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MiscMetabar 0.9.1 (in development)

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_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.

MiscMetabar 0.8.1

MiscMetabar 0.7 (in development)

BREAKING CHANGES

MiscMetabar 0.6.0

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

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

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.