Package index • microViz

Subsetting or sorting phyloseq samples Functions for filtering or reording samples in a phyloseq object. These characteristically start with “ps_”, which is short for phyloseq.
`ps_filter()`	Filter phyloseq samples by sample_data variables
`ps_arrange()`	Arrange samples in phyloseq by sample_data variables or taxon abundance
`ps_seriate()`	Arrange samples in a phyloseq by microbiome similarity
`ps_sort_ord()` `ord_order_samples()`	Sort phyloseq samples by ordination axes scores
`ps_reorder()`	Set order of samples in phyloseq object
`ps_dedupe()`	De-duplicate phyloseq samples
`ps_drop_incomplete()`	Deselect phyloseq samples with sample_data missings
Manipulating phyloseq sample_data Functions for modifying and augmenting the sample data within phyloseq objects. These also start with “ps_”, which is short for phyloseq.
`ps_select()`	Select phyloseq sample_data using dplyr::select syntax
`ps_mutate()`	Modify or compute new sample_data in phyloseq object
`ps_join()`	Join a dataframe to phyloseq sample data
`ps_otu2samdat()`	Copy phyloseq otu_table data to sample_data
`ps_melt()`	Melt phyloseq data object into large data.frame (tibble)
Manipulating taxa Functions for modifying the taxonomic information contained within phyloseq objects. These characteristically start with “tax_”, which is short for taxa.
`tax_fix()`	Replace unknown, NA, or short tax_table values
`tax_fix_interactive()`	Shiny app to help you use tax_fix
`tax_prepend_ranks()`	Add rank prefixes to phyloseq tax_table values
`tax_filter()`	Filter rare and/or low abundance taxa from a phyloseq object
`tax_agg()`	Aggregate taxa and track aggregation in psExtra
`tax_transform()`	Transform taxa in phyloseq object and record transformation
`tax_scale()`	Mean-center and SD-scale taxa in phyloseq
`tax_select()`	Subset phyloseq object by (partial) taxa names
`tax_mutate()`	Modify or compute new taxonomic ranks in phyloseq
`tax_rename()`	Make new phyloseq taxa names from classification and taxon abundance info
`tax_name()`	Simple way to set unique taxa_names for phyloseq object
`tax_sort()`	Sort taxa in phyloseq otu_table and tax_table
`tax_sort_ord()` `ord_order_taxa()`	Order taxa in phyloseq by their loading vectors
`tax_reorder()`	Reorder taxa in phyloseq object using vector of names
`tax_top()`	Get names of "top" n taxa
`tax_names2rank()`	Add taxa_names as last column in phyloseq tax_table
Ordination and related methods Functions for assessing and visualising overall microbiota composition and its associations with phyloseq sample data variables. dist_* functions calculate or use sample-sample distances/dissimilarities. ord_* functions calculate or use sample ordinations.
`dist_calc()`	Calculate distances between pairs of samples in phyloseq object
`dist_permanova()`	Calculate PERMANOVA after dist_calc()
`dist_bdisp()`	Wrapper for vegan::betadisper()
`ord_calc()`	Ordinate samples (arrange by similarity in multiple dimensions)
`ord_plot()`	Customisable ggplot2 ordination plot
`stat_chull()`	Draw convex hull for a set of points on a ggplot
`add_paths()`	Add paths connecting points on a ggplot scatterplot
`tax_lab_style()` `constraint_lab_style()`	Create list for ord_plot() *_lab_style arguments
`vec_constraint()` `vec_tax_sel()` `vec_tax_all()`	Create ordination plot vector styling lists
`ord_plot_iris()`	Circular compositional barplot sorted by ordination angle
`ord_explore()`	Interactively explore microbial compositions of ordinated samples
`scale_shape_girafe_filled()`	Filled shapes for ggiraph interactive plots
`ps_get()` `dist_get()` `ord_get()` `info_get()` `perm_get()` `bdisp_get()` `tax_models_get()` `tax_stats_get()` `taxatree_models_get()` `taxatree_stats_get()` `otu_get()` `tt_get()` `samdat_tbl()`	Extract elements from psExtra class
Taxon models and tree visualisations Functions for modelling and visualising associations between individual microbes and phyloseq sample data variables.
`tax_model()`	Statistical modelling for individual taxa in a phyloseq
`taxatree_models()`	Statistical modelling for individual taxa across multiple ranks
`taxatree_models2stats()` `tax_models2stats()`	Extract statistics from taxatree_models or tax_model output
`taxatree_stats_p_adjust()`	Adjust p values in taxatree_stats dataframe
`taxatree_plots()`	Plot statistical model results for all taxa on a taxonomic tree
`taxatree_plotkey()`	Draw labelled key to accompany taxatree_plots
`taxatree_label()`	Add logical label column to taxatree_stats dataframe
`taxatree_plot_labels()`	Add labels to taxatree plots/key
`taxatree_nodes()` `taxatree_edges()`	Create node and edge dataframes for taxatree_plots
`cor_test()`	Simple wrapper around cor.test for y ~ x style formula input
Heatmap plotting functions Functions for drawing and annotating heatmaps
`comp_heatmap()`	Draw heatmap of microbiome composition across samples
`cor_heatmap()`	Microbe-to-sample-data correlation heatmap
`taxAnnotation()`	Helper to specify a HeatmapAnnotation for taxa
`anno_tax_box()`	Helper to specify heatmap annotation for showing taxa abundance on boxplot
`anno_tax_prev()`	Helper to specify heatmap annotation for showing taxa prevalence as barplot
`anno_tax_density()`	Helper to specify heatmap annotation for showing taxa abundance density plot
`sampleAnnotation()`	Helper to specify a HeatmapAnnotation for samples in comp_heatmap
`anno_sample()`	Helper to specify simple comp_heatmap annotation for other sample data
`anno_sample_cat()`	Helper to specify comp_heatmap annotation for categorical sample data
`anno_cat()`	Create colored rectangle annotations for categorical data
`anno_cat_legend()`	Convenience function for generating a legend for anno_cat annotations.
`varAnnotation()`	Helper to specify a HeatmapAnnotation for variables in cor_heatmap
`anno_var_box()`	Helper to specify heatmap annotation for variable distribution boxplots
`anno_var_hist()`	Helper to specify heatmap annotation for variable distribution histograms
`anno_var_density()`	Helper to specify heatmap annotation for variable distribution density plot
`heat_palette()`	Easy palettes for ComplexHeatmap
`heat_numbers()`	Aesthetic settings for drawing numbers on heatmap tiles
`heat_grid()`	set options for drawing gridlines on heatmaps
`adjacent_side()`	Simple heatmap helper to get a default adjacent side for another annotation
Other functions Other assorted functions
`comp_barplot()`	Plot (grouped and ordered) compositional barplots
`distinct_palette()`	Colour palettes suitable for 20+ categories
`tax_palette()`	Make a fixed taxa colour palette e.g. for comp_barplot
`tax_palette_plot()`	tax_palette plotting helper function
`ps_calc_dominant()`	Calculate dominant taxon in each phyloseq sample
`ps_calc_diversity()`	Calculate diversity index and add to phyloseq sample data
`ps_calc_richness()`	Calculate richness estimate and add to phyloseq sample data
`phyloseq_validate()`	Check for (and fix) common problems with phyloseq objects
`prev()`	Calculate prevalence from numeric vector
Datasets
`shao19`	Gut microbiota relative abundance data from Shao et al. 2019
`ibd`	IBD study data in phyloseq object.
Other
`microViz-package` `microViz`	microViz: microbiome data analysis and visualization
`print(<psExtraInfo>)`	Print method for psExtraInfo object
`psExtra-class`	Define psExtra class S4 object
`upgrade_ps_extra_to_psExtra()`	Convert old format "ps_extra" objects to new "psExtra" objects
`dist_calc_seq()`	Calculate distances between sequential samples in ps_extra/phyloseq object
`tax_anno()` `anno_prev()` `anno_abund()` `var_anno()` `old_anno_var_hist()` `old_anno_var_box()`	DEPRECATED Heatmap annotations helpers

Reference

Subsetting or sorting phyloseq samples

Manipulating phyloseq sample_data

Manipulating taxa

Ordination and related methods

Taxon models and tree visualisations

Heatmap plotting functions

Other functions

Datasets

Other