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 |
|||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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