function_list.md

In leffj/mctoolsr: Microbial Community Data Analysis Tools

mctoolsr Function List

Dissimilarity calculation and manipulation

add_metadata_to_dm_clmns(): Add metadata to an additional column in column formatted dissimilarities dataframe

calc_dm(): Calculate a dissimilarity matrix from a taxa table

calc_mean_dissimilarities(): Calculate mean dissimilarities using a metadata factor

calc_ordination(): Calculate Point Coordinates in an Ordination

calc_pairwise_permanovas(): Calculate pairwise PERMANOVA results

convert_dm_to_3_column(): Convert dissimilarity matrix to 3 column format

filter_dm(): Filter samples from dissimilarity matrix

Diversity

calc_diversity(): Calculate diversity values

Load external data

load_2_dms(): Load two dissimilarity matrices for use with mctoolsr

load_dm(): Load a dissimilarity matrix for use with mctoolsr

load_taxa_table(): Load a taxa table for use with mctoolsr

load_tree(): Load in a phylogenetic tree

Misc analyses

calc_prop_shared_taxa(): Calculate mean proportions of shared taxa between paired samples

calc_prop_taxa_from_sample_type(): Calculate the proportion of taxa in a set of samples that are also observed in another sample type

calc_taxa_changes(): Calculate the changes in taxonomic relative abundances compared to controls

core_taxa(): Determine taxa that are common (core) across sample types

return_top_taxa(): Return the most abundant taxa in a dataset

Phylogeny

filter_tree(): Filter tips in phylogenetic tree

Plots

plot_dendrogram(): Generate a dendrogram based on a dissimilarity matrix

plot_diversity(): Plot diversity values

plot_nmds(): Generate an NMDS Plot Quickly

plot_ordination(): Generate an Ordination Plot

plot_taxa_bars(): Plot stacked bar plots to represent taxa compompositions

plot_ts_heatmap(): Plot taxa summary heatmap

plot_venn_diagram(): Plot Venn Diagrams

Taxa table manipulation

calc_taxa_means(): Calculate mean taxa values across a specified factor

export_taxa_table(): Export a taxa table as a text file

filter_data(): Filter samples from dataset

filter_samples_by_counts(): Filter samples from a dataset based on number of sequences

match_datasets(): Match up samples from two datasets

rename_samples(): Rename samples in an mctoolsr dataset

Taxa table normalization

convert_to_relative_abundances(): Convert taxa table to relative abundances

single_rarefy(): Rarefy samples in a taxa table

Taxonomy-based analyses

collapse_taxonomy(): Collapse taxonomy dataframe to character vector

filter_taxa_from_input(): Filter taxa from a loaded dataset

filter_taxa_from_table(): Filter taxa from an individual taxa summary table

summarize_taxonomy(): Calculate values for coarser taxonomic groupings

taxa_summary_by_sample_type(): Further summarize output from summarize_taxonomy by sample type

leffj/mctoolsr documentation built on Aug. 5, 2022, 1:27 a.m.