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 NA
s instead of odd error.
compare_groups
now ignores NA
s 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 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.
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 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)