The R package vegan includes the function ordiplot for making ordination plots using R’s base graphics. Additionally vegan provides several functions for enhancing the plots with spiders, hulls, and ellipses. It is even possible to overlay an ordination plot with a cluster diagram. (See my package ggordiplots on GitHub for making the same kinds of plots with ggplot graphics.) Vegan’s functions for adding these layers begin with “ordi”: ordispider, ordihull, ordiellipse, ordicluster. Earlier this year I discovered the package vegan3d. It makes use of rgl graphics which means that the plots it generates can be scaled and rotated with the mouse. This is not just fun – it allows you to see how well separated treatment groups are in the ordination space.
Vegan3d’s function ordirgl is similar to ordiplot – it draws the ordination plot depicting samples and/or species. Other functions beginning with “orgl” are similar to the ones beginning with “ordi” in vegan: orglpoints, orglspider, orglellipse, orglcluster. See the vegan3d documentation for full instructions on how to use these.
I made an interactive html page of a slightly enhanced version of the example given in the vegan3d documentation, viewable if you CLICK HERE. Some explanation of the last code block of the Rmarkdown file reproduced here is necessary.
open3d() # Opens a graphic device for the plot. ## wgl ## 8 par3d(windowRect = c(20, 40, 1000, 1200)) # left, top, right, bottom in pixels my.color <- c("red", "blue") ordirgl(ord, size=4, col = my.color[as.numeric(sam$Type)]) # plot points with(sam, orglspider(ord, Type, col = my.color[1:2], scaling = "sites")) # add spiders with(sam, orglellipse(ord, Type, col = my.color[1:2], kind = "se", conf = 0.95, scaling = "sites")) # add ellipses rglwidget() # You cannot run this line in RStudio.
The open3d command opens an rgl graphics window. If you are using RStudio, this window will open outside of RStudio. The next 5 lines build the plot in the graphics window. At any step after the line beginning with ordirgl you can zoom and rotate the plot in the graphics window. The last line, rglwidget(), is necessary to knit the html file. If you try to run it in RStudio, it will cause RStudio to freeze. If you try to use the RStudio menu to knit the html document, RStudio will freeze. So DO NOT do either of these things!
To knit the Rmarkdown file into an html file, you must enter the command in the console window. In this case the command is:
rmarkdown::render(input = "vegan3d_example.Rmd", output_format = "html_document", output_file = "vegan3d_example.html")