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