Man pages for david-barnett/microViz
Microbiome Data Analysis and Visualization
| add_paths | Add paths connecting points on a ggplot scatterplot |
| adjacent_side | Simple heatmap helper to get a default adjacent side for... |
| anno_cat | Create colored rectangle annotations for categorical data |
| anno_cat_legend | Convenience function for generating a legend for anno_cat... |
| anno_sample | Helper to specify simple comp_heatmap annotation for other... |
| anno_sample_cat | Helper to specify comp_heatmap annotation for categorical... |
| anno_tax_box | Helper to specify heatmap annotation for showing taxa... |
| anno_tax_density | Helper to specify heatmap annotation for showing taxa... |
| anno_tax_prev | Helper to specify heatmap annotation for showing taxa... |
| anno_var_box | Helper to specify heatmap annotation for variable... |
| anno_var_density | Helper to specify heatmap annotation for variable... |
| anno_var_hist | Helper to specify heatmap annotation for variable... |
| check_otutable_is_counts | Internal helper for ps_counts |
| comp_barplot | Plot (grouped and ordered) compositional barplots |
| comp_heatmap | Draw heatmap of microbiome composition across samples |
| cor_heatmap | Microbe-to-sample-data correlation heatmap |
| cor_test | Simple wrapper around cor.test for y ~ x style formula input |
| deprecated-heatmap-annotations | DEPRECATED Heatmap annotations helpers |
| dist_bdisp | Wrapper for vegan::betadisper() |
| dist_calc | Calculate distances between pairs of samples in phyloseq... |
| dist_calc_seq | Calculate distances between sequential samples in... |
| distinct_palette | Colour palettes suitable for 20+ categories |
| dist_permanova | Calculate PERMANOVA after dist_calc() |
| heat_grid | set options for drawing gridlines on heatmaps |
| heat_numbers | Aesthetic settings for drawing numbers on heatmap tiles |
| heat_palette | Easy palettes for ComplexHeatmap |
| ibd | IBD study data in phyloseq object. |
| microViz | microViz: microbiome data analysis and visualization |
| models2stats | Extract statistics from taxatree_models or tax_model output |
| new_psExtraInfo | Constructor for psExtraInfo list objects (internal use) |
| new_psExtraOrdInfo | Constructor for info list class used in ord_info element of... |
| ord_arrows | Create ordination plot vector styling lists |
| ord_calc | Ordinate samples (arrange by similarity in multiple... |
| ord_explore | Interactively explore microbial compositions of ordinated... |
| Ordination-labels | Create list for ord_plot() *_lab_style arguments |
| ordination-sorting-samples | Sort phyloseq samples by ordination axes scores |
| ordination-sorting-taxa | Order taxa in phyloseq by their loading vectors |
| ord_plot | Customisable ggplot2 ordination plot |
| ord_plot_iris | Circular compositional barplot sorted by ordination angle |
| ord_plot-label-helpers | Helpers for ord_plot label adjustments |
| phyloseq_validate | Check for (and fix) common problems with phyloseq objects |
| pipe | Pipe operator |
| prev | Calculate prevalence from numeric vector |
| ps_arrange | Arrange samples in phyloseq by sample_data variables or taxon... |
| ps_calc_diversity | Calculate diversity index and add to phyloseq sample data |
| ps_calc_dominant | Calculate dominant taxon in each phyloseq sample |
| ps_calc_richness | Calculate richness estimate and add to phyloseq sample data |
| ps_counts | Get phyloseq with counts if available |
| ps_dedupe | De-duplicate phyloseq samples |
| ps_drop_incomplete | Deselect phyloseq samples with sample_data missings |
| psExtra-accessors | Extract elements from psExtra class |
| psExtra-class | Define psExtra class S4 object |
| psExtraInfo | Print method for psExtraInfo object |
| ps_filter | Filter phyloseq samples by sample_data variables |
| ps_join | Join a dataframe to phyloseq sample data |
| ps_melt | Melt phyloseq data object into large data.frame (tibble) |
| ps_mutate | Modify or compute new sample_data in phyloseq object |
| ps_otu2samdat | Copy phyloseq otu_table data to sample_data |
| ps_reorder | Set order of samples in phyloseq object |
| ps_select | Select phyloseq sample_data using dplyr::select syntax |
| ps_seriate | Arrange samples in a phyloseq by microbiome similarity |
| samdatAsDataframe | Internal helper that gets phyloseq sample_data as a plain... |
| sampleAnnotation | Helper to specify a HeatmapAnnotation for samples in... |
| scale_shape_girafe_filled | Filled shapes for ggiraph interactive plots |
| shao19 | Gut microbiota relative abundance data from Shao et al. 2019 |
| stat_chull | Draw convex hull for a set of points on a ggplot |
| tax_agg | Aggregate taxa and track aggregation in psExtra |
| taxAnnotation | Helper to specify a HeatmapAnnotation for taxa |
| taxatree_funs | Create node and edge dataframes for taxatree_plots |
| taxatree_label | Add logical label column to taxatree_stats dataframe |
| taxatree_models | Statistical modelling for individual taxa across multiple... |
| taxatree_plotkey | Draw labelled key to accompany taxatree_plots |
| taxatree_plot_labels | Add labels to taxatree plots/key |
| taxatree_plots | Plot statistical model results for all taxa on a taxonomic... |
| taxatreePruneLabelArgs | Helper, removes unwanted arguments from geom_* call args list |
| taxatree_stats_p_adjust | Adjust p values in taxatree_stats dataframe |
| tax_filter | Filter rare and/or low abundance taxa from a phyloseq object |
| tax_fix | Replace unknown, NA, or short tax_table values |
| tax_fix_interactive | Shiny app to help you use tax_fix |
| tax_model | Statistical modelling for individual taxa in a phyloseq |
| tax_mutate | Modify or compute new taxonomic ranks in phyloseq |
| tax_name | Simple way to set unique taxa_names for phyloseq object |
| tax_names2rank | Add taxa_names as last column in phyloseq tax_table |
| tax_palette | Make a fixed taxa colour palette e.g. for comp_barplot |
| tax_palette_plot | tax_palette plotting helper function |
| tax_prepend_ranks | Add rank prefixes to phyloseq tax_table values |
| tax_rename | Make new phyloseq taxa names from classification and taxon... |
| tax_reorder | Reorder taxa in phyloseq object using vector of names |
| tax_scale | Mean-center and SD-scale taxa in phyloseq |
| tax_select | Subset phyloseq object by (partial) taxa names |
| tax_sort | Sort taxa in phyloseq otu_table and tax_table |
| tax_top | Get names of "top" n taxa |
| tax_transform | Transform taxa in phyloseq object and record transformation |
| upgrade_ps_extra_to_psExtra | Convert old format "ps_extra" objects to new "psExtra"... |
| varAnnotation | Helper to specify a HeatmapAnnotation for variables in... |
