High-Performance Open-Source Archive
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 subtaxa
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