3.7¶
Enhancements:¶
This release is full of new tracks and new parameters for existing tracks:
Brand new tracks:
fasta
: to display sequences with colored letters from a fasta file (Thanks @GDelevoye for his contribution).maf
(multiple alignment format): to display conservation between species.hic_matrix_square
: to display Hi-C matrices not in ‘triangle’ shape but in ‘square’ shape. This allow to display identical regions but also interactions between 2 different regions. This render plots close to hicPlotMatrix.
New parameters for existing tracks:
Related to
hic_matrix_square
: we implemented a newdisplay
mode forbed
andlinks_type
forlinks
:squares
. This allow to overlay TADs or loops on these Hi-C maps.For
bed
andgtf
:the
fontstyle
can be set toitalic
oroblique
.the
arrowhead_fraction
which controls the size of the arrowhead in the flybase style can be adjusted.the color of the backbone when you use flybase or UCSC style can be changed with
color_backbone
.
For
gtf
a new parametermerge_overlapping_exons = true
help to get a better display when all transcripts are merged.For
bedgraph_matrix
: whentype = lines
is set the colors of individual lines can be set byindividual_color
and the summary line bysummary_color
Minor enhancements:¶
pyGenomeTracks display better error message when rtf files are used.
the help message for BED has been improved to highlight the fact that the extension needs to be part of the output.
if the directory of the output file does not exists, it is created.
Drop support for python 3.6¶
The introduction of the new track for Maf forced us to drop support for python 3.6.
Relax version control on matplotlib:¶
Any version of matplotlib from 3.1.1 to 3.5.1 is now accepted.
Bugfixes:¶
The tick values for the x-axis are now accurate (see #333) and more informative.
The y values for tracks like bigwig are not restricted to one decimal. If needed, the scientific notation can be used.
pyGenomeTracks now allows to plot above chromosome size defined in bigwig or Hi-C matrices without raising an error.
pyGenomeTracks now works with gtf without exons.
pyGenomeTracks now closes figures after saving.
The plotting part does not modify the tracks anymore. This solves #393