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MiscMetabar 0.7 (in development)


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

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


  • 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.


  • 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

MiscMetabar 0.32

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.
  • 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

MiscMetabar 0.21

  • This is the first release of pkgdown.