R: Miscellaneous Functions for Metabarcoding Analysis

# Miscellaneous Functions for Metabarcoding Analysis

## Documentation for package ‘MiscMetabar’ version 0.16.8

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D F G H I K L M N O P R S T U V W

MiscMetabar-package | '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
aldex_pq | Run Aldex on a phyloseq object
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_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_mmseqs2 | Assign taxonomy using MMseqs2
assign_sintax | Assign Taxonomy using Sintax algorithm of Vsearch
assign_vsearch_lca | Assign taxonomy using LCA
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
css_pq | Cumulative Sum Scaling (CSS) normalization of a phyloseq object
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
divent_hill_matrix_pq | Compute Hill diversity numbers for all samples in an OTU table

## -- 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
filt_taxa_wo_NA | Filter taxa by cleaning taxa with NA at given taxonomic rank(s)
find_mmseqs2 | Find the MMseqs2 binary
find_vsearch | Find the vsearch binary
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
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
gmpr_pq | Geometric Mean of Pairwise Ratios (GMPR) normalization of a phyloseq object
graph_test_pq | Performs graph-based permutation tests on phyloseq object

## -- H --

hill_acc_pq | Hill diversity accumulation curve for a phyloseq object (default: q = 1)
hill_bar_pq | Bar plot of Hill diversity with SE, jittered points, and Kruskal-Wallis test
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)
install_mmseqs2 | Install MMseqs2 from GitHub releases
install_vsearch | Install vsearch binary
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_mmseqs2_installed | Check whether MMseqs2 is installed and callable
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()'
lefser_pq | Run LEfSe on a phyloseq object
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 --

mcknight_residuals_pq | Depth-robust alpha diversity residuals (McKnight / Mikryukov)
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
mmseqs2_clustering | Recluster sequences of a phyloseq object or cluster a list of DNA sequences using MMseqs2 software
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_ordination_pq | A wrapper of plot_ordination with vegan distance matrix
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_seq_ratio_pq | A diagnostic plot of the number of sequences per 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
profile_hill_pq | Hill diversity profile for a phyloseq object
psmelt_samples_pq | Build a sample information tibble from physeq object

## -- R --

rarefy_even_depth_pq | Rarefy a phyloseq object to even sequencing depth
rarefy_pq | Rarefy a phyloseq object, optionally averaging over repetitions
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_distinct_colors | Reorder fill and color scales to maximize perceptual contrast between adjacent segments
reorder_taxa_pq | Reorder taxa in otu_table/tax_table/refseq slot of a phyloseq object
resolve_vector_ranks | Resolve conflict in a vector of taxonomy values
ridges_pq | Ridge plot of a phyloseq object
ridges_sam_pq | Ridges plot of sample distribution across taxa
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
srs_pq | Scaling with Ranked Subsampling (SRS) normalization of a 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)'
tmm_pq | Trimmed Mean of M-values (TMM) normalization of a phyloseq object
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
transform_pq | Unified dispatcher for all OTU-table transformations and normalisations
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
unwanted_tax_patterns | Default patterns for unwanted taxonomic values
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
verify_tax_table | Verify the taxonomy table of a phyloseq object
vsearch_clustering | Recluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using vsearch software
vst_pq | Variance Stabilizing Transformation of a phyloseq object (DESeq2)
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.