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metacoder 0.2.1

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@zachary-foster zachary-foster released this 04 May 19:17
· 133 commits to master since this release
v0.2.1
e47458a

metacoder 0.2.1

Bug fixes

  • Fixes numerous bugs in heat_tree_matrix that happen when the input data is not exactly like that produced by compare_groups (issues #195, #196, #197).
  • Fixed how output_file was used with heat_tree_matrix. Now whole plot is saved instead of last subplot. (issue #203)
  • Fixed "unused argument" bug in parse_mothur_tax_summary when reading from a file path (issue #211).
  • Fixed bug when in zero_low_counts when using use_total = TRUE (issue #227).
  • Numerous other small fixes.
  • Fixed parse_phyloseq error when arbitrary rank names were used.

Improvements

  • Node and edge legends can now be excluded individually (Thanks @grabear!) (issue #202).
  • The output of heat_tree_matrix always has a 1:1 aspect ratio. (issue #205)
  • Numerous calculation functions added, with more consistent behavior.

metacoder 0.2.0

Bug fixes

  • Fixed bug in subtaxa that caused an error when all of subset is FALSE. (issue #143)
  • Fixed bug in filter_taxa that caused an error when all taxa are filtered out. (issue #144)

Breaking changes

  • All taxmap-related manipulation functions have been moved to the taxa package.
  • heat_tree now uses the taxmap class defined in the taxa package.
  • Numerous changes (i.e. upgrades) to primersearch

Improvements

  • Upgraded primersearch output to be cleaner and have info like the amplicon sequence and primer binding sites.
  • Added functions to identift and remove taxa with ambiguous names like "unknown"
  • code from ggrepel package now used to avoid overlapping labels. Thanks Kamil Slowikowski!
  • New function heat_tree_matrix to make plotting a pairwise matrix of heat trees for comparing treatments.
  • New parser named parse_mothur_tax_summary for mothur *.tax.summary file made by classify.seqs.
  • New parser named parse_mothur_taxonomy for mothur *.taxonomy file made by classify.seqs.
  • New parser named parse_qiime_biom for the QIIME BIOM output.
  • New parser named parse_phyloseq to convert phyloseq objects.
  • New parser named parse_newick to parse newick files.
  • New parser named parse_unite_general for unite general FASTA release. (issue #154)
  • New parser named parse_rdp for RDP FASTA release. (issue #160)
  • New parser named parse_silva_fasta for SILVA FASTA release. (issue #162)
  • New function calc_obs_props to calculate proportions from observation counts (issue #167
  • New parser named parse_greengenes for the Greengenes database. (issue #?)
  • New writer named write_greengenes to create an imitation of the Greengenes database format.
  • New writer named write_rdp to create an imitation of the RDP database format.
  • New writer named write_mothur_taxonomy to create an imitation of the mothur taxonomy format.
  • New writer named write_unite_general to create an imitation of the UNITE general FASTA release.
  • New writer named write_silva_fasta to create an imitation of the SILVA FASTA release.
  • New function named compare_treatments to compare multiple samples in multiple treatments, applying a user-defined function.
  • New function named calc_taxon_abund to sum observation values for each taxon.
  • Added col_names option to calc_taxon_abund to set names of output columns.
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