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metacoder 0.2.0
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@zachary-foster zachary-foster released this 08 Jan 19:19
· 170 commits to master since this release
0.2.0
5b917d1

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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