pycirclize - v1.9.1

Fixed

• Set epsilon to avoid unexpected exception in min-max range checks (#90)

- Python
Published by moshi4 about 1 year ago

pycirclize - v1.9.0

Added

• Added track.annotate() method

Changed

• Changed Circos.clear_savefig to pycirclize.config.clear_savefig

- Python
Published by moshi4 over 1 year ago

pycirclize - v1.8.0

Added

• Added track.raster() method

Fixed

• Set clip_on=False to enable Patch to be displayed outside of Axes (#80)
• Fixed unexpected ValueError due to rounding error

- Python
Published by moshi4 over 1 year ago

pycirclize - v1.7.2

Added

• Added recipe docs for comparative genomics

Fixed

• Set encoding="utf-8" explicitly to avoid Windows default encoding issue

- Python
Published by moshi4 over 1 year ago

pycirclize - v1.7.1

Change Log

Fixed

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

- Python
Published by moshi4 over 1 year ago

pycirclize - v1.7.0

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

- Python
Published by moshi4 over 1 year ago

pycirclize - v1.6.0

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)

- Python
Published by moshi4 about 2 years ago

pycirclize - v1.5.0

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)

- Python
Published by moshi4 about 2 years ago

pycirclize - v1.4.0

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)

- Python
Published by moshi4 about 2 years ago

pycirclize - v1.3.0

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)

- Python
Published by moshi4 over 2 years ago

pycirclize - v1.2.0

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)

- Python
Published by moshi4 over 2 years ago

pycirclize - v1.1.0

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)

- Python
Published by moshi4 over 2 years ago

pycirclize - v1.0.0

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 sectorsstartpos 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

- Python
Published by moshi4 over 2 years ago

pycirclize - v0.5.1

Change Log

Bug Fix

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

https://github.com/moshi4/pyCirclize/compare/v0.5.0...v0.5.1

- Python
Published by moshi4 almost 3 years ago

pycirclize - v0.5.0

Change Log

New Functionality

• Added track.stacked_bar() method for plotting vertical stacked bar
• Added track.stacked_barh() method for plotting horizontal stacked bar

Improvement

• Added exception handling for too large circos space
• Added dataframe property to Matrix class

Bug Fix

• Fixed to accept genbank TextIOWrapper object

https://github.com/moshi4/pyCirclize/compare/v0.4.0...v0.5.0

- Python
Published by moshi4 almost 3 years ago

pycirclize - v0.4.0

Change Log

New Functionality

• Added sector2clockwise option to enable plotting sector with anti-clockwise direction

Improvement

• Refactored GFF parsing logic to improve processing speed
• Replaced linter flake8 to ruff

https://github.com/moshi4/pyCirclize/compare/v0.3.1...v0.4.0

- Python
Published by moshi4 about 3 years ago

pycirclize - v0.3.1

Change Log

Improvement

• Added some methods to Genbank/Gff parser class for plotting genomic features in each contig/scaffold
• Added arc option to xxx.line() method to enable selecting arc or linear style
• Added mycoplasma_alvi.[gbk|gff] example to load_prokaryote_example_file() function

Bug Fix

• Fixed GCskew, GCcontent calculation error when biopython<=1.79 is installed

https://github.com/moshi4/pyCirclize/compare/v0.3.0...v0.3.1

- Python
Published by moshi4 about 3 years ago

pycirclize - v0.3.0

Change Log

New Functionality

• Added circos.colorbar() method
• Added track.grid() method

Improvement

• Added circos.ax property

Bug Fix

• Fixed track.line() bug when plotting minus direction

https://github.com/moshi4/pyCirclize/compare/v0.2.1...v0.3.0

- Python
Published by moshi4 about 3 years ago

pycirclize - v0.2.1

Change Log

Improvement

• Added link_kws_handler option to Circos.initialize_from_matrix()

https://github.com/moshi4/pyCirclize/compare/v0.2.0...v0.2.1

- Python
Published by moshi4 about 3 years ago

pycirclize - v0.2.0

Change Log

New Functionality

• Added sector.raster() method for plotting raster image
• Added utils.calc_group_spaces() function for easily grouping sector display
• Added circos.get_group_sectors_deg_lim() method for easily grouping sector display

Improvement

• Added ax option to circos.plotfig() method for plotting to user-defined matplotlib Axes
• Added order option to circos.initialize_from_matrix() method for plotting Chord Diagram
• Added adjust_rotation option to circos.text() method

https://github.com/moshi4/pyCirclize/compare/v0.1.3...v0.2.0

- Python
Published by moshi4 over 3 years ago

pycirclize - v0.1.3

Change Log

Minor Change

• Added side arg param to track.yticks() method

https://github.com/moshi4/pyCirclize/compare/v0.1.2...v0.1.3

- Python
Published by moshi4 over 3 years ago

pycirclize - v0.1.2

Change Log

Minor Change

• Added Circos.initialize_from_matrix() static method to plot Chord Diagram more easily
• Removed upper bound version constraint in dependencies

https://github.com/moshi4/pyCirclize/compare/v0.1.1...v0.1.2

- Python
Published by moshi4 over 3 years ago

pycirclize - v0.1.1

Change Log

Minor Change

• Added parse_fromto_table static method to Matrix parser class
• Fixed to not display Chord Diagram link if the matrix value is less than or equal to 0
• Fixed to not display the decimal point when the xticks interval value type is int

https://github.com/moshi4/pyCirclize/compare/v0.1.0...v0.1.1

- Python
Published by moshi4 over 3 years ago

pycirclize - v0.1.0

First Official Release

pyCirclize is a circular visualization python package implemented based on matplotlib.

- Python
Published by moshi4 over 3 years ago