Changelogs

Summary of developments of moonstone library.

v0.7

v0.7.0

• https://github.com/motleystate/moonstone/pull/78

• Phylogenetic Diversity (https://github.com/motleystate/moonstone/pull/81): * new argument force_computation allows to force diversity computation even when species are missing in the Tree * only accepting trees in skbio.TreeNode

• PlotTaxonomyCounts (https://github.com/motleystate/moonstone/pull/83): * new arguments: color_df and sep_series/sep_how added to plot_sample_composition_most_abundant_taxa * new plot_most_abundant_taxa method and renaming of the old one to plot_most_prevalant_taxa * mode argument for plot_most_abundant_taxa() and plot_most_prevalent_taxa() to plot the data as a boxplot or a violin plot, as well as a bargraph (https://github.com/motleystate/moonstone/pull/89)

• plot_complex_graph in the MatrixBarGraph class to display some metadata below the main graph (https://github.com/motleystate/moonstone/pull/83)

• 2 new arguments, group_col2 and groups2, for the analyse_groups method from the DiversityBase class and its descendants (https://github.com/motleystate/moonstone/pull/86)

• orientation argument for the plot_one_graph method of the GroupBaseGraph class and its descendants (https://github.com/motleystate/moonstone/pull/86)

v0.6

v0.6.0

• https://github.com/motleystate/moonstone/pull/66

• https://github.com/motleystate/moonstone/pull/69

• Build in visualization for taxonomy counts https://github.com/motleystate/moonstone/pull/72

• Faith’s PD and UniFrac https://github.com/motleystate/moonstone/pull/75

v0.5

v0.5.0

• Visualize metadata cat (https://github.com/motleystate/moonstone/pull/62)

• parser for metaphlan3 (https://github.com/motleystate/moonstone/pull/60)

• pvalue correction in analyse groups (https://github.com/motleystate/moonstone/pull/57)

• add HeatmapGraph (https://github.com/motleystate/moonstone/pull/56)

• Statistical tests for group comparison (https://github.com/motleystate/moonstone/pull/53)

• Mann - Whitney u test in alpha diversity (https://github.com/motleystate/moonstone/pull/50)

• Feature box plot alpha diversity (https://github.com/motleystate/moonstone/pull/46)

• More filtering methods : classes NaNPercentageFiltering and NumberOfDifferentValuesFiltering (https://github.com/motleystate/moonstone/pull/44)

v0.4

v0.4.0

• new features for AlphaDiversity class (https://github.com/motleystate/moonstone/pull/42):

  • visualize method now has two mode: histogram or violin

  • visualize_groups method allows visualization with violin plot based on metadata grouped by a chosen column

• There is now definition of index_col for MetadataParser to define which column to use as the index for the metadata (https://github.com/motleystate/moonstone/pull/42)

• class ``GenesToTaxonomy``to go from gene counts to taxonomy df (https://github.com/motleystate/moonstone/pull/36)

• add TaxonomyRandomSelection to allow random selection on multiindexed dataframe (https://github.com/motleystate/moonstone/pull/32)

• Classe AlphaDiversity and child classes ShannonIndex and SimpsonInverseIndex (https://github.com/motleystate/moonstone/pull/29)

• add RandomSelection to normalization module (https://github.com/motleystate/moonstone/pull/28)

v0.3

v0.3.0

• Refactor use of plotting_options : iteration through dict.keys() + exported in BaseGraph (Parent Class)

• plotting_options, output_file and show dealt with in plot_one_graph (instead of at instantiation)

• Refactoring of BarGraph

• Relocation of functions : check_list_of and add_x_to_plotting_options in utils/plot.py

• Relocation of method to bin series in utils/pandas/series.py

• Transition to autosummary in available classes

• Listing of plot classes in available classes

v0.2

v0.2.0

• Add base for each module (with visualize() method and data_report property)

• Use the new base for MeanFiltering module.

• Refactoring of Filtering class into several classes:

  • NoCountsFiltering that filters on rows or columns with no counts at all

  • NamesFiltering that filters on a given list of row or columns names

    • Either keep the names

    • Or exclude them

  • TaxonomyNamesFiltering that filters on a given list of index names at a chosen level

    • Either keep the names

    • Or exclude them

• Add base module for plots

• Add class BaseGraph and child classes Histogram and BarGraph

v0.1

v0.1.0

• First release of the work done on moonstone.

• Contains command line moonstone to run built-in analysis. See moonstone --help for more information.

• Starting modules to build your own analysis:

  • Parsers

    • Metadata

    • Counts

      • Qiime2

      • Kraken2

      • Picrust2

      • Metaphlan2

  • Normalization

    • GeometricMean

    • TotalCounts

    • StandardScalar

  • Filtering