track_domains {rGenomeTracks} | R Documentation |
Domain files are bed files represents TADS in the case of HiC analysis.
track_domains( file, title = NULL, height = 2, overlay_previous = "no", orientation = NULL, line_width = 0.5, color = "#1f78b4", max_value = NULL, show_data_range = TRUE, min_value = NULL, border_color = "black", prefered_name = "transcript_name", merge_transcripts = 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. 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. |
show_data_range |
Boolean. Default is TRUE. |
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. |
To remove the border, set 'border_color' parameter to "none".
genome_track
Omar Elashkar
tads_dir <- system.file("extdata", "tad_classification.bed", package = "rGenomeTracks" ) tads <- track_domains( file = tads_dir, border_color = "black", color = "#11FF34", height = 5 ) tads_i <- track_domains( file = tads_dir, border_color = "red", color = "#cccccc", height = 3, orientation = "inverted" ) tracks <- track_x_axis(where = "top") + tads + tads_i ## Not run: plot_gtracks(tracks, chr = "X", start = 30 * 10^5, end = 35 * 10^5) ## End(Not run)