Possible parameters

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.

parameter	x-axis	epilogos	links	domains	bed	narrow_peak	bigwig	bedgraph	bedgraph_matrix	hlines	hic_matrix	scalebar
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
links_type			arcs
line_width			not set	0.5	0.5	1				0.5		0.5
line_style			solid							solid
color			blue	#1f78b4	#1f78b4	#FF000080	#33a02c	#a6cee3		black		black
alpha			0.8				1	1		1		1
max_value			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
ylim			not set
compact_arcs_level			0
border_color				black	black
prefered_name				transcript_name	transcript_name
merge_transcripts				false	false
labels					true
style					flybase
display					stacked
max_labels					60
global_max_row					false
gene_rows					not set
arrow_interval					2
arrowhead_included					false
color_utr					grey
height_utr					1
arrow_length					not set
all_labels_inside					false
labels_in_margin					false
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
use_middle								false
rasterize								false	true		true
pos_score_in_bin									center
plot_horizontal_lines									false
colormap									viridis		RdYlBu_r
region											not set
depth											100000
show_masked_bins											false
scale_factor											1
transform											no
x_center												not set
size												not set
height												0.5

Some parameters can take only discrete values.

They are summarized here:

• where:

  • for x-axis: top, bottom

  • for scalebar: left, right, top, bottom

• orientation:

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

• links_type:

  • for links: arcs, triangles, loops

• line_style:

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

• compact_arcs_level:

  • for links: 0, 1, 2

• merge_transcripts:

  • for domains, bed: true, false

• style:

  • for bed: flybase, UCSC, tssarrow

• display:

  • for bed: collapsed, triangles, interleaved, stacked

• labels:

  • for bed: true, false

• global_max_row:

  • for bed: true, false

• arrowhead_included:

  • for bed: true, false

• all_labels_inside:

  • for bed: true, false

• labels_in_margin:

  • for bed: 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

• nans_to_zeros:

  • for bigwig, bedgraph: true, false

• use_middle:

  • for bedgraph: true, false

• rasterize:

  • for bedgraph, bedgraph_matrix, hic_matrix: true, false

• pos_score_in_bin:

  • for bedgraph_matrix: center, block

• plot_horizontal_lines:

  • for bedgraph_matrix: true, false

• transform:

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

• show_masked_bins:

  • for hic_matrix: true, false