v3.1.0

Highlights

• Ag3: Limit docstring widths for better wrapping in colab help tabs
  (GH186).
• Ag3: Return a copy of cached DataFrames to any subsequent user
  modifications do not affect the cached data
  (GH184).
• Ag3: Improving zooming behaviour of bokeh genome plots
  (GH189).
• Ag3: Add sample identifiers to CNV HMM heatmap plots
  (GH191).
• Ag3: Exclude high coverage variance samples by default in CNV HMM
  heatmap plots
  (GH178).
• Ag3: Standardise default width of bokeh genome plots
  (GH174).
• Ag3: Consistently capitalise plot labels
  (GH176).
• Ag3: Tidy title for CNV HMM heatmap plots when using multiple
  sample sets
  (GH175).
• Ag3: Fix a bug in loading of gene CNV frequencies where
  intermediate species samples are missing
  (GH183).

What's Changed

• CNV gene frequency bug fixes by @alimanfoo in #188
• Misc plotting improvements by @alimanfoo in #192
• Return copies of cached dataframes by @alimanfoo in #194
• Narrow docstrings by @alimanfoo in #195
• V3.1.0 prep by @alimanfoo in #199

Full Changelog: v3.0.0...v3.1.0

v3.0.0

Highlights

• Added a new function Ag3.plot_cnv_hmm_coverage() which generates a
  bokeh plot showing normalised coverage and HMM copy number for an
  individual sample.

• Added a new function Ag3.plot_cnv_hmm_heatmap() which generates a
  bokeh plot showing the HMM copy number for multiple samples as a
  heatmap.

• Added support for accessing genome regions to the CNV data access
  functions Ag3.cnv_hmm(), Ag3.gene_cnv(),
  Ag3.gene_cnv_frequencies() and Ag3.cnv_coverage_calls()
  (GH113). Please
  use the region parameter to specify a contig or contig region. The
  previous contig parameter is no longer supported.

• Added support for a region parameter to the Ag3.geneset()
  function.

• Added docstrings for Ag3.plot_genes() and Ag3.plot_transcript()
  (GH170).

• Set plot width and height automatically in
  Ag3.plot_frequencies_heatmap() based on the number of rows and
  columns.

What's Changed

• Ag3 CNV improvements by @alimanfoo in #171

Full Changelog: v2.2.0...v3.0.0

v2.2.0

Highlights

• Added a new function Ag3.plot_genes() which generates a bokeh plot
  of gene annotations
  (GH154).

• Added a new function Ag3.plot_transcript() which generates a bokeh
  plot of a gene model
  (GH155).

• Fixed a bug in the Ag3.gene_cnv_frequencies() function
  (GH166).

• CI improvements
  (GH150).

What's Changed

• Fix CNV frequencies bug by @alimanfoo in #167
• Add gene and transcript plotting functions by @alimanfoo in #168
• v2.2.0 release prep by @alimanfoo in #169

Full Changelog: v2.1.0...v2.2.0

v2.1.0

Highlights

• Ag3: Add support for giving a list of contigs to the contig
  parameter in gene_cnv() and gene_cnv_frequencies()
  (GH162).

• Ag3: Miscellaneous optimisations and documentation fixes
  (GH153,
  GH158,
  GH159,
  GH161).

What's Changed

• Add support for multiple contigs to Ag3 gene_cnv... functions by @alimanfoo in #163
• Misc maintenance 2022-03-07 by @alimanfoo in #164
• v2.1.0 release prep by @alimanfoo in #165

Full Changelog: v2.0.0...v2.1.0

v2.0.0

Highlights

New features and API changes

• Ag3: New functions have been added for space-time analysis of SNP
  allele frequencies and gene CNV frequencies
  (GH143).

  • The new function plot_frequencies_time_series() creates faceted time
    series plots of frequencies using plotly.

  • The new function plot_frequencies_interactive_map() creates an
    ipyleaflet map with coloured markers representing frequencies in
    different cohorts, with widgets to select the variant, taxon and
    time period of interest.

  • The new function plot_frequencies_map_markers() supports plotting
    frequency markers on an existing ipyleaflet map.

  • The new function snp_allele_frequencies_advanced() computes SNP
    allele frequencies in a transcript of interest and returns an
    xarray dataset which can be used as input to space and time
    plotting functions.

  • The new function aa_allele_frequencies_advanced() computes amino
    acid substitution frequencies in a transcript of interest and
    returns an xarray dataset which can be used as input to space and
    time plotting functions.

  • The new function gene_cnv_frequences_advanced() computes gene
    CNV frequencies for a given contig and returns an xarray dataset
    which can be used as input to space and time plotting functions.

  • The function aa_allele_frequencies() has been modified
    to better handle the case where SNPs at different genome positions
    cause the same amino acid change.

• Ag3: The function gene_cnv_frequencies() has been modified so
  that each row now represents a gene and variant (amplification or
  deletion), and columns are cohorts
  (GH139). Also
  a new parameter drop_invariant has been added, which is True by
  default, meaning that only records with some evidence of copy number
  variation in the given cohorts are returned.

• Ag3: Samples with high coverage variance are now removed by
  default when running the gene_cnv_frequencies(), and this can be
  controlled via a new max_coverage_variance parameter
  (GH141). To
  support this, the sample_coverage_variance variable has been added
  to the output of the gene_cnv() function
  (GH128).

• Ag3: All functions accepting a sample_sets parameter now check
  for the same sample set being selected more than once
  (GH144).

• Ag3: The functions which plot frequencies, including
  plot_frequencies_heatmap(), plot_frequencies_time_series(), and
  plot_frequencies_interactive_map(), have been modified to use
  consistent labels for variants
  (GH145).

• Ag3: The frequencies plotting functions now automatically set a
  title based on metadata from the input dataframe or dataset
  (GH146). The
  cohorts axis labels have also been moved to the bottom to make room
  for a title.

• Ag3: All column names in sample metadata dataframes are now lower
  case, and columns starting "adm" have been renamed to start with
  "admin" (e.g., "adm1_ISO" has been renamed to "admin1_iso") to have
  consistent naming of columns and parameter values relating to
  administrative units
  (GH142).

• Ag3: Functions cnv_hmm(), cnv_coverage_calls() and
  cnv_discordant_read_calls() support multiple contigs for the
  contig parameter and automatically concatenate datasets
  (GH90).

Bug fixes, maintenance and documentation

• Ag3: Function docstrings have been improved to document return
  values
  (GH84).

• Ag3: Improve repr methods
  (GH138).

Pull requests

• Add pf7 module by @kathryn1995 in #69
• Update version for pf7 pre-release by @kathryn1995 in #137
• Ag3 functions for space-time analysis of variant frequencies by @alimanfoo in #140
• Improve doc strings by @KellyLBennett in #135
• Fix plot_frequencies_heatmap return value by @alimanfoo in #147
• Support multiple contigs in CNV datasets by @KellyLBennett in #136
• Add sample coverage variance filtering to CNV frequencies methods by @alimanfoo in #148
• Check dup sample sets by @alimanfoo in #149
• Misc aesthetics by @alimanfoo in #151
• v2.0.0 release prep by @alimanfoo in #152

New Contributors

• @KellyLBennett made their first contribution in #135

Full Changelog: v1.0.1...v2.0.0

v1.0.1

What's Changed

• Expose more imshow parameters in plot_frequencies_heatmap by @alimanfoo in #134

Full Changelog: v1.0.0...v1.0.1

v1.0.0

Highlights

New features and API changes

• Ag3: Added support for genome regions when accessing data
  (GH14). N.B.,
  the contig parameter is no longer supported, instead use the
  region parameter which can be a contig ID (e.g., "3L"), a contig
  region (e.g., "3L:1000000-2000000"), a gene ID ("AGAP004070"), or a
  list of any of the above. This affects methods including
  snp_sites(), site_filters(), snp_genotypes() and
  snp_dataset(). Contributed by Nace
  Kranjc.

• Ag3: The parameters for specifying which species analysis version
  is used have changed
  (GH55). This
  affects species_calls(), sample_metadata(),
  snp_allele_frequencies() and gene_cnv_frequencies(). In most
  cases the default values for these parameters should be appropriate
  and so no changes to your code should be needed.

• Ag3: The names of the columns in dataframes containing data
  related to species calling have changed to make it clearer which
  species calling method has been used. This affects dataframes
  returned by species_calls() and sample_metadata(). See
  GH93
  for further details.

• Ag3: The latest cohorts metadata are now automatically loaded and
  joined in with the sample metadata when calling
  sample_metadata(). See
  GH94
  for further details.

• Ag3: SNP effects are now automatically included in the output
  dataframe from snp_allele_frequencies()
  (GH95).

• Ag3: Added a new sample_query parameter to methods returning
  frequencies to allow for making a sub-selection of samples
  (GH96).

• Ag3: Added a new method aa_allele_frequencies() to return a
  dataframe of amino acid substitution allele frequencies
  (GH101).

• Ag3: Added a new method plot_frequencies_heatmap() for creating
  a heatmap plot of allele frequencies
  (GH102).

• Ag3: The Google Cloud Storage URL ("gs://vo_agam_release") is now
  the default value when instantiating the Ag3 class
  (GH103). So
  now you don't need to provide it if you are accessing data from
  GCS. I.e., you can just do:

import malariagen_data
ag3 = malariagen_data.Ag3()

• Ag3: The identifiers used for data releases have been changed to
  use "3.0" instead of "v3", "3.1" instead of "v3.1",
  etc. (GH104)

• The Ag3 and Amin1 classes have a better repr
  (GH111).

• Ag3: All dataframe columns containing allele frequency values are
  now prefixed with "frq_" to allow for easier selection of frequency
  columns
  (GH116).

• Ag3: When computing frequencies, automatically drop columns for
  cohorts below the minimum cohort size
  (GH118).

• Amin1: Added support for region parameter instead of contig
  (GH119).

• Ag3: The snp_sites() method no longer returns a tuple of arrays
  if the field parameter is not provided, please provide an explicit
  field parameter or use the snp_calls() method instead
  (recommended).

Bug fixes, maintenance and documentation

• Ag3: Move default values for analysis parameters to constants
  (GH70).

• Ag3: Check for manifest.tsv when discovering a release
  (GH74).

• Ag3: Decode sample IDs when building snp_calls() dataset
  (GH82).

• Ag3: Fix snp_calls() cannot take multiple releases for
  sample_set parameter
  (GH85).

• Ag3: Fix chunks parameter appears to be ignored
  (GH86).

• Support Python 3.9
  (GH91).

• Ag3: Fix pandas performance warnings
  (GH108).

• Ag3: Fix bug involving inconsistent array lengths before and after
  computation
  (GH114).

• Ag3: Fix compatibility with zarr 2.11.0
  (GH129).

• Some optimisations to speed up the test suite a bit
  (GH122).

Pull requests

• Add variance vars to CNV HMM by @leehart in #83
• Support multiple releases via the sample_sets parameter by @alimanfoo in #88
• Upgrade CI by @alimanfoo in #92
• Improve species metadata by @alimanfoo in #97
• Check release manifest by @alimanfoo in #98
• Decode sample_id to str in Ag3.snp_calls() dataset by @alimanfoo in #99
• Add effects to allele frequencies by @alimanfoo in #100
• Support genomic regions by @nkran in #106
• snp_allele_frequencies() Pandas Warning - fragmented dataframe by @cclarkson in #110
• Add cohorts to sample_metadata() by @cclarkson in #109
• Misc minor improvements by @alimanfoo in #112
• Add "frq_" to columns in frequency generating methods by @cclarkson in #117
• Drop cohorts columns below min cohort size when computing frequencies by @cclarkson in #120
• Fix bug with optimised dask compress by @alimanfoo in #121
• ag3.aa_allele_frequencies() method by @cclarkson in #124
• Add sample_query parameter to allele frequencies by @alimanfoo in #126
• ag3.plot_frequencies_heatmap() by @cclarkson in #125
• Zarr 2.11.0 compatibility by @alimanfoo in #130
• v1.0.0 release notes by @alimanfoo in #131
• Refactor region support and add region support to Amin1 by @alimanfoo in #132

New Contributors

• @leehart made their first contribution in #83
• @nkran made their first contribution in #106

Full Changelog: v0.15.0...v1.0.0

v0.15.0

Updates default cohorts_analysis parameter to latest analysis (20211101).

What's Changed

• Update cohorts_analysis to latest version by @cclarkson in #79
• v0.15.0 release by @cclarkson in #81

Full Changelog: v0.14.1...v0.15.0

v0.14.1

What's Changed

• Fix bug in applying site_mask parameter in Amin1 by @alimanfoo in #77

Full Changelog: v0.14.0...v0.14.1

v0.14.0

Highlights

• Adds the Amin1 class providing access to the Anopheles minimus
  Amin1 SNP data release.

Pull requests

• Amin1 by @alimanfoo in #75

Full Changelog: v0.12.1...v0.14.0