metacoder 0.2.0

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.