Package: microViz 0.12.4

microViz: Microbiome Data Analysis and Visualization

Microbiome data visualization and statistics tools built upon phyloseq.

Authors:David Barnett [aut, cre]

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microViz.pdf |microViz.html✨
microViz/json (API)
NEWS

# Install 'microViz' in R:

install.packages('microViz', repos = c('https://david-barnett.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/david-barnett/microviz/issues

Datasets:

ibd - IBD study data in phyloseq object.
shao19 - Gut microbiota relative abundance data from Shao et al. 2019

On CRAN:

microbiome microbiome-analysis microbiota

108 exports 99 stars 4.13 score 133 dependencies 358 scripts

Last updated 2 months agofrom:739f3881b6. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 29 2024
R-4.5-win	NOTE	Aug 29 2024
R-4.5-linux	NOTE	Aug 29 2024
R-4.4-win	NOTE	Aug 29 2024
R-4.4-mac	NOTE	Aug 29 2024
R-4.3-win	ERROR	Aug 29 2024
R-4.3-mac	ERROR	Aug 29 2024

Exports:%>%add_paths adjacent_side anno_abund anno_cat anno_cat_legend anno_prev anno_sample anno_sample_cat anno_tax_box anno_tax_density anno_tax_prev anno_var_box anno_var_density anno_var_hist bdisp_get comp_barplot comp_heatmap constraint_lab_style cor_heatmap cor_test dist_bdisp dist_calc dist_calc_seq dist_get dist_permanova distinct_palette heat_grid heat_numbers heat_palette info_get old_anno_var_box old_anno_var_hist ord_calc ord_explore ord_get ord_order_samples ord_plot ord_plot_iris otu_get perm_get phyloseq_validate prev ps_arrange ps_calc_diversity ps_calc_dominant ps_calc_richness ps_dedupe ps_drop_incomplete ps_filter ps_get ps_join ps_melt ps_mutate ps_otu2samdat ps_reorder ps_select ps_seriate ps_sort_ord samdat_tbl sampleAnnotation scale_shape_girafe_filled stat_chull tax_agg tax_anno tax_filter tax_fix tax_fix_interactive tax_lab_style tax_model tax_models_get tax_models2stats tax_mutate tax_name tax_names2rank tax_palette tax_palette_plot tax_prepend_ranks tax_rename tax_reorder tax_scale tax_select tax_sort tax_sort_ord tax_stats_get tax_top tax_transform taxAnnotation taxatree_edges taxatree_label taxatree_models taxatree_models_get taxatree_models2stats taxatree_nodes taxatree_plot_labels taxatree_plotkey taxatree_plots taxatree_stats_get taxatree_stats_p_adjust textAngleCalc textHjustCalc tt_get upgrade_ps_extra_to_psExtra var_anno varAnnotation vec_constraint vec_tax_all vec_tax_sel

Dependencies:ade4 ape askpass backports base64enc bayesm Biobase BiocGenerics biomformat Biostrings broom bslib ca cachem circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap compositions cowplot cpp11 crayon curl data.table DEoptimR digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach fs gclus generics GenomeInfoDb GenomeInfoDbData GetoptLong ggiraph ggplot2 GlobalOptions glue gtable highr htmltools htmlwidgets httpuv httr igraph IRanges isoband iterators jquerylib jsonlite knitr labeling later lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv microbiome mime multtest munsell nlme openssl permute phyloseq pillar pixmap pkgconfig plyr png promises purrr qap R6 rappdirs RColorBrewer Rcpp RcppArmadillo registry reshape2 rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown robustbase Rtsne S4Vectors sass scales seriation shape shiny sourcetools sp stringi stringr survival sys systemfonts tensorA tibble tidyr tidyselect tinytex TSP UCSC.utils utf8 uuid vctrs vegan viridisLite withr xfun xtable XVector yaml zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

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