NEWS.md

News

metacoder 0.3.7

• Maintenance release to fix CRAN check issues.

metacoder 0.3.6

• When an ordered factor is supplied to the groups argument of compare_groups, the order of levels is used to arrange the results. This can be used to change the order of groups when the output is used with heat_tree_matrix (issue #323).
• Added calc_diff_abund_deseq2 function to use DESeq2 to produce output like compare_group useful for heat_tree_matrix
• Fixed error with primersearch and primersearch_raw when there is a single match to a single query (issue #326)
• Fixed Error in grid.Call.graphics(C_setviewport, vp, TRUE) : non-finite location and/or size for viewport when using heat_tree_matrix with only a single comparison. Now a single differential heat tree is made instead of a matrix #328).
• Replace use of depreciated n_extra in print.

metacoder 0.3.5

• Replaced depreciated as.tbl function from dplyr'
• Added node_legend_title and edge_legend_title options to heat_tree to specify the title for each legend.
• Added options to heat_tree to set the number of significant figures used for the numbers in the legend.
• Reintegrated the functionality of the taxa package in order to prepare for releasing a rewritten version of taxa.
• Reduced the number of dependencies and made some optional.

metacoder 0.3.4

• Added parsing of taxon ranks to the UNITE parser
• Various minor bug fixes

metacoder 0.3.3

• Fixed a bug in calc_n_samples and calc_prop_samples that caused an error when group names had spaces in them.
• calc_prop_samples default output column name changed from "n_samples" to "prop_samples".

metacoder 0.3.2

• calculation functions that use the groups option now warn if groups is used without cols.
• Fixed a bug in some calculation functions that would name columns incorrectly in some data sets when the groups option was used. (issue #233).

metacoder 0.3.1

Bug fixes

• calc_taxon_abund no longer errors when a taxon has no observations associated with it.
• New heat_tree_matrix options to change size and color of row and column labels.
• Fixed a bug causing the size legend not to be shown (issue #249.
• Now when a node_color_interval is set but a edge_color_interval is not and edge_color is not used, the edge_color_interval is the same as the node_color_interval.

New features

• Added parser for dada2 results called parse_dada2 and writers to convert back called make_dada2_asv_table and make_dada2_tax_table.

Changes

• Started using the viridis colors for heat_tree by default (issue #133.

metacoder 0.3.0

Bug fixes

• Fixed bug in calc_n_samples where the message reported the number of taxa instead of the number of rows in the table.
• Fixed bug in heat_tree_matrix that happened when factors were used for treatments (issue #240.
• zero_low_counts now ignores NAs instead of odd error.
• compare_groups now ignores NAs instaed of returning NaN

Improvements

• Added more_than option to calc_n_samples so that users can set the minimum threshold for whether a sample is counted or not instead of it always 1.
• Added calc_prop_samples function for calculating the proportion of samples with a value greater than 0 (issues #233.
• primersearch is faster and takes less memory by using ape::DNAbin objects internally.
• Made calc_taxon_abund about 5x faster.

New features

• taxmap objects can be converted to phyloseq objects using as_phyloseq.
• Added parser for uBiome data.

Changes

• primersearch now takes and returns a taxmap object with results added as tables. primersearch_raw is a new function that behaves like the old primersearch did, returning a table.
• The dataset option of many functions has been renamed to data to match the option name in the taxa package.
• Numerous spelling fixes.

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.

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)