metacoder 0.3.8

Maintenance release to get metacoder back on CRAN after dependency taxize was temporarily removed from CRAN.

metacoder 0.3.6

Notable changes made:

• 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 fingures 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
• Versious minor bug fixes

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

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 0.2.0

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.

metacoder 0.1.3

Mostly minor improvements and bug fixes. Larger changes are waiting on the taxa package to be done, which will be the new home of the taxmap class and the associated dplyr-like manipulating functions like filter_taxa.

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.