News
- Maintenance release to fix CRAN check issues.
- Maintenance release to fix CRAN check issues.
- 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.
- 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.
- Added parsing of taxon ranks to the UNITE parser
- Various 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)