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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).calc_diff_abund_deseq2 function to use DESeq2 to produce output like compare_group useful for heat_tree_matrixprimersearch and primersearch_raw when there is a single match to a single query (issue #326)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).n_extra in print.as.tbl function from dplyr’node_legend_title and edge_legend_title options to heat_tree to specify the title for each legend.heat_tree to set the number of significant figures used for the numbers in the legend.taxa package in order to prepare for releasing a rewritten version of taxa.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”.groups option now warn if groups is used without cols.groups option was used. (issue #233).calc_taxon_abund no longer errors when a taxon has no observations associated with it.heat_tree_matrix options to change size and color of row and column labels.dada2 results called parse_dada2 and writers to convert back called make_dada2_asv_table and make_dada2_tax_table.viridis colors for heat_tree by default (issue #133.calc_n_samples where the message reported the number of taxa instead of the number of rows in the table.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 NaNmore_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.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.calc_taxon_abund about 5x faster.taxmap objects can be converted to phyloseq objects using as_phyloseq.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.dataset option of many functions has been renamed to data to match the option name in the taxa package.heat_tree_matrix that happen when the input data is not exactly like that produced by compare_groups (issues #195, #196, #197).output_file was used with heat_tree_matrix. Now whole plot is saved instead of last subplot. (issue #203)parse_mothur_tax_summary when reading from a file path (issue #211).zero_low_counts when using use_total = TRUE (issue #227).parse_phyloseq error when arbitrary rank names were used.heat_tree_matrix always has a 1:1 aspect ratio. (issue #205)subtaxa that caused an error when all of subset is FALSE. (issue #143)filter_taxa that caused an error when all taxa are filtered out. (issue #144)heat_tree now uses the taxmap class defined in the taxa package.primersearchprimersearch output to be cleaner and have info like the amplicon sequence and primer binding sites.heat_tree_matrix to make plotting a pairwise matrix of heat trees for comparing treatments.parse_mothur_tax_summary for mothur *.tax.summary file made by classify.seqs.parse_mothur_taxonomy for mothur *.taxonomy file made by classify.seqs.parse_qiime_biom for the QIIME BIOM output.parse_phyloseq to convert phyloseq objects.parse_newick to parse newick files.parse_unite_general for unite general FASTA release. (issue #154)parse_rdp for RDP FASTA release. (issue #160)parse_silva_fasta for SILVA FASTA release. (issue #162)calc_obs_props to calculate proportions from observation counts (issue #167parse_greengenes for the Greengenes database. (issue #?)write_greengenes to create an imitation of the Greengenes database format.write_rdp to create an imitation of the RDP database format.write_mothur_taxonomy to create an imitation of the mothur taxonomy format.write_unite_general to create an imitation of the UNITE general FASTA release.write_silva_fasta to create an imitation of the SILVA FASTA release.compare_treatments to compare multiple samples in multiple treatments, applying a user-defined function.calc_taxon_abund to sum observation values for each taxon.col_names option to calc_taxon_abund to set names of output columns.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 onceheat_tree now gives a warning if infinite values are given to itextract_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 labelsextract_taxonomy: added batch_size option to help deal with invalid IDs betterheat_tree option margin_size funcion now takes four values instead of 2.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.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 suppliedprimersearch that cased the wrong primer sequence to be returned when primers match in the reverse directionparse_mothur_summary where “unclassified” had got changed to “untaxmap” during a search and replaceextract_taxonomymutate_taxa and mutate_obs that made replacing columns result in new columns with duplicate names.plot_taxonomy and the plot method have been renamed heat_tree.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.n_subtaxa and n_subtaxa_1 functionstaxmap objects!print method for taxmap objectsextract_taxonomy works on SeqFastadna class from seqinrparse_mothur_summary function: parses the mothur summary tableremove_redundant_names function: removes components of names of taxa in subtaxaThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.