News

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.

metacoder 0.1.3

Improvements

• Provided helpful error message when the evaluation nested too deeply: infinite recursion / options(expressions=)? occurs due to too many labels being printed.
• heat_tree: improved how the predicted bondries of text is calcuated, so text with any rotation, justification, or newlines influences margins correctly (i.e. does not get cut off).
• heat_tree: Can now save multiple file outputs in different formats at once

Minor changes

• heat_tree now gives a warning if infinite values are given to it
• extract_taxonomy: There is now a warning message if class regex does not match (issue #123)
• heat_tree: Increased lengend text size and reduced number of labels
• extract_taxonomy: added batch_size option to help deal with invalid IDs better
• Added CITATION file

Breaking changes

• The heat_tree option margin_size funcion now takes four values instead of 2.

Bug fixes

• heat_tree: Fixed bug when color is set explicitly (e.g. “grey”) instead of raw numbers and the legend is not removed. Now a mixure of raw numbers and color names can be used.
• Fixed bugs caused by dplyr version update
• Fixed bug in heat_tree that made values not in the input taxmap object not associate with the right taxa. See this post.
• extract_taxonomy: Fixed an error that occured when not all inputs could be classified and sequences were supplied
• Fixed bug in primersearch that cased the wrong primer sequence to be returned when primers match in the reverse direction
• Fixed a bug in parse_mothur_summary where “unclassified” had got changed to “untaxmap” during a search and replace
• Fixed outdated example code for extract_taxonomy
• Fixed a bug in mutate_taxa and mutate_obs that made replacing columns result in new columns with duplicate names.

metacoder 0.1.2

Breaking changes

• plot_taxonomy and the plot method have been renamed heat_tree.

New features

• New introduction vignette
• Various minor bug fixes

metacoder 0.1.1

Breaking changes

• taxon_levels have been replaced with n_supertaxa to make names conceptually consistent. Note that this means what was 1 as taxon_levels is now 0 as n_supertaxa.

New features

• Added n_subtaxa and n_subtaxa_1 functions
• Added taxonomy parsing examples to vignettes

metacoder 0.1.0

Breaking changes

• Many options and functions have been renamed (#115)

New features

• dplyr functions for taxmap objects!
• Added a print method for taxmap objects
• new SILVA example data set
• extract_taxonomy works on SeqFastadna class from seqinr
• parse_mothur_summary function: parses the mothur summary table
• remove_redundant_names function: removes components of names of taxa in subtaxa

Changes

• Core functions are much faster
• More tests
• Updated vignettes
• Many bug fixes and minor upgrades
• Legend now moves into plot if there is room (#118)