News
- 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.
- Added parsing of taxon ranks to the UNITE parser
- Versious minor bug fixes
- 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”.
- 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).
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.
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.
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.
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.
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 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 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.
Breaking changes
plot_taxonomy and the plot method have been renamed heat_tree.
New features
- New introduction vignette
- Various minor bug fixes
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
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 seqinrparse_mothur_summary function: parses the mothur summary tableremove_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)