Man pages for leffj/mctoolsr
Microbial Community Data Analysis Tools

add_metadata_to_dm_clmnsAdd metadata to an additional column in column formatted...
calc_diversityCalculate diversity values
calc_dmCalculate a dissimilarity matrix from a taxa table
calc_mean_dissimilaritiesCalculate mean dissimilarities using a metadata factor
calc_ordinationCalculate Point Coordinates in an Ordination
calc_pairwise_permanovasCalculate pairwise PERMANOVA results
calc_prop_shared_taxaCalculate mean proportions of shared taxa between paired...
calc_prop_taxa_from_sample_typeCalculate the proportion of taxa in a set of samples that are...
calc_taxa_changesCalculate the changes in taxonomic relative abundances...
calc_taxa_meansCalculate mean taxa values across a specified factor
collapse_taxonomyCollapse taxonomy dataframe to character vector
convert_dm_to_3_columnConvert dissimilarity matrix to 3 column format
convert_to_relative_abundancesConvert taxa table to relative abundances
core_taxaDetermine taxa that are common (core) across sample types
export_otu_tableExport an OTU table as a text file [DEPRECATED]
export_taxa_tableExport a taxa table as a text file
filter_dataFilter samples from dataset
filter_dmFilter samples from dissimilarity matrix
filter_samples_by_countsFilter samples from a dataset based on number of sequences
filter_taxa_from_inputFilter taxa from a loaded dataset
filter_taxa_from_tableFilter taxa from an individual taxa summary table
filter_treeFilter tips in phylogenetic tree
fruits_veggiesFruits and Vegetables Bacterial Community Data
fruits_veggies_OTUs_treeFruits and Vegetables Bacterial Phylotype Tree
load_2_dmsLoad two dissimilarity matrices for use with mctoolsr
load_dmLoad a dissimilarity matrix for use with mctoolsr
load_taxa_tableLoad a taxa table for use with mctoolsr
load_treeLoad in a phylogenetic tree
match_datasetsMatch up samples from two datasets
mctoolsrMicrobial Community Data Analysis Tools
plot_dendrogramGenerate a dendrogram based on a dissimilarity matrix
plot_diversityPlot diversity values
plot_nmdsGenerate an NMDS Plot Quickly
plot_ordinationGenerate an Ordination Plot
plot_taxa_barsPlot stacked bar plots to represent taxa compompositions
plot_ts_heatmapPlot taxa summary heatmap
plot_venn_diagramPlot Venn Diagrams
rename_samplesRename samples in an mctoolsr dataset
return_top_taxaReturn the most abundant taxa in a dataset
single_rarefyRarefy samples in a taxa table
summarize_taxonomyCalculate values for coarser taxonomic groupings
sumtax_example_dataTaxa Summary from Produce Dataset
taxa_summary_by_sample_typeFurther summarize output from summarize_taxonomy by sample...
leffj/mctoolsr documentation built on Nov. 30, 2017, 1:31 a.m.