Package index

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

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