GGPLOT2 Shepard's Plot Example

GGPLOT2 Shepard's Plot Example

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This tutorial shows how you can create Shepard's Plot using GGPLOT2.

Here is an example to plot a very similar plot using ggplot2.The method was to get the structure of the stressplot(example_NMDS) and extract the data stored in that object.

Shepard's Plot Using GGPLOT2 Example

The below example uses the tidyverse package that includes ggplot and other packages such as tidyr that contains the pivot_longer function.

library(vegan)
library(tidyverse)

# Analyze the structure of the stressplot
# Notice there's an x, y and yf list
str(stressplot(example_NMDS))

# Create a tibble that contains the data from stressplot
df <- tibble(x = stressplot(example_NMDS)$x, y = stressplot(example_NMDS)$y, yf = stressplot(example_NMDS)$yf) %>%
  # Change data to long format
  pivot_longer(cols = c(y, yf),
               names_to = "var")

# Create plot
df %>%
  ggplot(aes(x = x,
             y = value)) +
  # Add points just for y values
  geom_point(data = df %>%
               filter(var == "y")) +
  # Add line just for yf values
  geom_step(data = df %>%
              filter(var == "yf"),
            col = "red",
            direction = "vh") +
  # Change axis labels
  labs(x = "Observed Dissimilarity", y = "Ordination Distance") +
  # Add bw theme
  theme_bw()

Output:

Chart - Shepard's Plot using GGPLOT2

Credit: Jonathan V. Solórzano