In wilkox/unionplot: Draw union plots

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)

A union plot is like a Venn diagram, in that it shows the overlap between three groups. Unlike a Venn diagram, the number of overlapping members is not indicated by a number but by a point drawn for each member, which can then be coloured by a factor of interest. If there are too many members to display easily, each point can represent more than one member (as in the example above).

The package is designed for displaying microbial ecology data (OTUs in samples), but can be adapted for other applications.

Installation

Install unionplot from GitHub:

devtools::install_github("wilkox/unionplot")

Walkthrough

For any union plot, you'll need a data frame containing at least these columns: - A factor column named 'OTU', containing the OTUs (or other set members); - A factor column, containing exactly three levels, which will be the three groups in the plot; - A factor column, by which the points will be coloured.

Union plots only display presence/absence of an OTU (or other set member), not counts. Any 'Count' or 'Relative abundance' column will be ignored. Any row in the data frame containing an OTU and a sample will be assumed to imply that the OTU is present in that sample. So, if your OTU table contains rows with count or relative abundance '0' should be filtered out before drawing the plot.

For this example plot, we'll use a randomly generated OTU table with three samples and three taxonomic families.

library(unionplot)
data(OTUTable)
head(OTUTable)

Drawing the plot is accomplished with the unionplot() function:

unionplot(OTUTable, group = "Sample", colour = "Family")

The plot is drawn with ggplot, so you can save it easily with ggsave.

The plot includes labels for each region, but they're placed with no consideration for aesthetics so you'll probably need to do some polishing work in a vector graphics program. The number in parentheses is the actual number of OTUs in each region, and does not change even if the points represent more than one OTU (the collapse argument).

wilkox/unionplot documentation built on May 4, 2019, 5:26 a.m.