Miscellaneous Functions for Metabarcoding Analysis

Documentation for package ‘MiscMetabar’ version 0.12.1

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'MiscMetabar' package

-- A --

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
add_blast_info	Add information from 'blast_pq()' to the 'tax_table' slot of a _phyloseq_ object
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 ...)
add_funguild_info	Add information about Guild for FUNGI the FUNGuild databse
add_info_to_sam_data	Add information to sample_data slot of a phyloseq-class object
add_new_taxonomy_pq	Add new taxonomic rank to a phyloseq object.
adonis_phyloseq	Deprecated function(s) in the MiscMetabar package
adonis_pq	Permanova on a phyloseq object
adonis_rarperm_pq	Permanova (adonis) on permutations of rarefaction even depth
all_object_size	List the size of all objects of the GlobalEnv.
ancombc_pq	Run ANCOMBC2 on phyloseq object
are_modality_even_depth	Test if the mean number of sequences by samples is link to the modality of a factor
assign_idtaxa	A wrapper of 'IdTaxa'
assign_sintax	Assign Taxonomy using Sintax algorithm of Vsearch
assign_vsearch_lca	Assign taxonomy using LCA _à la_ stampa
asv2otu	Recluster sequences of an object of class 'physeq' or a list of DNA sequences
as_binary_otu_table	Transform the otu_table of a 'phyloseq-class' object into a 'phyloseq-class' object with a binary otu_table.

-- B --

biplot_physeq	Deprecated function(s) in the MiscMetabar package
biplot_pq	Visualization of two samples for comparison
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.
build_phytree_pq	Build phylogenetic trees from refseq slot of a phyloseq object

-- C --

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
circle_pq	Plot OTU circle for 'phyloseq-class' object
clean_physeq	Deprecated function(s) in the MiscMetabar package
clean_pq	Clean phyloseq object by removing empty samples and taxa
compare_pairs_pq	Compare samples in pairs using diversity and number of ASV including shared ASV.
count_seq	Count sequences in fasta or fastq file
cutadapt_remove_primers	Remove primers using cutadapt

-- D --

data_fungi	Fungal OTU in phyloseq format
data_fungi_mini	Fungal OTU in phyloseq format
data_fungi_sp_known	Fungal OTU in phyloseq format
diff_fct_diff_class	Compute different functions for different class of vector.
distri_1_taxa	Distribution of sequences across a factor for one taxon
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

-- F --

fac2col	Translates a factor into colors.
filter_asv_blast	Filter undesirable taxa using blast against a custom database.
filter_taxa_blast	Filter undesirable taxa using blast against a custom database.
filter_trim	A wrapper of the function 'dada2::filterAndTrim()' to use in targets pipeline
filt_taxa_pq	Filter taxa of a phyloseq object based on the minimum number of sequences/samples
formattable_pq	Create a visualization table to describe taxa distribution across a modality
funguild_assign	Assign Guilds to Organisms Based on Taxonomic Classification
funky_color	Funky palette color

-- G --

get_file_extension	Get the extension of a file
get_funguild_db	Retrieve the FUNGuild database
ggaluv_pq	Alluvial plot for taxonomy and samples factor vizualisation
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
ggVenn_phyloseq	Deprecated function(s) in the MiscMetabar package
ggvenn_pq	Venn diagram of 'phyloseq-class' object using 'ggVennDiagram::ggVennDiagram' function
glmutli_pq	Automated model selection and multimodel inference with (G)LMs for phyloseq
graph_test_pq	Performs graph-based permutation tests on phyloseq object

-- H --

hill_curves_pq	Hill Diversities and Corresponding Accumulation Curves for phyloseq
hill_phyloseq	Deprecated function(s) in the MiscMetabar package
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_phyloseq	Deprecated function(s) in the MiscMetabar package
hill_tuckey_pq	Calculate hill number and compute Tuckey post-hoc test

-- I --

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

-- K --

krona

Make Krona files using KronaTools.

-- L --

LCBD_pq	Compute and test local contributions to beta diversity (LCBD) of samples
learn_idtaxa	A wrapper of 'DECIPHER::LearnTaxa()'
list_fastq_files	List fastq files
lulu	Post Clustering Curation of Amplicon Data.
lulu_phyloseq	Deprecated function(s) in the MiscMetabar package
lulu_pq	Lulu reclustering of class 'physeq'

-- M --

merge_krona	Merge Krona files using KronaTools.
merge_samples2	Merge samples by a sample variable or factor
merge_samples2-method	Merge samples by a sample variable or factor
merge_taxa_vec	Merge taxa in groups (vectorized version)
merge_taxa_vec-method	Merge taxa in groups (vectorized version)
MiscMetabar-deprecated	Deprecated function(s) in the MiscMetabar package
multipatt_pq	Test and plot multipatt result
multiplot	Multiple plot function
multitax_bar_pq	Plot taxonomic distribution across 3 taxonomic levels and optionally one sample factor
multi_biplot_pq	Visualization of a collection of couples of samples for comparison
mumu_pq	MUMU reclustering of class 'physeq'

-- N --

normalize_prop_pq	Normalize OTU table using samples depth
no_legend	Discard legend in ggplot2

-- O --

otu_circle

Deprecated function(s) in the MiscMetabar package

-- P --

perc	Convert a value (or a fraction x/y) in percentage
phyloseq_to_edgeR	Convert phyloseq OTU count data into DGEList for edgeR package
physeq_graph_test	Deprecated function(s) in the MiscMetabar package
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_ancombc_pq	Plot ANCOMBC2 result for phyloseq object
plot_complexity_pq	Plot kmer complexity of references sequences of a phyloseq object
plot_deseq2_phyloseq	Deprecated function(s) in the MiscMetabar package
plot_deseq2_pq	Plot DESeq2 results for a phyloseq or a DESeq2 object.
plot_edgeR_phyloseq	Deprecated function(s) in the MiscMetabar package
plot_edgeR_pq	Plot edgeR results for a phyloseq or a edgeR object.
plot_guild_pq	Plot information about Guild from tax_table slot previously created with 'add_funguild_info()'
plot_LCBD_pq	Plot and test local contributions to beta diversity (LCBD) of samples
plot_mt	Plot the result of a mt test 'phyloseq::mt()'
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_SCBD_pq	Plot species contributions to beta diversity (SCBD) of samples
plot_tax_pq	Plot taxonomic distribution in function of a factor with stacked bar in %
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
postcluster_pq	Recluster sequences of an object of class 'physeq' or a list of DNA sequences
psmelt_samples_pq	Build a sample information tibble from physeq object

-- R --

rarefy_sample_count_by_modality	Rarefy (equalize) the number of samples per modality of a factor
read_phyloseq	Deprecated function(s) in the MiscMetabar package
read_pq	Read phyloseq object from multiple csv tables and a phylogenetic tree in Newick format.
rename_samples	Rename the samples of a phyloseq slot
rename_samples_otu_table	Rename samples of an otu_table
reorder_taxa_pq	Reorder taxa in otu_table/tax_table/refseq slot of a phyloseq object
ridges_pq	Ridge plot of a phyloseq object
rotl_pq	rotl wrapper for phyloseq data

-- S --

sample_data_with_new_names	Load sample data from file and rename samples using names of samples and an optional order
sam_data_matching_names	Match sample names from sam_data and fastq files
sankey_phyloseq	Deprecated function(s) in the MiscMetabar package
sankey_pq	Sankey plot of 'phyloseq-class' object
save_pq	A wrapper of write_pq to save in all three possible formats
search_exact_seq_pq	Search for exact matching of sequences
select_one_sample	Select one sample from a physeq object
select_taxa	Select a subset of taxa in a specified order where possible
select_taxa-method	Select a subset of taxa in a specified order where possible
signif_ancombc	Filter ancombc_pq results
simplify_taxo	Simplify taxonomy by removing some unused characters such as "k__"
SRS_curve_pq	Scaling with ranked subsampling (SRS) curve of phyloseq object
subsample_fastq	Subsample a fastq file copying the n_seq first sequences in a given folder
subset_samples_pq	Subset samples using a conditional boolean vector.
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
summary_plot_phyloseq	Deprecated function(s) in the MiscMetabar package
summary_plot_pq	Summarize a 'phyloseq-class' object using a plot.
swarm_clustering	Re-cluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using SWARM

-- T --

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
taxa_only_in_one_level	Show taxa which are present in only one given level of a modality
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
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
Tengeler2020_pq	This tutorial explores the dataset from Tengeler et al. (2020) available in the 'mia' package. obtained using 'mia::makePhyloseqFromTreeSE(Tengeler2020)'
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
transp	Adds transparency to a vector of colors
treemap_pq	Plot treemap of 2 taxonomic levels
tsne_pq	Compute tSNE position of samples from a phyloseq object

-- U --

umap_pq	Computes a manifold approximation and projection (UMAP) for phyloseq object
unique_or_na	Get the unique value in x or NA if none
upset_pq	Make upset plot for phyloseq object.
upset_test_pq	Test for differences between intersections

-- V --

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_phyloseq	Deprecated function(s) in the MiscMetabar package
venn_pq	Venn diagram of 'phyloseq-class' object
verify_pq	Verify the validity of a phyloseq object
vsearch_clustering	Recluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using vsearch software
vs_search_global	Search for a list of sequence in a fasta file against physeq reference sequences using vsearch

-- W --

write_phyloseq	Deprecated function(s) in the MiscMetabar package
write_pq	Save phyloseq object in the form of multiple csv tables.