Man pages for leffj/mctoolsr
Microbial Community Data Analysis Tools
| add_metadata_to_dm_clmns | Add metadata to an additional column in column formatted... |
| calc_diversity | Calculate diversity values |
| 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 |
| calc_prop_shared_taxa | Calculate mean proportions of shared taxa between paired... |
| calc_prop_taxa_from_sample_type | Calculate the proportion of taxa in a set of samples that are... |
| calc_taxa_changes | Calculate the changes in taxonomic relative abundances... |
| calc_taxa_means | Calculate mean taxa values across a specified factor |
| collapse_taxonomy | Collapse taxonomy dataframe to character vector |
| convert_dm_to_3_column | Convert dissimilarity matrix to 3 column format |
| convert_to_relative_abundances | Convert taxa table to relative abundances |
| core_taxa | Determine taxa that are common (core) across sample types |
| export_otu_table | Export an OTU table as a text file [DEPRECATED] |
| export_taxa_table | Export a taxa table as a text file |
| filter_data | Filter samples from dataset |
| filter_dm | Filter samples from dissimilarity matrix |
| filter_samples_by_counts | Filter samples from a dataset based on number of sequences |
| filter_taxa_from_input | Filter taxa from a loaded dataset |
| filter_taxa_from_table | Filter taxa from an individual taxa summary table |
| filter_tree | Filter tips in phylogenetic tree |
| fruits_veggies | Fruits and Vegetables Bacterial Community Data |
| fruits_veggies_OTUs_tree | Fruits and Vegetables Bacterial Phylotype Tree |
| 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 |
| match_datasets | Match up samples from two datasets |
| mctoolsr | Microbial Community Data Analysis Tools |
| 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 |
| rename_samples | Rename samples in an mctoolsr dataset |
| return_top_taxa | Return the most abundant taxa in a dataset |
| single_rarefy | Rarefy samples in a taxa table |
| summarize_taxonomy | Calculate values for coarser taxonomic groupings |
| sumtax_example_data | Taxa Summary from Produce Dataset |
| taxa_summary_by_sample_type | Further summarize output from summarize_taxonomy by sample... |
