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 new display mode for bed and links_type for links: squares.
    This allow to overlay TADs or loops on these Hi-C maps.

  • For bed and gtf:

    • the fontstyle can be set to italic or oblique.

    • 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 parameter merge_overlapping_exons = true help to get a better display when all transcripts are merged.

  • For bedgraph_matrix: when type = lines is set the colors of individual lines can be set by individual_color and the summary line by summary_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.