Microbiome Data Analysis and Visualization


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Documentation for package ‘microViz’ version 0.12.6

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A B C D H I M O P S T U V

microViz-package microViz: microbiome data analysis and visualization

-- A --

add_paths Add paths connecting points on a ggplot scatterplot
adjacent_side Simple heatmap helper to get a default adjacent side for another annotation
anno_abund DEPRECATED Heatmap annotations helpers
anno_cat Create colored rectangle annotations for categorical data
anno_cat_legend Convenience function for generating a legend for anno_cat annotations.
anno_prev DEPRECATED Heatmap annotations helpers
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_tax_box Helper to specify heatmap annotation for showing taxa abundance on boxplot
anno_tax_density Helper to specify heatmap annotation for showing taxa abundance density plot
anno_tax_prev Helper to specify heatmap annotation for showing taxa prevalence as barplot
anno_var_box Helper to specify heatmap annotation for variable distribution boxplots
anno_var_density Helper to specify heatmap annotation for variable distribution density plot
anno_var_hist Helper to specify heatmap annotation for variable distribution histograms

-- B --

bdisp_get Extract elements from psExtra class

-- C --

comp_barplot Plot (grouped and ordered) compositional barplots
comp_heatmap Draw heatmap of microbiome composition across samples
constraint_lab_style Create list for ord_plot() *_lab_style arguments
cor_heatmap Microbe-to-sample-data correlation heatmap
cor_test Simple wrapper around cor.test for y ~ x style formula input

-- D --

deprecated-heatmap-annotations DEPRECATED Heatmap annotations helpers
distinct_palette Colour palettes suitable for 20+ categories
dist_bdisp Wrapper for vegan::betadisper()
dist_calc Calculate distances between pairs of samples in phyloseq object
dist_calc_seq Calculate distances between sequential samples in ps_extra/phyloseq object
dist_get Extract elements from psExtra class
dist_permanova Calculate PERMANOVA after dist_calc()

-- H --

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

-- I --

ibd IBD study data in phyloseq object.
info_get Extract elements from psExtra class

-- M --

microViz microViz: microbiome data analysis and visualization

-- O --

old_anno_var_box DEPRECATED Heatmap annotations helpers
old_anno_var_hist DEPRECATED Heatmap annotations helpers
Ordination-arrows Create ordination plot vector styling lists
Ordination-labels Create list for ord_plot() *_lab_style arguments
ord_calc Ordinate samples (arrange by similarity in multiple dimensions)
ord_explore Interactively explore microbial compositions of ordinated samples
ord_get Extract elements from psExtra class
ord_order_samples Sort phyloseq samples by ordination axes scores
ord_order_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
otu_get Extract elements from psExtra class

-- P --

perm_get Extract elements from psExtra class
phyloseq_validate Check for (and fix) common problems with phyloseq objects
prev Calculate prevalence from numeric vector
print.psExtraInfo Print method for psExtraInfo object
psExtra-accessors Extract elements from psExtra class
psExtra-class Define psExtra class S4 object
ps_arrange Arrange samples in phyloseq by sample_data variables or taxon abundance
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_dedupe De-duplicate phyloseq samples
ps_drop_incomplete Deselect phyloseq samples with sample_data missings
ps_filter Filter phyloseq samples by sample_data variables
ps_get Extract elements from psExtra class
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
ps_sort_ord Sort phyloseq samples by ordination axes scores

-- S --

samdat_tbl Extract elements from psExtra class
sampleAnnotation Helper to specify a HeatmapAnnotation for samples in comp_heatmap
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

-- T --

taxAnnotation Helper to specify a HeatmapAnnotation for taxa
taxatree_edges Create node and edge dataframes for taxatree_plots
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 ranks
taxatree_models2stats Extract statistics from taxatree_models or tax_model output
taxatree_models_get Extract elements from psExtra class
taxatree_nodes Create node and edge dataframes for taxatree_plots
taxatree_plotkey Draw labelled key to accompany taxatree_plots
taxatree_plots Plot statistical model results for all taxa on a taxonomic tree
taxatree_plot_labels Add labels to taxatree plots/key
taxatree_stats_get Extract elements from psExtra class
taxatree_stats_p_adjust Adjust p values in taxatree_stats dataframe
tax_agg Aggregate taxa and track aggregation in psExtra
tax_anno DEPRECATED Heatmap annotations helpers
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_lab_style Create list for ord_plot() *_lab_style arguments
tax_model Statistical modelling for individual taxa in a phyloseq
tax_models2stats Extract statistics from taxatree_models or tax_model output
tax_models_get Extract elements from psExtra class
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 abundance info
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_sort_ord Order taxa in phyloseq by their loading vectors
tax_stats_get Extract elements from psExtra class
tax_top Get names of "top" n taxa
tax_transform Transform taxa in phyloseq object and record transformation
tt_get Extract elements from psExtra class

-- U --

upgrade_ps_extra_to_psExtra Convert old format "ps_extra" objects to new "psExtra" objects

-- V --

varAnnotation Helper to specify a HeatmapAnnotation for variables in cor_heatmap
var_anno DEPRECATED Heatmap annotations helpers
vec_constraint Create ordination plot vector styling lists
vec_tax_all Create ordination plot vector styling lists
vec_tax_sel Create ordination plot vector styling lists