In david-barnett/microViz: Microbiome Data Analysis and Visualization

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

This article shows you how to quickly get started with interactive exploration of your data/ ordination plot.

library(phyloseq)
library(microViz)

Example

Example data loaded from the corncob package. All you need is a valid phyloseq object, and to run tax_fix to ensure the tax_table doesn't contain problematic names.

pseq <- microViz::ibd %>%
  tax_fix() %>%
  phyloseq_validate()

The gif animation below shows the result of running ord_explore, the animation starts immediately after interactively selecting "Genus" level aggregation, "clr" transformation, and the "PCA" ordination method from the "Edit" menu.

ord_explore(pseq)

Another (old) example

Get example dataset from the phyloseq package and clean up the taxa just a little.

data("enterotype", package = "phyloseq")
taxa_names(enterotype)[1] <- "Unclassified" # replace strange "-1" name
ps <- tax_fix(enterotype) # remove NA taxa and similar

Create simple Bray-Curtis PCoA to explore interactively.

ord1 <- ps %>%
  tax_transform("identity", rank = "Genus") %>%
  dist_calc("bray") %>% # bray curtis
  ord_calc() # automagically picks PCoA

Start interactive Shiny app. Note that the gif animation shown is from an outdated version of microViz. More recent versions of ord_explore allow editing the ordination shown, and generating ord_plot code.

ord_explore(data = ord1, auto_caption = NA)

Session info

devtools::session_info()

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.