Changes in version 0.3.9 (2026-04-11) - Maintenance release to fix CRAN check issues. Changes in version 0.3.8 (2025-02-11) - Maintenance release to fix CRAN check issues. Changes in version 0.3.7 (2024-02-20) - Maintenance release to fix CRAN check issues. Changes in version 0.3.6 (2023-04-04) - 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. Changes in version 0.3.5 (2021-06-23) - 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. Changes in version 0.3.4 (2020-04-29) - Added parsing of taxon ranks to the UNITE parser - Various minor bug fixes Changes in version 0.3.3 (2019-07-18) - 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". Changes in version 0.3.2 (2019-04-08) - 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). Changes in version 0.3.1 (2019-01-04) 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. Changes in version 0.3.0 (2018-08-28) 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. Changes in version 0.2.1 (2018-05-02) 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. Changes in version 0.2.0 (2018-01-05) 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. Changes in version 0.1.3 (2017-05-23) 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. Changes in version 0.1.2 (2016-08-27) Breaking changes - plot_taxonomy and the plot method have been renamed heat_tree. New features - New introduction vignette - Various minor bug fixes Changes in version 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 Changes in version 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)