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
.
- the
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
- 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.
- The introduction of the new track for Maf forced us to drop support for python 3.6.
- Any version of matplotlib from 3.1.1 to 3.5.1 is now accepted.
- 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