Built in visualization for taxonomy counts

[khillion]

Description

Description of the Pull Request content. Especially give details for what changed since the description done in the related issue.

Changelogs

• Filter taxonomy counts on mean among sample (moonstone.filtering.TaxonomyMeanFiltering)
• moonstone.plot.graphs.bargraph.MatrixBarGraph : Visualization of matrix with stacked bar charts
• moonstone.plot.counts.PlotTaxonomyCounts : Visualization of taxonomy counts abdundances with bar charts

  plotter = PlotTaxonomyCounts(taxonomy_df)
  plotter.plot_most_abundant_taxa()
  plotter.plot_sample_composition_most_abundant_taxa()

• PLOT_CLASS class attribute in parsers: allows to perform visualization for data using .plotter property:

  parser = YourParser(file_path)
  parser.plotter.make_awesome_plot()

• Quick visualization of top taxa (total sum among samples). Example of use:

  parser = Metaphlan3Parser(metaphlan_file_path)
  parser.plotter.plot_most_abundant_taxa()

Issue(s)

Fixes #71

Definition of Done

• [x] New code is tested with unit tests
• [x] Documentation has been updated
• [ ] Pull Request has been revised by a maintainer of the project

[codecov-commenter]

Codecov Report

Merging #72 (bbb818e) into master (fddf1f3) will increase coverage by 0.21%. The diff coverage is 73.09%.

@@            Coverage Diff             @@
##           master      #72      +/-   ##
==========================================
+ Coverage   57.78%   57.99%   +0.21%     
==========================================
  Files          59       60       +1     
  Lines        2307     2419     +112     
==========================================
+ Hits         1333     1403      +70     
- Misses        974     1016      +42     

Flag	Coverage Δ
unittests	57.99% <73.09%> (+0.21%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
moonstone/normalization/reads/downsize_dir.py	0.00% <0.00%> (ø)
moonstone/plot/graphs/bargraph.py	63.63% <45.00%> (-30.81%)	:arrow_down:
moonstone/plot/counts.py	63.23% <56.14%> (-20.98%)	:arrow_down:
moonstone/parsers/base.py	77.77% <57.14%> (-22.23%)	:arrow_down:
moonstone/filtering/taxonomy_filtering.py	94.11% <86.66%> (-5.89%)	:arrow_down:
moonstone/utils/colors.py	94.44% <94.44%> (ø)
moonstone/parsers/counts/taxonomy/base.py	100.00% <100.00%> (ø)
moonstone/parsers/counts/taxonomy/kraken2.py	100.00% <100.00%> (ø)
moonstone/parsers/counts/taxonomy/metaphlan.py	100.00% <100.00%> (ø)
moonstone/parsers/counts/taxonomy/qiime.py	100.00% <100.00%> (ø)
... and 5 more

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