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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
verify_pq()
Verify the validity of a phyloseq object

Transform phyloseq object

Taxonomy

add_new_taxonomy_pq()
Add new taxonomic rank to a phyloseq object.
add_blast_info()
Add information from blast_pq() to the tax_table slot of a phyloseq object
blast_to_phyloseq()
Blast some sequence against refseq slot of a phyloseq-class object.
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.
filter_asv_blast()
Filter undesirable taxa using blast against a custom database.

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

Subset/merge taxa

subset_taxa_pq()
Subset taxa using a conditional named boolean vector.
subset_taxa_tax_control()
Subset taxa using a taxa control (e.g. truffle root tips) through 3 methods.
select_taxa()
Select a subset of taxa in a specified order where possible
merge_taxa_vec()
Merge taxa in groups (vectorized version)

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

asv2otu()
Recluster sequences of an object of class physeq or a list of DNA sequences
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
lulu_pq()
Lulu reclustering of class physeq
lulu()
Post Clustering Curation of Amplicon Data.
mumu_pq()
MUMU reclustering of class physeq

Remove chimera using vsearch

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

Sample data

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

Phylogenetic tree

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

Others

add_dna_to_phyloseq()
Add dna in refseq slot of a physeq object using taxa names and renames taxa using ASV_1, ASV_2, …
clean_pq()
Clean phyloseq object by removing empty samples and taxa

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_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 an 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
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
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
plot_var_part_pq()
Plot the partition the variation of a phyloseq object
venn_pq()
Venn diagram of phyloseq-class object

Differential abundance analysis

multipatt_pq()
Test and plot multipatt result
phyloseq_to_edgeR()
Convert phyloseq OTU count data into DGEList for edgeR package
plot_edgeR_pq()
Plot edgeR results for a phyloseq or a edgeR object.
plot_deseq2_pq()
Plot DESeq2 results for a phyloseq or a DESeq2 object.
plot_mt()
Plot the result of a mt test phyloseq::mt()
ancombc_pq()
Run ANCOMBC2 on phyloseq object
signif_ancombc()
Filter ancombc_pq results
plot_ancombc_pq()
Plot ANCOMBC2 result for phyloseq object

Taxonomy

ggaluv_pq()
Alluvial plot for taxonomy and samples factor vizualisation
heat_tree_pq()
Heat tree from metacoder package using tax_table slot
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 using complement, reverse and reverse-complement
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() 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

list_fastq_files()
List fastq files
filter_trim()
A wrapper of the function dada2::filterAndTrim() to use in targets pipeline
cutadapt_remove_primers()
Remove primers using cutadapt
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

rename_samples_otu_table()
Rename samples of an otu_table
rename_samples()
Rename the samples of a phyloseq slot
sample_data_with_new_names()
Load sample data from file and rename samples using names of samples and an optional order
psmelt_samples_pq()
Build a sample information tibble from physeq object

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_sp_known
Fungal OTU in phyloseq format
data_fungi_mini data_fungi_mini
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

funky_color()
Funky palette color
fac2col()
Translates a factor into colors.
transp()
Adds transparency to a vector of colors

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

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.
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
are_modality_even_depth()
Test if the mean number of sequences by samples is link to the modality of a factor
MiscMetabar-package
MiscMetabar package

Deprecated

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