Possible parametersΒΆ

Here is a table to summarize which are the parameters that can be use for each of the file_type and which is the default value: Empty means this parameter is not used. not set means that by default the parameter is commented. This table is available as csv here.

parameter

x_axis

epilogos

links

domains

bed

gtf

narrow_peak

bigwig

bedgraph

bedgraph_matrix

hlines

hic_matrix

hic_matrix_square

maf

scalebar

vlines

vhighlight

overlay_previous

no

no

no

no

no

no

no

no

no

no

no

no

no

no

no

where

bottom

left

fontsize

15

12

12

12

categories_file

not set

orientation

not set

not set

not set

not set

not set

not set

not set

not set

not set

not set

not set

not set

not set

links_type

arcs

line_width

not set

0.5

0.5

0.5

1

0.5

0.5

0.5

0.5

0.5

line_style

solid

solid

dashed

color

blue

#1f78b4

#1f78b4

#1f78b4

#FF000080

#33a02c

#a6cee3

black

black

black

yellow

alpha

0.8

1

1

1

1

0.7

0.5

max_value

not set

not set

not set

not set

not set

not set

not set

not set

not set

not set

min_value

not set

not set

not set

not set

not set

not set

not set

not set

not set

ylim

not set

compact_arcs_level

0

use_middle

false

false

region2

not set

not set

border_color

black

black

black

none

prefered_name

transcript_name

transcript_name

transcript_name

merge_transcripts

false

false

false

labels

true

true

style

flybase

flybase

display

stacked

stacked

max_labels

60

60

merge_overlapping_exons

false

false

global_max_row

false

false

gene_rows

not set

not set

arrow_interval

2

2

arrowhead_included

false

false

arrowhead_fraction

0.004

0.004

color_utr

grey

grey

color_backbone

black

black

height_utr

1

1

arrow_length

not set

not set

all_labels_inside

false

false

labels_in_margin

false

false

fontstyle

normal

normal

show_data_range

true

true

true

true

true

show_labels

true

use_summit

true

width_adjust

1.5

type

peak

fill

fill

matrix

negative_color

not set

not set

nans_to_zeros

false

false

summary_method

mean

not set

number_of_bins

700

700

transform

no

no

no

no

log_pseudocount

0

0

y_axis_values

transformed

transformed

second_file*

not set

not set

operation*

file

file

grid

false

false

rasterize

false

true

true

true

pos_score_in_bin

center

plot_horizontal_lines

false

colormap

viridis

RdYlBu_r

RdYlBu_r

individual_color

grey

summary_color

#1f77b4

depth

100000

show_masked_bins

false

false

scale_factor

1

1

file_index

not set

color_identical

black

color_mismatch

grey

color_gap

lightgrey

species_order

not set

species_labels

not set

species_order_only

false

display_ref_seq

false

x_center

not set

size

not set

scalebar_start_position

not set

scalebar_end_position

not set

zorder

10

-100

* While pyGenomeTracks can convert coverage tracks on the fly, this might be a time-consuming step, especially on large files and if you want to replot many times. In this situation, we recommend using the deepTools suite to convert your files in advance. For example bamCoverage or bamCompare

Some parameters can take only discrete values.

They are summarized here:

  • overlay_previous:

    • for x_axis, epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, hic_matrix_square, maf, scalebar, fasta, spacer: no, yes, share-y

  • where:

    • for x_axis: top, bottom

    • for scalebar: left, right, top, bottom

  • orientation:

    • for epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, hic_matrix_square, maf: inverted, not set

  • links_type:

    • for links: arcs, triangles, loops, squares

  • line_style:

    • for links, hlines, vlines: solid, dashed, dotted, dashdot

  • compact_arcs_level:

    • for links: 0, 1, 2

  • use_middle:

    • for links, bedgraph: true, false

  • merge_transcripts:

    • for domains, bed, gtf: true, false

  • style:

    • for bed, gtf: flybase, UCSC, tssarrow

  • display:

    • for bed: collapsed, triangles, interleaved, stacked, squares

    • for gtf: collapsed, triangles, interleaved, stacked

  • fontstyle:

    • for bed, gtf: normal, italic, oblique

  • labels:

    • for bed, gtf: true, false

  • global_max_row:

    • for bed, gtf: true, false

  • arrowhead_included:

    • for bed, gtf: true, false

  • all_labels_inside:

    • for bed, gtf: true, false

  • labels_in_margin:

    • for bed, gtf: true, false

  • merge_overlapping_exons:

    • for bed, gtf: true, false

  • type:

    • for narrow_peak: peak, box

    • for bedgraph_matrix: matrix, lines

  • show_data_range:

    • for narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines: true, false

  • show_labels:

    • for narrow_peak: true, false

  • use_summit:

    • for narrow_peak: true, false

  • summary_method:

    • for bigwig: mean, average, max, min, stdev, dev, coverage, cov, sum

    • for bedgraph: mean, average, max, min, stdev, dev, coverage, cov, sum, not set

  • transform:

    • for bigwig, bedgraph: no, log, log1p, -log, log2, log10

    • for hic_matrix, hic_matrix_square: no, log, log1p, -log

  • y_axis_values:

    • for bigwig, bedgraph: original, transformed

  • nans_to_zeros:

    • for bigwig, bedgraph: true, false

  • grid:

    • for bigwig, bedgraph: true, false

  • rasterize:

    • for bedgraph, bedgraph_matrix, hic_matrix, hic_matrix_square: true, false

  • pos_score_in_bin:

    • for bedgraph_matrix: center, block

  • plot_horizontal_lines:

    • for bedgraph_matrix: true, false

  • show_masked_bins:

    • for hic_matrix, hic_matrix_square: true, false

  • species_order_only:

    • for maf: true, false

  • display_ref_seq:

    • for maf: true, false