NEWS.md

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

MiscMetabar 0.13.0 (in development)

• Add function [assign_blastn()] and add a method blast in the function [add_new_taxonomy_pq()].
• Add function [resolve_vector_ranks()] to resolve conflict in a vector of taxonomy values

MiscMetabar 0.12.1 (in development)

• Add parameter name min_bootstrap in [add_new_taxonomy_pq()]
• Bug fix in [assign_idtaxa()]
• Add parameters pattern_to_remove and remove_NA to [simplify_taxo()]

MiscMetabar 0.12.0

• Add function [assign_idtaxa()] and [learn_idtaxa()] to facilitate the taxonomic assignation using the idtaxa algorithm from the DECIPHER R package.
• Add option idtaxa to method in [add_new_taxonomy_pq()]
• Add function [tbl_sum_taxtable()] to summarize tax_table from a phyloseq object
• In function [assign_sintax()], add params too_few (default value "align_start") and too_many (default "merge") to authorize db with variable numbers of rank and parenthesis in taxonomic name,

MiscMetabar 0.11.1

• Add param suffix to add_blast_info() allowing multiple use of the function on the same phyloseq object (e.g. in order to used different database)
• Add param return_DNAStringSet to write_temp_fasta() function to return a DNAStringSet object in place of a temporary file.
• Add a vignette pkgnet-report.
• Add the possibility to send fasta.gz file to count_seq()

MiscMetabar 0.11

• Add function filt_taxa_pq() to filter taxa based on the number of sequences/occurences
• Add functions no_legend() and hill_curves_pq() to plot hill diversity accumulation curves for phyloseq
• Add function umap_pq() to compute Dimensionality Reduction with UMAP
• Add function plot_complexity_pq() to plot kmer complexity of references sequences of a phyloseq object
• Add param type to ridge_pq() to plot a cumulative version (type="ecdf") version of ridge
• Introduce the idea of a pq-verse: some other packages will complete the MiscMetabar packages to make package maintenance easier. The comparpq package will facilitate the comparison of phyloseq object with different taxonomy, different clustering methods, different samples with same modality or different primers.
• Add functions [assign_vsearch_lca()], [assign_sintax()] and internal function [write_temp_fasta()]
• Add param method to add_new_taxonomy_pq() to allow the use of [dada2::assign_taxonomy()] (default, precedent only method available), [assign_sintax()] or [assign_vsearch_lca()]

MiscMetabar 0.10.4

• Add functions 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.

MiscMetabar 0.10.3

• Add params 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.
• Add automatic report in json for the function cutadapt_remove_primers().
• Add param verbose to track_wkflow() and improve examples for track_wkflow() and list_fastq_files

MiscMetabar 0.10.2

• Improve code thanks to {lintr} package
• Add option return_file_path to cutadapt_remove_primers() in order to facilitate targets pipeline
• Add function sam_data_matching_names() to match and verify congruence between fastq files names and sample metadata (sam_data)

MiscMetabar 0.10.1

CRAN 2024-09-10

• Delete function heat_tree_pq() because {metacoder} package is archived from CRAN.

MiscMetabar 0.9.4

• Set a seed in the example of 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"))
• Make some storage amelioration by replacing list() by vector(list, ...)

MiscMetabar 0.9.3

CRAN 2024-09-09

• Homogenize terminology replacing ASV by taxa/taxon in documentation and code
• Build an alias function filter_taxa_blast() for filter_asv_blast()
• Build an alias function postcluster_pq() for asv2otu()
• Add param return_data_for_venn in function ggvenn_pq in order to make more customizable plot following ggVennDiagram tutorial

BREAKING CHANGES

• Replacing misnamed param rename_asv by rename_taxons in clean_pq()
• Replacing misnamed param reorder_asv by reorder_taxons in clean_pq()

MiscMetabar 0.9.2

• Add param 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.
• Add param 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.
• Add param vioplot to hill_pq() function to allow violin plot instead of boxplot.
• Modify rarefy_sample_count_by_modality to debug the case of modality with level of length one.

MiscMetabar 0.9.1

CRAN 2024-04-28

New functions

• 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

New parameters

• 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_p() 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.

MiscMetabar 0.8.1

• 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()]

MiscMetabar 0.7

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.

BREAKING CHANGES

• 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

MiscMetabar 0.6.0

• 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

MiscMetabar 0.52

• 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

MiscMetabar 0.51

• 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.

MiscMetabar 0.5

• Phyloseq object are converted in taxa_are_columns in the ggvenn_pq() thanks to issue #31

BREAKING CHANGES

• Rename param log_10 in function biplot_pq() into log10trans
• Rename param log10transform in function circle_pq() into log10trans

MiscMetabar 0.42

• 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

MiscMetabar 0.41

• 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.

MiscMetabar 0.40

• 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.

BREAKING CHANGES

• 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

MiscMetabar 0.34

• 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.

MiscMetabar 0.33

• 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.

MiscMetabar 0.32

• 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.

MiscMetabar 0.31

• 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)

MiscMetabar 0.3

• Change some function names, mainly replacing physeq by pk. \tabular{rl}{ graph_test_pq() \tab now a synonym for physeq_graph_test\cr adonis_pq() \tab now a synonym for adonis_phyloseq\cr clean_pq() \tab now a synonym for clean_physeq\cr lulu_pq() \tab now a synonym for lulu_phyloseq\cr circle_pq() \tab now a synonym for otu_circle\cr biplot_pq() \tab now a synonym for biplot_physeq\cr read_pq() \tab now a synonym for read_phyloseq\cr write_pq() \tab now a synonym for write_phyloseq\cr sankey_pq() \tab now a synonym for sankey_phyloseq\cr summary_plot_pq() \tab now a synonym for summary_plot_phyloseq\cr plot_edgeR_pq() \tab now a synonym for plot_edgeR_phyloseq\cr plot_deseq2_pq() \tab now a synonym for plot_deseq2_phyloseq\cr venn_pq() \tab now a synonym for venn_phyloseq\cr ggvenn_pq() \tab now a synonym for ggVenn_phyloseq\cr hill_tuckey_pq() \tab now a synonym for hill_tuckey_phyloseq\cr hill_pq() \tab now a synonym for hill_phyloseq\cr heat_tree_pq() \tab now a synonym for physeq_heat_tree\cr compare_pairs_pq() \tab now a synonym for multiple_share_bisamples\cr }
• 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

MiscMetabar 0.24

• 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

MiscMetabar 0.23

• 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()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())

MiscMetabar 0.22

• 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.

MiscMetabar 0.21

• This is the first release of pkgdown.

adrientaudiere/MiscMetabar documentation built on Feb. 7, 2025, 5:47 p.m.