- Add functions [taxa_as_rows()] and [taxa_as_columns()] to replace verbose called to [clean_pq()]
- Add function [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.
- Add functions [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. - Add function [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.
- Add function [rarefy_sample_count_by_modality()] to equalize the number of samples for each levels of a modality (factor)
- Add function [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)
- Add function [adonis_rarperm_pq()] to compute multiple Permanova analyses on different sample depth rarefaction.
- Add function [ggaluv_pq()] to plot taxonomic distribution in alluvial fashion with ggplot2 (using the [ggalluvial] package)
- Add function [glmutli_pq()] to use automated model selection and multimodel inference with (G)LMs for phyloseq object

- Add param
`taxa_ranks`

in function [psmelt_samples_pq()] to group results by samples AND taxonomic ranks. - Add param
`hill_scales`

in functions [hill_tuckey_pq()] and [hill_pq()] to choose the level of the hill number. - Add param
`na_remove`

in function`hill_pq()`

to remove samples with NA in the factor fact.

- Add param
`plot_with_tuckey`

to`hill_pq()`

., - Add function
`formattable_pq()`

to make beautiful table of the distribution of taxa across a modality using visualization inside in the table. - Add functions
`fac2col()`

and`transp()`

to facilitate manipulation of colors, especially in function`formattable_pq()`

- Add functions
`signif_ancombc()`

and`plot_ancombc_pq()`

to plot significant results from`ancombc_pq()`

function - Add function
`distri_1_taxa()`

to summarize the distribution of one given taxa across level of a modality - Add function
`normalize_prop_pq()`

to implement the method proposed by McKnight et al. 2018 - Add function
`psmelt_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). - Replace param
`variable`

by`fact`

in function`ggbetween_pq()`

and`hill_pq()`

(keeping the variable option in`hill_pq()`

for backward compatibility) - Fix a bug in the class of the return object of function
`chimera_removal_vs()`

. Now it return a matrix to be able to be parsed on to [dada2::getUniques()]

- 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.

- Harmonization of parameters names:
`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 0.05`sequences`

->`seq2search`

in function`search_exact_seq_pq()`

`seq_names`

->`dna_seq`

in function`asv2otu`

- Removing the function
`install_pkg_needed()`

which do not comply with CRAN policies

- Add function
`ancombc_pq()`

to simplify the call to`ANCOMBC::ancombc2()`

: ANalysis of COmpositions of Microbiomes with Bias Correction 2 - Add param
`taxa_names_from_physeq`

(default FALSE) to`subset_taxa_pq()`

- Add param
`rarefy_by_sample`

(default FALSE) to function`ggbetween_pq()`

- Add function
`are_modality_even_depth()`

to test if samples depth significantly vary among the modalities of a factor - Add functions
`merge_taxa_vec()`

and`merge_samples2()`

from the speedyseq package into MiscMetabar to decrease package dependencies (Thanks to Mike R. Mclaren) - Add function
`reorder_taxa_pq()`

in order to replace the unique call to package MicroViz to decrease package dependencies. - Add functions
`get_funguild_db()`

and`funguild_assign()`

from the FUNGuildR package into MiscMetabar to decrease package dependencies - Remove all dependencies from packages not available on CRAN or Bioconductor. Improve code using
`goodpractice::gp`

() and`devtools::check()`

function - Add messages in various cases (NA in samples data, low number of sequences in samples, low number of sequences by taxa) when using
`verify_pq()`

with args`verbose=TRUE`

- Fix a bug in
`multitax_bar_pq()`

when using`nb_seq = FALSE`

- Add function
`ggbetween_pq()`

to facilitate comparison of hill number using the power of`ggstatsplot::ggbetweenstats()`

- Add function
`plot_SCBD_pq()`

to plot species contributions to beta diversity (SCBD) of samples

- Add function
`LCBD_pq()`

and`plot_LCBD_pq()`

to compute, test and plot local contributions to beta diversity (LCBD) of samples - Add function
`tbl_sum_samdata()`

to summarize information from sample data in a table - Add function
`mumu_pq()`

to use mumu, a fast and robust C++ implementation of lulu. - Add (a mostly internal) function
`install_pkg_needed()`

to install pkg (mostly for package list in*Suggest*in DESCRIPTION) if needed by a function. - Add function
`add_funguild_info()`

and`plot_guild_pq()`

to add and plot fungal guild information from taxonomy using`FUNGuild`

package - Add function
`build_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.

- Phyloseq object are converted in taxa_are_columns in the
`ggvenn_pq()`

thanks to issue #31

- Rename param
`log_10`

in function`biplot_pq()`

into`log10trans`

- Rename param
`log10transform`

in function`circle_pq()`

into`log10trans`

- Add argument
`one_plot`

(default FALSE, same behavior than before) to`hill_pq`

function in order to return an unique ggplot2 object with the four plots inside. - Add argument
`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. - Add function
`multitax_bar_pq()`

to plot 3 levels of taxonomy in function of samples attributes - Add function
`ridges_pq()`

to plot ridges of one taxonomic level in function of samples attributes - Add function
`treemap_pq`

to plot treemap of two taxonomic levels

- Add function
`iNEXT_pq()`

to calculate hill diversity using the iNEXT package. - Add argument
`pairs`

to`multi_biplot_pq()`

in order to indicate all pairs of samples we want to print. - Improve
`compare_pairs_pq()`

with information about the number of shared sequences among pairs. - Add function
`upset_pq()`

to plot upset of phyloseq object using the ComplexUpset package. - Add function
`upset_test_pq`

to test for differences between intersections (wrapper of`ComplexUpset::upset_test()`

for`phyloseq-object`

). - Add info (param
`add_info`

) in subtitle of the`hill_pq()`

function. - Add argument
`remove_space`

to`simplify_taxo()`

function. - Add argument
`simplify_taxo`

to`clean_pq()`

function. - Change argument
`rarefy_nb_seq`

by`rarefy_before_merging`

and add arguments`rarefy_after_merging`

and`add_nb_seq`

to`ggvenn_pq()`

function. - Add arguments
`rarefy_after_merging`

to`biplot_pq()`

and`upset_pq()`

functions. - Add argument
`taxa_fill`

to`upset_pq()`

function in order to fill the bar with taxonomic rank. - Add a function
`subsample_fastq()`

to make subset of fastq files in order to test your pipeline with all samples but with a low number of reads. - Add a function
`accu_samp_threshold()`

to compute the number of sequence to obtain a given proportion of ASV in accumulation curves (`accu_plot). - Add a function
`tax_bar_pq()`

in order to plot taxonomic distribution across samples.

- Add function
`multi_biplot_pq()`

to visualize a collection of couples of samples for comparison through a list of`biplot_pq()`

. - Add options
`add_info`

,`na_remove`

, and`clean_pq`

to`plot_tax_pq()`

function. - Add options
`vsearch_cluster_method`

and`vsearch_args`

to`otu2asv()`

for more detailed control of the vsearch software. - Suppression of buggy function
`MM_idtaxa()`

. - Add a wrapper of
`write_pq()`

called`save_pq()`

to save a*phyloseq*object in the three possible formats () at the same time- 4 separate tables
- 1 table version
- 1 RData file

- Add a function
`add_blast_info()`

to add information from`blast_pq()`

to the`tax_table`

slot of a*phyloseq*object. - Add option
`keep_temporary_files`

in`asv2otu()`

function. - Improve the documentation of
`asv2otu()`

and fix a little bug in the name of the conserved ASV after`asv2otu()`

. - Test coverage largely improved leading to numerous minor bug fixes.
- Add function
`search_exact_seq_pq()`

to search for exact matching of sequences using complement, reverse and reverse-complement against a phyloseq object. - Add function
`add_new_taxonomy_pq()`

to add new taxonomic rank to a phyloseq object. For example to add taxonomic assignment from a new database. - Add a battery of test using
`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)`

):- vsearch_cluster_method = “–cluster_size”
- tax_adjust = 0

- Add option
`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. - Add option
`args_makedb`

and`args_blastn`

to functions`blast_pq()`

,`blast_to_phyloseq()`

,`blast_to_derep()`

and`filter_asv_blast()`

. - Add option
`rarefy_nb_seqs`

to`ggven_pq()`

in order to rarefy samples before plotting. - Add function
`SRS_curve_pq()`

to plot scaling with ranked subsampling (SRS) curves using the`SRS::SRS_curve()`

function (see citation(“SRS”) for reference). - Add option
`nb_samples_info`

to`biplot_pq()`

in order to add the number of samples merged by level of factors. - Add a message when two modalities differ greatly (more than x2) in their number of sequences in
`biplot_pq()`

and`ggvenn_pq()`

. - Add options
`na_remove`

,`dist_method`

(including Aitchinson and robust-Aitchinson distance),`correction_for_sample_size`

and`rarefy_nb_seqs`

options to`adonis_pq()`

function. - Add option
`na_remove`

to`graph_test_pq()`

function.

- Add function
`plot_tax_pq()`

to plot taxonomic distribution (nb of sequences or nb of ASV) across factor. - Add option
`add_points`

and make better axis of`hill_pq()`

function - Add function
`blast_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 |

- Add functions
`tsne_pq()`

and`plot_tsne_pq()`

to quickly visualize results of the t-SNE multidimensional analysis based on the`Rtsne::Rtsne()`

function.

- Add the possibility to select a folder in the function
`count_seq()`

- Add functions
`track_wkflow_samples()`

and`select_one_sample()`

- Add option
`sam_data_first`

in function`write_pq()`

- Add option
`reorder_asv`

and`rename_asv`

to in function`write_pq()`

and`clean_pq`

- Add a function
`rotl_pq()`

to build a phylogenetic tree using the ASV binomial names of a physeq object and the Open Tree of Life tree.

- Argument
`split_by`

to make multiple plot given a variable in`sam_data`

slot (function`ggvenn_pq()`

)

- Argument
`seq_names`

in`asv2otu()`

function allow to clusterize sequences from a character vector of DNA. - Add a
`blast_pq()`

function to blast the sequences of the`@ref_seq`

slot against a custom database - Add a
`filter_asv_blast()`

function to filter ASV in*phyloseq*dataset using blast against a custom database - Add a
`subset_taxa_pq()`

function to filter ASV based on a named conditional vector. Used in`filter_asv_blast()`

. - Add parameter
`force_taxa_as_columns`

(default FALSE) and`force_taxa_as_rows`

(default FALSE) to`clean_pq()`

. - Add a first version of the function
`count_fastq_seq()`

to count sequences from fastq.gz files directly from R. - Add taxonomic info to
`track_wkflow()`

function (parameter`taxonomy_rank`

)

- Change some function names, mainly replacing
`physeq`

by`pk`

. - Improve documentation using some rules documented in the Rules vignettes.
- Add a option
`sam_names()`

to`read_pq()`

- Correction of
`data_fungi`

and`data_fungi_sp_known`

metadata

- Add supplementary info in summary_plot_physeq()`
- Better arguments in biplot_physeq()`)
- Add merge_sample_by argument in biplot_physeq()`
- Better documentation with more example.
- For other minors bugs fixes and addition, see the list of commits

Adapt 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()`

functionAdd some functions useful for the targets package

Add a

`biplot_physeq()`

function to visualize of two samples for comparison of physeq objectAdd an argument

*modality*in the`tax_datatable()`

function to split OTU abundancy by level of the sample modalityAdd a function

`multiple_share_bisamples()`

to help compare samples by pairsAdd 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()`

)

- Add badge to set the development lifecycle of each function
- Add the lulu_phyloseq function to make easy the reclustering of phyloseq object using the lulu algorithm (https://www.nature.com/articles/s41467-017-01312-x) from the lulu package.

- This is the first release of pkgdown.