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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_matrix
primersearch
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 NA
s instead of
odd error.compare_groups
now ignores NA
s instaed of
returning NaN
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.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.primersearch
primersearch
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_taxonomy
mutate_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 seqinr
parse_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.
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