_dir <- system.file("extdata", "tad_classification.bed", package = "rGenomeTracks" ) genes_dir <- system.file("extdata", "dm3_genes.bed.gz", package = "rGenomeTracks" ) links_dir <- system.file("extdata", "test.arcs", package = "rGenomeTracks" ) tads <- track_domains(tads_dir, color = "#cccccc", border_color = "red") links_overlay <- track_links(links_dir, color = "red", line_width = 3, links_type = "loop", overlay_previous = "share-y" ) links <- track_links(links_dir, color = "blue", line_width = 3, height = 3 ) genes <- track_bed(genes_dir, height = 7, style = "flybase", fontsize = 10 ) vlines <- track_vlines(genes_dir) ## Not run: plot_gtracks(tads + links_overlay + links + genes + vlines, chr = "X", start = 30 * 10^5, end = 35 * 10^5) ## End(Not run)