A double dash on itself "--" signals end of the options and start of file names (if present). You can use
a single dash "-" as STDIN placeholder. Available options and a short description are listed here:
-h,--help
Show summary of options.
--version
Shows current version and exits.
-v,--verbose
Verbose mode, a full report is sent to standard error (default is set to showing only WARNINGS).
-V,--logs-filename<filename>
Report is written to a log file.
-q,--quiet
Quiet mode, do not show any message/warning to standard error (reporting only ERRORS).
-p,--page-size<format_name>
Setting a page size among pre-defined ones see below for a list of available page formats).
--margin-left<length>--margin-right<length>--margin-top<length>--margin-bottom<length>
Setting each page margin to <length>. If no units are provided, points are assumed, you can use
points, milimeters, centimeters or inches (pt, mm, cm or in, respectively).
-B,--background-color<color>
Background color.
-F,--foreground-color<color>
Foreground color.
-T,--title<string>
Definning plot title.
-t,--subtitle<string>
Definning plot subtitle.
-X,--x-label<string>
Defining X-axis label.
-Y,--y-label<Y-Label>
Defining Y-axis label.
-L,--percent-box-label<string>
Defining percent-box label.
-l,--extra-box-label<XBox-Label>
Definning Extra-Box Label.
-x,--x-sequence-coords<pos..pos>-S,--start-x-sequence<pos>
Sets X-sequence first nucleotide.
-E,--end-x-sequence<pos>
Sets X-sequence last nucleotide.
-y,---y-sequence-coords<pos..pos>-s,--start-y-sequence<pos>
Sets Y-sequence first nucleotide.
-e,--end-y-sequence<pos>
Sets Y-sequence last nucleotide.
--x-sequence-zoom<pos..pos>--y-sequence-zoom<pos..pos>-Z,--zoom[[-S<pos>][-E<pos>][-s<pos>][-e<pos>]]
This option zooms an area you have selected with -S,-E,-s,-e (all 4 are optional).
-z,--zoom-area[[-S<pos>][-E<pos>][-s<pos>][-e<pos>]]
This option marks a zoom area on your plot, but does not make a zoom.
-A,--alignment-name<SeqXName:SeqYName>
Defining which alignment is going to be plotted if you have more than one alignment in your gff
input.
-N,--x-sequence-name<SeqXName>
Defining which sequence is going to be plotted at X-axis.
-n,--y-sequence-name<SeqYName>
Defining which sequence is going to be plotted at Y-axis.
-r,--aplot-xy-noteq
By default X and Y axes have same length, this option disables such behaviour, so X and Y sequence
will have axes-lengths proportional to their nucleotide lengths.
-R,--xy-axes-scale<X/Yratio>
This option allows one to set a different scale between X and Y axes lengths (by default is '1').
Below 1 values make Y larger than X, and larger than 1 result in getting X larger than Y. # Must
be explained better.
-W,--aln-scale-width
Scaling score on width for Aplot lines.
-w,--aln-scale-color
Scaling score on color for Aplot lines.
-K,--show-ribbons<ribbon_type>
Force Ribbons for all features on axes to be: (N)one, (L)ines, (R)ibbons, (B)oth.
-G,--show-grid
Switches 'on' grid (default is 'off').
-g,--hide-grid
Switches 'off' grid (if switched on from customization files).
-I,--show-percent-box
Switches 'on' Percent box (default is 'off').
-i,--hide-percent-box
Switches 'off' Percent box (if set to 'on' on custom files).
-O,--show-extra-box
Switches 'on' Extra box (default is 'off').
-o,--hide-extra-box
Switches 'off' Extra box (if set to 'on' on custom files).
-D,--aplot-box-color<color>
Aplot main box background color.
-d,--percent-box-color<color>
Percent box background color.
-b,--extra-box-color<color>
Extra box background color.
--nopswarnings
Switch off warnings that may appear on the final PostScript figure when X sequence, Y sequence
and/or alignment input data is missing.
-a,--hide-credits
Switch off gff2aplot credits line on plot.
--debug
Reporting variable contents when testing the program. Requires that log report file option was
also activated.
--layout-var'<variable=value>'--sequence-var'<sequence::variable=value>'--source-var'<source::variable=value>'--strand-var'<strand::variable=value>'--group-var'<group::variable=value>'--feature-var'<feature::variable=value>'
Loading a feature/group/strand/source/sequence/layout customization variable from command-line.
You can set several variables by repeating any of these options, i.e.:
... --feature-var 'cds::feature_shape=box'
--feature-var 'cds::feature_color=blue' ...
-C,--custom-filename<filename>
Loading customization parameters from a given file (if default ".gff2aplotrc" exists is loaded
before it).
Those are the colors defined in gff2aplot:
+ Default Colors: black white.
+ Color Palette:
grey pink magenta violet blue skyblue cyan seagreen
green limegreen yellow orange red brown
You can get up to nine color shades from Variable Colors with "verydeep", "deep", "verydark",
"dark", "light", "verylight", "pale" and "verypale" prefixes, as example:
verydeepblue, deepblue, verydarkblue, darkblue, blue, lightblue, verylightblue, paleblue and
verypaleblue.
+ Dynamic colors: gradient rainbow.
The following page sizes are available: from A0 to A10, from B0 to B10, 10x14, executive, folio,
ledger, legal, letter, quarto, statement and tabloid.
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