bed

Description

A track for all bed-like files (with first column chromosome, second start and third end). If the other columns fit the requirement as defined in UCSC additional fields can be used. For example, the 5th and 9th column can be used to change the color of intervals, the 6th column indicate the strand… By default, intervals without strand are displayed as rectangle and for intervals with strand an arrow is added at the extremity (not included in the interval). In case of BED12 format, the introns are displayed into another color. But other styles are available.

Parameters

Necessary:

  • file

Optional:

  • title: Put here a title which will apprear on the right.

  • height: 0.5 (default) or float above 0.

  • overlay_previous: no (default) or yes or share-y.

  • fontsize: 12 (default) or any float above 0

  • orientation: by default this option is not set but you can also put: inverted.

  • line_width: 0.5 (default) or any float above 0

  • color: #1f78b4 (default)

  • max_value: by default this option is not set but you can also put: any float

  • min_value: by default this option is not set but you can also put: any float

  • border_color: black (default)

  • prefered_name: transcript_name (default)

  • merge_transcripts: false (default) or true.

  • labels: true (default) or false.

  • style: flybase (default) or UCSC or tssarrow.

  • display: stacked (default) or collapsed, triangles or interleaved.

  • max_labels: 60 (default) or any integer above 0

  • global_max_row: false (default) or true.

  • gene_rows: by default this option is not set but you can also put: any integer above 0

  • arrow_interval: 2 (default) or any integer above 1

  • arrowhead_included: false (default) or true.

  • color_utr: grey (default)

  • height_utr: 1 (default) or any float above 0 below 1

  • arrow_length: by default this option is not set but you can also put: any integer above 0

  • all_labels_inside: false (default) or true.

  • labels_in_margin: false (default) or true.

Output of make_tracks_file:

# title of track (plotted on the right side)
title =
# height of track in cm (ignored if the track is overlay on top the previous track)
height = 2
# if you want to plot the track upside-down:
# orientation = inverted
# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
# Otherwise, each plot use its own scale
#overlay_previous = yes

# If the bed file contains the exon
# structure (bed 12) then this is plotted. Otherwise
# a region **with direction** is plotted.
# If the bed file contains a column for color (column 9), then this color can be used by
# setting:
#color = bed_rgb
# if color is a valid colormap name (like RbBlGn), then the score (column 5) is mapped
# to the colormap.
# In this case, the the min_value and max_value for the score can be provided, otherwise
# the maximum score and minimum score found are used.
#color = RdYlBu
#min_value=0
#max_value=100
# If the color is simply a color name, then this color is used and the score is not considered.
color = darkblue
# whether printing the labels
labels = false
# optional:
# by default the labels are not printed if you have more than 60 features.
# to change it, just increase the value:
#max_labels = 60
# optional: font size can be given to override the default size
fontsize = 10
# optional: line_width
#line_width = 0.5
# the display parameter defines how the bed file is plotted.
# Default is 'stacked' where regions are plotted on different lines so
# we can see all regions and all labels.
# The other options are ['collapsed', 'interleaved', 'triangles']
# These options assume that the regions do not overlap.
# `collapsed`: The bed regions are plotted one after the other in one line.
# `interleaved`: The bed regions are plotted in two lines, first up, then down, then up etc.
# optional, default is black. To remove the border, simply set 'border_color' to none
# Not used in tssarrow style
#border_color = black
# style to plot the genes when the display is not triangles
#style = UCSC
#style = flybase
#style = tssarrow
# maximum number of gene rows to be plotted. This
# field is useful to limit large number of close genes
# to be printed over many rows. When several images want
# to be combined this must be set to get equal size
# otherwise, on each image the height of each gene changes
#gene_rows = 10
# by default the ymax is the number of
# rows occupied by the genes in the region plotted. However,
# by setting this option, the global maximum is used instead.
# This is useful to combine images that are all consistent and
# have the same number of rows.
#global_max_row = true
# If you want to plot all labels inside the plotting region:
#all_labels_inside = true
# If you want to display the name of the gene which goes over the plotted
# region in the right margin put:
#labels_in_margin = true
# if you use UCSC style, you can set the relative distance between 2 arrows on introns
# default is 2
#arrow_interval = 2
# if you use tssarrow style, you can choose the length of the arrow in bp
# (default is 4% of the plotted region)
#arrow_length = 5000
# if you use flybase or tssarrow style, you can choose the color of non-coding intervals:
#color_utr = grey
# as well as the proportion between their height and the one of coding
# (by default they are the same height):
#height_utr = 1
# By default, for oriented intervals in flybase style,
# or bed files with less than 12 columns, the arrowhead is added
# outside of the interval.
# If you want that the tip of the arrow correspond to
# the extremity of the interval use:
# arrowhead_included = true
# optional. If not given is guessed from the file ending.
file_type = bed