Change Log

Fixed

• Fixed chord links calc bug in Matrix.parse_fromto_table() method (#75)

Change Log

Changed

• Dropped python3.8 support
• Switched package manager poetry to rye

Fixed

• Fixed to ignore features that have no location
• Fixed get_seqid2seq() method incorrect return type

Change Log

Improvement

• Added clear_savefig class variable to enable rendering figure in notebook even when savefig() method is called
• Added is_pseudo_feature() utils function
• Fixed to enable changing text properties of colorbar (#71)

Change Log

Improvement

• Changed Circos init argument sectors to enable set range tuple
• Removed Circos init argument sector2start_pos
• Added vmin argument to Circos.radar_chart() method

Bug Fix

• Fixed sector range error bug due to rounding error (#67, #27)

Change Log

New Functionality

• Added Circos.radar_chart() static method for radar chart plot

Improvement

• Fixed to enable set figsize of matplotlib figure
• Added Circos.chord_diagram() method as an alias for Circos.initialize_from_matrix()
• Refactored Genbank and Gff genomic parser class (min_range, max_range is no longer used)

Change Log

New Functionality

• Added show_confidence() method to TreeViz class (#48)

Improvement

• Fixed too many points in vector curves to reduce SVG file size (#56)

Bug Fix

• Fixed Matrix.parse_fromto_table() to ignore 0 values and not throw an ZeroDivisionError (#49)

Change Log

New Functionality

• Added circos.link_line() method (#45)

Bug Fix

• Fixed error caused by removal of strand property in SeqFeature (BioPython v1.82)

Change Log

Improvement

• Added label_formatter argument to Circos.initialize_from_tree() & track.tree() methods
• Fixed track.genomic_features() method to accept SeqFeature (not only list[SeqFeature])
• Fixed example tree file to shorten long species names

Bug Fix

• Fixed calculation error of GC contents and GC skew for short sequence in Genbank class (#43)

Change Log

New Functionality

• Reimplemented track.tree() method to enhance tree annotation functionality (Breaking Change)
• Added TreeViz class for handling tree property & annotation
• Added Circos.initialize_from_tree() staticmethod to more easily plot phylogenetic tree
• Added load_example_tree_file() function

Improvement

• Changed Circos init argument sectors_start_pos to sector2start_pos (Breaking Change)
• Added hs1 & mm39 dataset in load_eukaryote_example_dataset() function
• Added show_endlabel argument to track.xticks_by_interval() method
• Added width argument to track.heatmap() method
• Added center & r_center properties to Track class
• Added center property to Sector class
• Added warning message when adding a track with r > 100
• Fixed track.heatmap() method to accept numerical list and numpy 1d-array
• Fixed circos.savefig() method to suppress memory leak during multiple plots
• Refined the documentation site overall

Change Log

Bug Fix

• Fixed a bug that gff.get_seqid2size() got incorrect multi-contig size (#33)

v0.5.0...v0.5.1