track_bed {rGenomeTracks} | R Documentation |
Generate genome_track object from a bed file.
track_bed( file, title = NULL, height = 2, overlay_previous = "no", fontsize = 12, orientation = NULL, line_width = 0.5, color = "#1f78b4", max_value = NULL, min_value = NULL, border_color = "black", prefered_name = "transcript_name", merge_transcripts = FALSE, labels = TRUE, style = "flybase", display = "stacked", max_labels = 60, global_max_row = FALSE, gene_rows = NULL, arrow_interval = 2, arrowhead_included = FALSE, color_utr = 0, height_utr = 1, arrow_length = 0, all_labels_inside = FALSE, labels_in_margin = 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". |
fontsize |
Numeric value to font size of tracks's text. |
orientation |
String. Set to "inverted" to make the track upside down. Default is NULL. |
line_width |
Numeric. Default is 0.5. |
color |
String. Hex color or string color. Default is "#1f78b4". |
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. |
border_color |
String. default is "black" |
prefered_name |
String. Denote which column to get elements names. Default is "transcript_name". |
merge_transcripts |
Boolean. Default is FALSE. |
labels |
Boolean. Default is FALSE. |
style |
String. Options are "flybase" (default), or "UCSV" or "tassarrow". |
display |
String. options are "stacked" (default) or "collapsed", "triangles" or "interleaved". |
max_labels |
Numeric. Any integer about 1. Default is 60. |
global_max_row |
Boolean. Default is FALSE. |
gene_rows |
Numeric. Default is NULL. |
arrow_interval |
Numeric. Should be above 1. Default is 2 |
arrowhead_included |
Boolean. Default is FALSE |
color_utr |
String. Hex color or string. Default is "grey" |
height_utr |
Numeric. Between 0 and 1. Default is 1. |
arrow_length |
Numeric. Default is NULL. |
all_labels_inside |
Boolean. Default is FALSE |
labels_in_margin |
Boolean. Default is FALSE. |
track_bed()
supports all common bed files with minimal of
3 columns and maximum of 12 columns.
genome_track
fontsize
argument can be overriden by the same
argument in plot_gtracks()
Omar Elashkar
bed12_dir <- system.file("extdata", "dm3_genes.bed.gz", package = "rGenomeTracks" ) bed4_dir <- system.file("extdata", "dm3_genes.bed4.gz", package = "rGenomeTracks" ) bed6_dir <- system.file("extdata", "dm3_genes.bed6.gz", package = "rGenomeTracks" ) # Create bed track using bed4 file bed4 <- track_bed( file = bed4_dir, height = 3, title = "bed4", color = "cyan", , border_color = "#9ACD32", line_width = 1.5 ) # Create bed track using bed6 file bed6 <- track_bed( file = bed6_dir, height = 3, title = "bed4", fontsize = 8, color = "red", border_color = "yellow", arrowhead_included = TRUE ) # Create bed track using bed12 file bed12 <- track_bed( file = bed12_dir, height = 3, title = "bed12", style = "UCSC", arrow_interval = 10, fontsize = 10 ) # Create a spacer track space <- track_spacer(height = 1) ## Not run: # Plotting the tracks plot_gtracks(bed4 + space + bed6 + space + bed12 + space, chr = "X", start = 300 * 10^4, end = 330 * 10^4, verbose = TRUE ) ## End(Not run)