gtf

Description

A track for gtf files.

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)

  • 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

  • merge_overlapping_exons: false (default) or true.

  • 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.

  • arrowhead_fraction: 0.004 (default) or any float above 0

  • color_utr: grey (default)

  • color_backbone: black (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.

  • fontstyle: normal (default) or italic or oblique.

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

# By default the transcript_name is used.
# If you want to use the gene_name:
prefered_name = gene_name
# By default, the gtf is transformed to transcripts
# If you want to use see only one structure per gene
# merge_transcripts = true
# Sometimes merging transcripts without merging overlapping
# exons may give unexpected output especially when
# multiple 3' exons overlap. We recommand to use:
# merge_overlapping_exons = true
# You can change the color of coding sequences by:
color = darkblue
# height of track in cm
height = 5
# 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 gtf 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 gtf regions are plotted one after the other in one line.
# `interleaved`: The gtf 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 want to use italic for your labels:
#fontstyle = italic
# 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
# if you use flybase or UCSC style, you can choose the color of the backbone
#color_backbone = red
# 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
# By default the size of this arrow is 0.4% of the plotted region.
# This size is also used to put space between the bed regions and
# their labels.
# To increase it:
#arrowhead_fraction = 0.01
# optional. If not given is guessed from the file ending.
file_type = gtf