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Created with Raphaël 2.2.016Sep8Nov620Oct191364318Sep1412Dec2May29Apr281412117525Mar24231817151494225Feb219Jan1821JulSave notes.codon_agg_classescodon_agg_classesChange default output of group_codons_by_class.Remove side effect of remove_codons.Fixing groupby axis.Update group_codons_by_class based on groupby.Update version number and copyright.Linting code.Remove unused imports.Remove files in buil directory.Comment asserts since normalization is not really working on skewed distributions nowAdd little docu to new fonctionsAdd functions to group codons by sum given classesDelete libcodonusage.pyDelete __init__.pyPlot more components in PCAplot more components in PCAAdded global R4 computation.mastermasterOptional fillna in exclude_all_nan_cols.Also compute global RSCU.Added computing of R4 (sensu Suzuki et al 2005).Add function to split table with info in index.Fix variable name.Add checks on column formats.Made load_bias_table a wrapper.Added code to compute RSCU.Try to fix detection of clustering diffs.Optional codon influence in PCA.17009_only17009_onlyMore easy to choose fig formats.Option to exclude columns for PCA.Start fixing aa usage violin plots.PCA, filtering by chromosome.More output from bias-calculating functions.Option to return proportions too, not just biases.Mention references.Figure size tweaks, violins by chromosome.Further forward violin plot kwargs.Forward arguments to violin plot.Fix aa and codon order, better long form.Fix violin order. Legend issues.Function to compare clusterings.