Man pages for adrientaudiere/MiscMetabar
Miscellaneous Functions for Metabarcoding Analysis
| accu_plot | Plot accumulation curves for 'phyloseq-class' object |
| accu_plot_balanced_modality | Plot accumulation curves with balanced modality and depth... |
| accu_samp_threshold | Compute the number of sequence to obtain a given proportion... |
| add_blast_info | Add information from 'blast_pq()' to the 'tax_table' slot of... |
| add_dna_to_phyloseq | Add dna in 'refseq' slot of a 'physeq' object using taxa... |
| 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... |
| add_new_taxonomy_pq | Add new taxonomic rank to a phyloseq object. |
| 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... |
| as_binary_otu_table | Transform the otu_table of a 'phyloseq-class' object into a... |
| biplot_pq | Visualization of two samples for comparison |
| blast_pq | Blast all sequence of 'refseq' slot of a 'phyloseq-class'... |
| blast_to_derep | Blast some sequence against sequences from of a 'derep-class'... |
| blast_to_phyloseq | Blast some sequence against 'refseq' slot of a... |
| build_phytree_pq | Build phylogenetic trees from refseq slot of a phyloseq... |
| chimera_detection_vs | Detect for chimera taxa using vsearch |
| chimera_removal_vs | Search for a list of sequence in an object to remove chimera... |
| circle_pq | Plot OTU circle for 'phyloseq-class' object |
| clean_pq | Clean phyloseq object by removing empty samples and taxa |
| compare_pairs_pq | Compare samples in pairs using diversity and number of ASV... |
| count_seq | Count sequences in fasta or fastq file |
| cutadapt_remove_primers | Remove primers using cutadapt |
| 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. |
| dist_bycol | Compute paired distances among matrix (e.g. otu_table) |
| dist_pos_control | Calculate ecological distance among positive controls vs... |
| distri_1_taxa | Distribution of sequences across a factor for one taxon |
| fac2col | Translates a factor into colors. |
| filter_asv_blast | Filter undesirable taxa using blast against a custom... |
| filter_trim | A wrapper of the function 'dada2::filterAndTrim()' to use in... |
| formattable_pq | Create a visualization table to describe taxa distribution... |
| funguild_assign | Assign Guilds to Organisms Based on Taxonomic Classification |
| funky_color | Funky palette color |
| 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... |
| ggscatt_pq | Scatterplot with marginal distributions and statistical... |
| ggvenn_pq | Venn diagram of 'phyloseq-class' object using... |
| glmutli_pq | Automated model selection and multimodel inference with... |
| graph_test_pq | Performs graph-based permutation tests on phyloseq object |
| hill_pq | Graphical representation of hill number 0, 1 and 2 across a... |
| hill_test_rarperm_pq | Test multiple times effect of factor on Hill diversity with... |
| hill_tuckey_pq | Calculate hill number and compute Tuckey post-hoc test |
| 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. |
| krona | Make Krona files using KronaTools. |
| LCBD_pq | Compute and test local contributions to beta diversity (LCBD)... |
| list_fastq_files | List fastq files |
| lulu | Post Clustering Curation of Amplicon Data. |
| lulu_pq | Lulu reclustering of class 'physeq' |
| merge_krona | Merge Krona files using KronaTools. |
| merge_samples2 | Merge samples by a sample variable or factor |
| merge_taxa_vec | Merge taxa in groups (vectorized version) |
| MiscMetabar-deprecated | Deprecated function(s) in the MiscMetabar package |
| MiscMetabar-package | 'MiscMetabar' package |
| multi_biplot_pq | Visualization of a collection of couples of samples for... |
| multipatt_pq | Test and plot multipatt result |
| multiplot | Multiple plot function |
| multitax_bar_pq | Plot taxonomic distribution across 3 taxonomic levels and... |
| mumu_pq | MUMU reclustering of class 'physeq' |
| normalize_prop_pq | Normalize OTU table using samples depth |
| perc | Convert a value (or a fraction x/y) in percentage |
| phyloseq_to_edgeR | Convert phyloseq OTU count data into DGEList for edgeR... |
| physeq_or_string_to_dna | Return a DNAStringSet object from either a character vector... |
| 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_guild_pq | Plot information about Guild from tax_table slot previously... |
| plot_LCBD_pq | Plot and test local contributions to beta diversity (LCBD) of... |
| plot_mt | Plot the result of a mt test 'phyloseq::mt()' |
| plot_SCBD_pq | Plot species contributions to beta diversity (SCBD) of... |
| plot_tax_pq | Plot taxonomic distribution in function of a factor with... |
| plot_tsne_pq | Plot a tsne low dimensional representation of a phyloseq... |
| 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... |
| psmelt_samples_pq | Build a sample information tibble from physeq object |
| rarefy_sample_count_by_modality | Rarefy (equalize) the number of samples per modality of a... |
| read_pq | Read phyloseq object from multiple csv tables and a... |
| 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... |
| ridges_pq | Ridge plot of a phyloseq object |
| rotl_pq | rotl wrapper for phyloseq data |
| sample_data_with_new_names | Load sample data from file and rename samples using names of... |
| 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-methods | 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... |
| SRS_curve_pq | Scaling with ranked subsampling (SRS) curve of phyloseq... |
| subsample_fastq | Subsample a fastq file copying the n_seq first sequences in a... |
| 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_pq | Summarize a 'phyloseq-class' object using a plot. |
| swarm_clustering | Re-cluster sequences of an object of class 'physeq' or... |
| taxa_as_columns | Force taxa to be in columns in the otu_table of a physeq... |
| taxa_as_rows | Force taxa to be in columns in the otu_table of a physeq... |
| taxa_only_in_one_level | Show taxa which are present in only one given level of a... |
| tax_bar_pq | Plot the distribution of sequences or ASV in one taxonomic... |
| tax_datatable | Make a datatable with the taxonomy of a 'phyloseq-class'... |
| tbl_sum_samdata | Summarize information from sample data in a table |
| Tengeler2020_pq | This tutorial explores the dataset from Tengeler et al.... |
| track_wkflow | Track the number of reads (= sequences), samples and cluster... |
| track_wkflow_samples | Track the number of reads (= sequences), samples and cluster... |
| 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 |
| 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 |
| var_par_pq | Partition the Variation of a phyloseq object by 2, 3, or 4... |
| var_par_rarperm_pq | Partition the Variation of a phyloseq object with rarefaction... |
| 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... |
| vs_search_global | Search for a list of sequence in a fasta file against physeq... |
| write_pq | Save phyloseq object in the form of multiple csv tables. |
