Package index • MiscMetabar

Describe phyloseq object

See also vignette on exploring data

summary_plot_pq(): Summarize a phyloseq-class object using a plot.

tbl_sum_samdata(): Summarize information from sample data in a table

tbl_sum_taxtable(): Summarize a tax_table (taxonomic slot of phyloseq object) using gtsummary

Transform phyloseq object

Verify and clean phyloseq object

clean_pq(): Clean phyloseq object by removing empty samples and taxa

verify_pq(): Verify the validity of a phyloseq object

Taxonomy

add_blast_info(): Add information from blast_pq() to the tax_table slot of a phyloseq object

add_new_taxonomy_pq(): Add new taxonomic rank to a phyloseq object.

assign_blastn(): Assign taxonomy using blastn algorithm and the blast software

assign_dada2(): Assign taxonomy with dada2 using 2 steps assignTaxonomy and assignSpecies

assign_idtaxa(): A wrapper of IdTaxa

assign_sintax(): Assign Taxonomy using Sintax algorithm of Vsearch

assign_vsearch_lca(): Assign taxonomy using LCA

blast_pq(): Blast all sequence of refseq slot of a phyloseq-class object against a custom database.

blast_to_derep(): Blast some sequence against sequences from of a derep-class object.

blast_to_phyloseq(): Blast some sequence against refseq slot of a phyloseq-class object.

filter_asv_blast() filter_taxa_blast(): Filter undesirable taxa using blast against a custom database.

learn_idtaxa(): A wrapper of DECIPHER::LearnTaxa()

resolve_vector_ranks(): Resolve conflict in a vector of taxonomy values

Function to add information from taxonomy

add_funguild_info(): Add information about Guild for FUNGI the FUNGuild databse

funguild_assign(): Assign Guilds to Organisms Based on Taxonomic Classification

get_funguild_db(): Retrieve the FUNGuild database

Transform OTU table only

as_binary_otu_table(): Transform the otu_table of a phyloseq-class object into a phyloseq-class object with a binary otu_table.

normalize_prop_pq(): Normalize OTU table using samples depth

taxa_as_columns(): Force taxa to be in columns in the otu_table of a physeq object

taxa_as_rows(): Force taxa to be in columns in the otu_table of a physeq object

Subset/merge taxa

filt_taxa_pq(): Filter taxa of a phyloseq object based on the minimum number of sequences/samples

filt_taxa_wo_NA(): Filter taxa by cleaning taxa with NA at given taxonomic rank(s)

merge_taxa_vec(): Merge taxa in groups (vectorized version)

select_taxa(): Select a subset of taxa in a specified order where possible

subset_taxa_pq(): Subset taxa using a conditional named boolean vector.

subset_taxa_tax_control(): Subset taxa using a taxa control or distribution based method

Subset/merge samples

merge_samples2(): Merge samples by a sample variable or factor

rarefy_sample_count_by_modality(): Rarefy (equalize) the number of samples per modality of a factor

select_one_sample(): Select one sample from a physeq object

subset_samples_pq(): Subset samples using a conditional boolean vector.

(Re)clustering OTU table

postcluster_pq() asv2otu(): Recluster sequences of an object of class physeq or a list of DNA sequences

lulu(): Post Clustering Curation of Amplicon Data.

lulu_pq(): Lulu reclustering of class physeq

mumu_pq(): MUMU reclustering of class physeq

swarm_clustering(): Re-cluster sequences of an object of class physeq or cluster a list of DNA sequences using SWARM

vsearch_clustering(): Recluster sequences of an object of class physeq or cluster a list of DNA sequences using vsearch software

Remove chimera using vsearch

chimera_detection_vs(): Detect for chimera taxa using vsearch

chimera_removal_vs(): Search for a list of sequence in an object to remove chimera taxa using vsearch

Sample data

add_info_to_sam_data(): Add information to sample_data slot of a phyloseq-class object

sam_data_matching_names(): Match sample names from sam_data and fastq files

Phylogenetic tree

build_phytree_pq(): Build phylogenetic trees from refseq slot of a phyloseq object

References sequences

add_dna_to_phyloseq(): Add dna in refseq slot of a physeq object using taxa names and renames taxa using prefix_taxa_names and number (default Taxa_1, Taxa_2 ...)

plot_complexity_pq(): Plot kmer complexity of references sequences of a phyloseq object

plot_refseq_extremity_pq(): Plot the nucleotide proportion at both extremity of the sequences

plot_refseq_pq(): Plot the nucleotide proportion of references sequences

plot_seq_ratio_pq(): A diagnostic plot of the number of sequences per samples

Explore phyloseq object

alpha-diversity

accu_plot(): Plot accumulation curves for phyloseq-class object

accu_plot_balanced_modality(): Plot accumulation curves with balanced modality and depth rarefaction

accu_samp_threshold(): Compute the number of sequence to obtain a given proportion of ASV in accumulation curves

ggbetween_pq(): Box/Violin plots for between-subjects comparisons of Hill Number

ggscatt_pq(): Scatterplot with marginal distributions and statistical results against Hill diversity of phyloseq object

glmutli_pq(): Automated model selection and multimodel inference with (G)LMs for phyloseq

hill_curves_pq(): Hill Diversities and Corresponding Accumulation Curves for phyloseq

hill_pq(): Graphical representation of hill number 0, 1 and 2 across a factor

hill_test_rarperm_pq(): Test multiple times effect of factor on Hill diversity with different rarefaction even depth

hill_tuckey_pq(): Calculate hill number and compute Tuckey post-hoc test

iNEXT_pq(): iNterpolation and EXTrapolation of Hill numbers (with iNEXT)

beta-diversity

adonis_pq(): Permanova on a phyloseq object

adonis_rarperm_pq(): Permanova (adonis) on permutations of rarefaction even depth

biplot_pq(): Visualization of two samples for comparison

circle_pq(): Plot OTU circle for phyloseq-class object

compare_pairs_pq(): Compare samples in pairs using diversity and number of ASV including shared ASV.

formattable_pq(): Create a visualization table to describe taxa distribution across a modality

ggvenn_pq(): Venn diagram of phyloseq-class object using ggVennDiagram::ggVennDiagram function

graph_test_pq(): Performs graph-based permutation tests on phyloseq object

LCBD_pq(): Compute and test local contributions to beta diversity (LCBD) of samples

multi_biplot_pq(): Visualization of a collection of couples of samples for comparison

plot_LCBD_pq(): Plot and test local contributions to beta diversity (LCBD) of samples

plot_SCBD_pq(): Plot species contributions to beta diversity (SCBD) of samples

plot_tsne_pq(): Plot a tsne low dimensional representation of a phyloseq object

plot_var_part_pq(): Plot the partition the variation of a phyloseq object

ridges_pq(): Ridge plot of a phyloseq object

SRS_curve_pq(): Scaling with ranked subsampling (SRS) curve of phyloseq object

tsne_pq(): Compute tSNE position of samples from a phyloseq object

umap_pq(): Computes a manifold approximation and projection (UMAP) for phyloseq object

upset_pq(): Make upset plot for phyloseq object.

upset_test_pq(): Test for differences between intersections

var_par_pq(): Partition the Variation of a phyloseq object by 2, 3, or 4 Explanatory Matrices

var_par_rarperm_pq(): Partition the Variation of a phyloseq object with rarefaction permutations

venn_pq(): Venn diagram of phyloseq-class object

Differential abundance analysis

ancombc_pq(): Run ANCOMBC2 on phyloseq object

multipatt_pq(): Test and plot multipatt result

phyloseq_to_edgeR(): Convert phyloseq OTU count data into DGEList for edgeR package

plot_ancombc_pq(): Plot ANCOMBC2 result for phyloseq object

plot_deseq2_pq(): Plot DESeq2 results for a phyloseq or a DESeq2 object.

plot_edgeR_pq(): Plot edgeR results for a phyloseq or a edgeR object.

plot_mt(): Plot the result of a mt test phyloseq::mt()

signif_ancombc(): Filter ancombc_pq results

Taxonomy

ggaluv_pq(): Alluvial plot for taxonomy and samples factor vizualisation

krona(): Make Krona files using KronaTools.

merge_krona(): Merge Krona files using KronaTools.

multitax_bar_pq(): Plot taxonomic distribution across 3 taxonomic levels and optionally one sample factor

physeq_or_string_to_dna(): Return a DNAStringSet object from either a character vector of DNA sequences or the refseq slot of a phyloseq-class object

plot_guild_pq(): Plot information about Guild from tax_table slot previously created with add_funguild_info()

plot_tax_pq(): Plot taxonomic distribution in function of a factor with stacked bar in %

rotl_pq(): rotl wrapper for phyloseq data

sankey_pq(): Sankey plot of phyloseq-class object

search_exact_seq_pq(): Search for exact matching of sequences

tax_bar_pq(): Plot the distribution of sequences or ASV in one taxonomic levels

tax_datatable(): Make a datatable with the taxonomy of a phyloseq-class object

treemap_pq(): Plot treemap of 2 taxonomic levels

vs_search_global(): Search for a list of sequence in a fasta file against physeq reference sequences using vsearch

Zoom on given taxa

distri_1_taxa(): Distribution of sequences across a factor for one taxon

taxa_only_in_one_level(): Show taxa which are present in only one given level of a modality

Improve reproducibility using targets pipeline

Processing fastq files

cutadapt_remove_primers(): Remove primers using cutadapt

filter_trim(): A wrapper of the function dada2::filterAndTrim() to use in targets pipeline

list_fastq_files(): List fastq files

subsample_fastq(): Subsample a fastq file copying the n_seq first sequences in a given folder

Import/export phyloseq object

read_pq(): Read phyloseq object from multiple csv tables and a phylogenetic tree in Newick format.

save_pq(): A wrapper of write_pq to save in all three possible formats

write_pq(): Save phyloseq object in the form of multiple csv tables.

Track info along pipeline

count_seq(): Count sequences in fasta or fastq file

track_wkflow(): Track the number of reads (= sequences), samples and cluster (e.g. ASV) from various objects including dada-class and derep-class.

track_wkflow_samples(): Track the number of reads (= sequences), samples and cluster (e.g. ASV) for each sample

Sample data management

psmelt_samples_pq(): Build a sample information tibble from physeq object

rename_samples(): Rename the samples of a phyloseq slot

rename_samples_otu_table(): Rename samples of an otu_table

sample_data_with_new_names(): Load sample data from file and rename samples using names of samples and an optional order

Taxonomy management

simplify_taxo(): Simplify taxonomy by removing some unused characters such as "k__"

reorder_taxa_pq(): Reorder taxa in otu_table/tax_table/refseq slot of a phyloseq object

Datasets

data_fungi: Fungal OTU in phyloseq format

data_fungi_mini: Fungal OTU in phyloseq format

data_fungi_sp_known: Fungal OTU in phyloseq format

Tengeler2020_pq: This tutorial explores the dataset from Tengeler et al. (2020) available in the mia package. obtained using mia::makePhyloseqFromTreeSE(Tengeler2020)

Other utilities

Color management

fac2col(): Translates a factor into colors.

funky_color(): Funky palette color

transp(): Adds transparency to a vector of colors

Fasta taxonomic database

format2dada2(): Format a fasta database in dada2 format

format2dada2_species(): Format a fasta database in dada2 format for Species assignment

format2sintax(): Format a fasta database in sintax format

File management

get_file_extension(): Get the extension of a file

External software management

is_cutadapt_installed(): Test if cutadapt is installed.

is_falco_installed(): Test if falco is installed.

is_krona_installed(): Test if krona is installed.

is_mumu_installed(): Test if mumu is installed.

is_swarm_installed(): Test if swarm is installed.

is_vsearch_installed(): Test if vsearch is installed.

Plot management

multiplot(): Multiple plot function

no_legend(): Discard legend in ggplot2

Variable management

diff_fct_diff_class(): Compute different functions for different class of vector.

perc(): Convert a value (or a fraction x/y) in percentage

unique_or_na(): Get the unique value in x or NA if none

Others

all_object_size(): List the size of all objects of the GlobalEnv.

are_modality_even_depth(): Test if the mean number of sequences by samples is link to the modality of a factor

dist_bycol(): Compute paired distances among matrix (e.g. otu_table)

dist_pos_control(): Calculate ecological distance among positive controls vs distance for all samples

MiscMetabar-package: MiscMetabar package

Deprecated

physeq_graph_test(): Deprecated function(s) in the MiscMetabar package