Table 2.
Table of exported functions and their descriptions available through the animalcules R package
| Data and interface | |
| run_animalcules() | Initiates a local instance of the animalcules Shiny application |
| Data summary and manipulation | |
| filter_summary_bar_density() | Visualize sample/microbe data with a bar plot (categorical) or density plot (continuous) |
| filter_summary_pie_box() | Visualize sample/microbe data with a pie chart (categorical) or box plot (continuous) |
| filter_categorize() | Convert continuous variables into a various number of factors |
| counts_to_logcpm() | Covert counts table to a log counts per million table |
| counts_to_relabu() | Covert counts table to a relative abundances table |
| upsample_counts() | Up-sample counts table to a higher taxon level |
| find_taxonomy() | Find taxonomy for unlimited ids |
| find_taxon_mat() | Find taxonomy information matrix for unlimited ids |
| mae_pick_samples() | Isolate or discard samples from a multi-assay experiment object |
| mae_pick_organisms() | Isolate or discard microbes from a multi-assay experiment object |
| Sample level visualization | |
| relabu_barplot() | Generate stacked bar plots of sample and group level microbe relative abundances |
| relabu_boxplot() | Generate box plots comparing organism prevalence across groups of samples |
| relabu_heatmap() | Generate a sample by microbe heatmap of counts |
| dimred_pca() | Return a 2D/3D scatter plot for dimensionality reduction through PCA |
| dimred_pcoa() | Return a 2D/3D scatter plot for dimensionality reduction through PCoA |
| dimred_umap() | Return a 2D/3D scatter plot for dimensionality reduction through UMAP |
| dimred_tsne() | Return a 2D/3D scatter plot for dimensionality reduction through t-SNE |
| Alpha and beta diversity | |
| diversities() | Return alpha diversity |
| do_alpha_div_test() | Compute various statistical tests for alpha diversity |
| alpha_div_boxplot() | Generate box plots comparing alpha diversity across groups of samples |
| diversity_beta_test() | Compute various statistical tests for beta diversity |
| diversity_beta_boxplot() | Generate box plots comparing beta diversity across groups of samples |
| diversity_beta_heatmap() | Generate a heatmap comparing beta diversity across groups of samples |
| Differential abundance analysis | |
| differential_abundance() | Performs differential abundance analysis across groups of samples |
| Biomarker discovery | |
| find_biomarker() | Identifies microbes as potential biomarkers for groups of samples |