ordination: Create an Ordination with Ellipses for Groups

In supportR: Support Functions for Wrangling and Visualization

Create an Ordination with Ellipses for Groups

Description

Produces a Nonmetric Multidimensional Scaling (NMS) or Principal Coordinate Analysis (PCoA) for up to 10 groups. Draws an ellipse around the standard deviation of the points in each group. By default, assigns a unique color (colorblind-safe) and point shape for each group. If the user supplies colors/shapes then the function can support more than 10 groups. For NMS ordinations, includes the stress as the legend title (see ?vegan::metaMDS for explanation of "stress"). For PCoA ordinations includes the percent variation explained parenthetically in the axis labels.

Usage

ordination(mod = NULL, grps = NULL, ...)

Arguments

mod	(pcoa | monoMDS/metaMDS) object returned by ape::pcoa or vegan::metaMDS
grps	(vector) vector of categorical groups for data. Must be same length as number of rows in original data object
...	additional arguments passed to graphics::plot, graphics::points, scales::alpha, vegan::ordiellipse, or graphics::legend. Open a GitHub Issue if function must support additional arguments

Value

(plot) base R ordination with an ellipse for each group

Examples

# Use data from the vegan package
utils::data("varespec", package = 'vegan')

# Make some columns of known number of groups
treatment <- c(rep.int("Trt1", (nrow(varespec)/4)),
               rep.int("Trt2", (nrow(varespec)/4)),
               rep.int("Trt3", (nrow(varespec)/4)),
               rep.int("Trt4", (nrow(varespec)/4)))

# And combine them into a single data object
data <- cbind(treatment, varespec)

# Get a distance matrix from the data
dist <- vegan::vegdist(varespec, method = 'kulczynski')

# Perform PCoA / NMS
pcoa_mod <- ape::pcoa(dist)
nms_mod <- vegan::metaMDS(data[-1], autotransform = FALSE, expand = FALSE, k = 2, try = 50)

# Create PCoA ordination (with optional agruments)
ordination(mod = pcoa_mod, grps = data$treatment, 
           bg = c("red", "blue", "purple", "orange"),
           lty = 2, col = "black")

# Create NMS ordination
ordination(mod = nms_mod, grps = data$treatment, alpha = 0.3, 
           x = "topright", legend = LETTERS[1:4])

supportR documentation built on June 22, 2024, 10:17 a.m.