Add function [plot_seq_ratio_pq()] to explore the number of sequences per samples using difference ratio of the number of sequences per samples ordered by the number of sequences.
Fix a bug in [subset_taxa_pq()] when the condition was TRUE only for one taxon
Fix warnings in [graph_test_pq()] with ggplot2 v.4.0.0
Fix a bug in [upseq_pq()] when using min_nb_seq
parameter.
Add params discard_genus_alone,
pattern_to_remove_tip and
pattern_to_remove_node to [rotl_pq()] to enhance the
default naming of nodes and tips
Improve documentation consistency following the style guide
Fix a bug in blast function by allowing value to be equal (not
strictly greater) to the threshold values id_cut,
bit_score_cut, min_cover_cut and
e_value_cut.
species_colnames by
taxonomic_ranks in [rotl_pq()]plot_mt() and
krona()
plot_mt(): alpha → pval
(aligns with existing pval pattern in other functions)krona(): file → file_path
(aligns with existing file_path pattern)text_size and
text_size_info to expand or minimize text annotation in
[summary_plot_pq()].from_sintax is TRUEaitchison and
robust.aitchison.vote_algorithm to choose the algo resolving conflict.pattern_to_remove in [format2dada2()]method are used.dada2_2steps in
function [add_new_taxonomy_pq()] which use [assign_dada2()]
function.blast
in the function [add_new_taxonomy_pq()].min_bootstrap in
[add_new_taxonomy_pq()]pattern_to_remove and
remove_NA to [simplify_taxo()]idtaxa to method in
[add_new_taxonomy_pq()]too_few
(default value “align_start”) and too_many (default
“merge”) to authorize db with variable numbers of rank and parenthesis
in taxonomic name,suffix to add_blast_info()
allowing multiple use of the function on the same phyloseq object
(e.g. in order to used different database)return_DNAStringSet to
write_temp_fasta() function to return a DNAStringSet object
in place of a temporary file.count_seq()filt_taxa_pq() to filter taxa based on the
number of sequences/occurencesno_legend() and
hill_curves_pq() to plot hill diversity accumulation curves
for phylosequmap_pq() to compute Dimensionality
Reduction with UMAPplot_complexity_pq() to plot kmer
complexity of references sequences of a phyloseq objecttype to ridge_pq() to plot a
cumulative version (type=“ecdf”) version of ridgemethod to add_new_taxonomy_pq()
to allow the use of [dada2::assign_taxonomy()] (default, precedent only
method available), [assign_sintax()] or [assign_vsearch_lca()]plot_refseq_pq() and
plot_refseq_extremity_pq() to plot the proportion of each
nucleotide and the diversity of nucleotides from @refseq of
a phyloseq object.type, na_remove and
verbose to ggvenn_pq(). The type = “nb_seq”
allow to plot Venn diagram with the number of shared sequences instead
of shared ASV.cutadapt_remove_primers().verbose to track_wkflow() and
improve examples for track_wkflow() and
list_fastq_filesreturn_file_path to
cutadapt_remove_primers() in order to facilitate targets
pipelinesam_data_matching_names() to match and
verify congruence between fastq files names and sample metadata
(sam_data)CRAN 2024-09-10
heat_tree_pq() because {metacoder}
package is archived from CRAN.build_tree_pq to resubmit
to CRAN Add a param return_a_vector in function
filter_trim() to make possible to return a vector of path
as it is useful when used with
targets::tar_targets(..., format="file"))list() by
vector(list, ...)CRAN 2024-09-09
filter_taxa_blast() for
filter_asv_blast()postcluster_pq() for
asv2otu()return_data_for_venn in function
ggvenn_pq in order to make more customizable plot following
ggVennDiagram
tutorialrename_asv by
rename_taxons in clean_pq()reorder_asv by
reorder_taxons in clean_pq()default_fun in function
merge_samples2() in order to replace the default function
that change the sample data in case of merging. A useful parameter is
default_fun=diff_fct_diff_class.kruskal_test to hill_pq()
function to prevent user to mis-interpret Tuckey HSD result (and
letters) if the global effect of the tested factor on Hill diversity is
non significant.vioplot to hill_pq() function to allow violin
plot instead of boxplot.rarefy_sample_count_by_modality to debug the
case of modality with level of length one.CRAN 2024-04-28
taxa_as_rows() and
taxa_as_columns() to replace verbose called to
clean_pq()ggscatt_pq() to plot and test for effect
of a numerical columns in sam_data on Hill number. Its the equivalent
for numerical variables of ggbetween_pq() which focus on
the effect of a factor.var_par_pq() ,
var_par_rarperm_pq() and plot_var_part_pq() to
compute the partition of the variation of community and plot it. It
introduce the notion of rarperm part in the function name.
It refers to the fact that this function compute permutation of samples
depth rarefaction to measure the variation due to the random process in
rarefaction.hill_test_rarperm_pq() to test the effect
of a factor on hill diversity accounting for the variation due to random
nature of the rarefaction by sample depth.rarefy_sample_count_by_modality() to
equalize the number of samples for each levels of a modality
(factor)accu_plot_balanced_modality() to plot
accumulation curves with balanced modality (same number of samples per
level) and depth rarefaction (same number of sequences per sample)adonis_rarperm_pq() to compute multiple
Permanova analyses on different sample depth rarefaction.ggaluv_pq() to plot taxonomic distribution
in alluvial fashion with ggplot2 (using the [ggalluvial] package)glmutli_pq() to use automated model
selection and multimodel inference with (G)LMs for phyloseq objecttaxa_ranks in function
psmelt_samples_pq() to group results by samples AND
taxonomic ranks.hill_scales in functions
hill_tuckey_pq() and hill_p() to choose the
level of the hill number.na_remove in function hill_pq()
to remove samples with NA in the factor fact.plot_with_tuckey to
hill_pq().,formattable_pq() to make beautiful table
of the distribution of taxa across a modality using visualization inside
in the table.fac2col() and transp() to
facilitate manipulation of colors, especially in function
formattable_pq()signif_ancombc() and
plot_ancombc_pq() to plot significant results from
ancombc_pq() functiondistri_1_taxa() to summarize the
distribution of one given taxa across level of a modalitynormalize_prop_pq() to implement the
method proposed by McKnight et
al. 2018psmelt_samples_pq() to build data frame of
samples information including the number of sequences (Abundance) and
Hill diversity metrics. Useful to use with the ggstatsplot
packages (see examples).variable by fact in function
ggbetween_pq() and hill_pq() (keeping the
variable option in hill_pq() for backward
compatibility)chimera_removal_vs(). Now it return a matrix to be able to
be parsed on to [dada2::getUniques()]CRAN 2024-03-08
Add functions chimera_detection_vs() and
chimera_removal_vs() to process chimera detection and
removal using vsearch
software
Add functions filter_trim(),
sample_data_with_new_names() and
rename_samples() to facilitate the use of targets for bioinformatic
pipeline.
Add function add_info_to_sam_data() to expand
sam_data slot using a data.frame and using nb_asv and nb_seq
Add functions swarm_clustering() and
vsearch_clustering() and add swarm method in
the function asv2otu()
Add function physeq_or_string_to_dna() mostly for
internal use
Add function cutadapt_remove_primers() to remove
primers using cutadapt
Add internal functions is_swarm_installed(),
is_cutadapt_installed(),
is_vsearch_installed() and
is_falco_installed() to test for the availability of
external software in order to run examples and test from
testthat.
Submit to CRAN and change code to comply with their rules (patch 0.7.1 to 0.7.9)
Numerous examples and tests are skipped on CRAN because it spends to much time to run. Rules vignettes is updated to details the strategy for this.
add_nb_sequences -> add_nb_seq in
ggvenn_pq()db -> db_url in
get_funguild_db()db -> db_funguild in
get_funguild_db()file -> file_path in
get_file_extension()n_seq -> nb_seq in
subsample_fastq()otutable -> otu_table in
lulu()alpha -> pval in
plot_edgeR_pq() and plot_deseq2_pq() and
change default value from 0.01 to more classical 0.05sequences -> seq2search in function
search_exact_seq_pq()seq_names -> dna_seq in function
asv2otuinstall_pkg_needed() which do not
comply with CRAN policiesancombc_pq() to simplify the call to
ANCOMBC::ancombc2() : ANalysis of COmpositions of
Microbiomes with Bias Correction 2taxa_names_from_physeq (default FALSE) to
subset_taxa_pq()rarefy_by_sample (default FALSE) to function
ggbetween_pq()are_modality_even_depth() to test if
samples depth significantly vary among the modalities of a factormerge_taxa_vec() and
merge_samples2() from the speedyseq package into
MiscMetabar to decrease package dependencies (Thanks to Mike R.
Mclaren)reorder_taxa_pq() in order to replace the
unique call to package MicroViz to decrease package dependencies.get_funguild_db() and
funguild_assign() from the FUNGuildR package into
MiscMetabar to decrease package dependenciesgoodpractice::gp() and
devtools::check() functionverify_pq() with args verbose=TRUEmultitax_bar_pq() when using
nb_seq = FALSEggbetween_pq() to facilitate comparison of
hill number using the power of
ggstatsplot::ggbetweenstats()plot_SCBD_pq() to plot species
contributions to beta diversity (SCBD) of samplesLCBD_pq() and plot_LCBD_pq()
to compute, test and plot local contributions to beta diversity (LCBD)
of samplestbl_sum_samdata() to summarize information
from sample data in a tablemumu_pq() to use mumu, a fast and robust
C++ implementation of lulu.install_pkg_needed()
to install pkg (mostly for package list in Suggest in
DESCRIPTION) if needed by a function.add_funguild_info() and
plot_guild_pq() to add and plot fungal guild information
from taxonomy using FUNGuild packagebuild_phytree_pq() to build 3 phylogenetic
trees (NJ, UPGMA and ML using phangorn R package) from the
refseq slot of a phyloseq object, possibly
with bootstrap values. See the vignettes Tree
visualization for an introduction to tree visualization using
ggtree R package.ggvenn_pq() thanks to issue #31log_10 in function
biplot_pq() into log10translog10transform in function
circle_pq() into log10transone_plot (default FALSE, same behavior
than before) to hill_pq function in order to return an
unique ggplot2 object with the four plots inside.correction_for_sample_size (default TRUE,
same behavior than before) to hill_pq and
hill_tuckey_pq function to allow removing any correction
for uneven sampling depth.multitax_bar_pq() to plot 3 levels of
taxonomy in function of samples attributesridges_pq() to plot ridges of one
taxonomic level in function of samples attributestreemap_pq to plot treemap of two
taxonomic levelsiNEXT_pq() to calculate hill diversity
using the iNEXT
package.pairs to multi_biplot_pq() in
order to indicate all pairs of samples we want to print.compare_pairs_pq() with information about the
number of shared sequences among pairs.upset_pq() to plot upset of phyloseq
object using the ComplexUpset
package.upset_test_pq to test for differences
between intersections (wrapper of
ComplexUpset::upset_test() for
phyloseq-object).add_info) in subtitle of the
hill_pq() function.remove_space to
simplify_taxo() function.simplify_taxo to clean_pq()
function.rarefy_nb_seq by
rarefy_before_merging and add arguments
rarefy_after_merging and add_nb_seq to
ggvenn_pq() function.rarefy_after_merging to
biplot_pq() and upset_pq() functions.taxa_fill to upset_pq()
function in order to fill the bar with taxonomic rank.subsample_fastq() to make subset of
fastq files in order to test your pipeline with all samples but with a
low number of reads.accu_samp_threshold() to compute the
number of sequence to obtain a given proportion of ASV in accumulation
curves (`accu_plot).tax_bar_pq() in order to plot taxonomic
distribution across samples.multi_biplot_pq() to visualize a
collection of couples of samples for comparison through a list of
biplot_pq().add_info, na_remove, and
clean_pq to plot_tax_pq() function.vsearch_cluster_method and
vsearch_args to otu2asv() for more detailed
control of the vsearch software.MM_idtaxa().write_pq() called
save_pq() to save a phyloseq object in the three
possible formats () at the same time
add_blast_info() to add information from
blast_pq() to the tax_table slot of a
phyloseq object.keep_temporary_files in
asv2otu() function.asv2otu() and fix a little
bug in the name of the conserved ASV after asv2otu().search_exact_seq_pq() to search for exact
matching of sequences using complement, reverse and reverse-complement
against a phyloseq object.add_new_taxonomy_pq() to add new taxonomic
rank to a phyloseq object. For example to add taxonomic assignment from
a new database.test_that package and
improve code compatibility with cran recommendations.asv2otu() with method="vsearch" change two
default values (to repeat the precedent behavior, use
asv2otu(..., vsearch_cluster_method = "--cluster_fast", tax_adjust = 1)):
add_nb_samples to ggvenn_pq()
which add the number of samples to level name in the plot. Useful to see
disequilibrium in the number of samples among the factor’s levels.args_makedb and args_blastn to
functions blast_pq(), blast_to_phyloseq(),
blast_to_derep() and filter_asv_blast().rarefy_nb_seqs to ggven_pq() in
order to rarefy samples before plotting.SRS_curve_pq() to plot scaling with ranked
subsampling (SRS) curves using the SRS::SRS_curve()
function (see citation(“SRS”) for reference).nb_samples_info to biplot_pq()
in order to add the number of samples merged by level of factors.biplot_pq() and
ggvenn_pq().na_remove, dist_method
(including Aitchinson and robust-Aitchinson distance),
correction_for_sample_size and rarefy_nb_seqs
options to adonis_pq() function.na_remove to graph_test_pq()
function.plot_tax_pq() to plot taxonomic
distribution (nb of sequences or nb of ASV) across factor.add_points and make better axis of
hill_pq() functionblast_to_derep() in order to facilitate
searching some fasta sequences in dereplicated sequences (obtained by
dada2::derepFastq)| Database (makeblastdb) | Sequences to blast (blastn) | |
|---|---|---|
blast_to_phyloseq() |
Built from ref_seq slot(physeq-class) |
Custom fasta file |
blast_to_derep() |
Built from dereplicate sequences (derep-class) | Custom fasta file |
blast_pq() |
Custom database or custom fasta file | ref_seq slot of a physeq object |
tsne_pq() and plot_tsne_pq()
to quickly visualize results of the t-SNE multidimensional analysis
based on the Rtsne::Rtsne() function.count_seq()track_wkflow_samples() and
select_one_sample()sam_data_first in function
write_pq()reorder_asv and rename_asv to
in function write_pq() and clean_pqrotl_pq() to build a phylogenetic tree
using the ASV binomial names of a physeq object and the Open Tree of
Life tree.split_by to make multiple plot given a
variable in sam_data slot (function
ggvenn_pq())seq_names in asv2otu() function
allow to clusterize sequences from a character vector of DNA.blast_pq() function to blast the sequences of the
@ref_seq slot against a custom databasefilter_asv_blast() function to filter ASV in
phyloseq dataset using blast against a custom databasesubset_taxa_pq() function to filter ASV based on
a named conditional vector. Used in
filter_asv_blast().force_taxa_as_columns (default FALSE) and
force_taxa_as_rows (default FALSE) to
clean_pq().count_fastq_seq()
to count sequences from fastq.gz files directly from R.track_wkflow() function
(parameter taxonomy_rank)physeq by
pk. sam_names() to read_pq()data_fungi and
data_fungi_sp_known metadataAdapt the function asv2otu() to IdClusters
change in the DECIPHER package (commit
254100922f2093cc789d018c18a26752a3cda1e3). Then change the
IdClusters function that was removed from DECIPHER to
Clusterize function.
Better functioning of blast_to_phyloseq() when none
query sequences are founded.
Add tax_adjust argument to
asv2otu()function
Add some functions useful for the targets package
Add a biplot_physeq() function to visualize of two
samples for comparison of physeq object
Add an argument modality in the
tax_datatable() function to split OTU abundancy by level of
the sample modality
Add a function multiple_share_bisamples() to help
compare samples by pairs
Add a new function (ggVenn_phyloseq()) for better
venn diagram but without area calculation (use
venn_phyloseq() in this case).
Add two functions helpful for beta-diversity analysis
(adonis_phyloseq() and
physeq_graph_test())
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