ggordiplots

Make ggplot Versions of Vegan's Ordiplots

https://github.com/jfq3/ggordiplots

Repository

Make ggplot Versions of Vegan's Ordiplots

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# ggordiplots


[![R-CMD-check](https://github.com/jfq3/ggordiplots/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jfq3/ggordiplots/actions/workflows/R-CMD-check.yaml)
[![Github All Releases](https://img.shields.io/github/downloads/jfq3/ggordiplots/total.svg)])


The `vegan` package includes several functions for adding features to ordination plots: `ordiarrows()`,  `ordiellipse()`, `ordihull()`, `ordispider()` and `ordisurf()`. This package adds these same features to ordination plots made with `ggplot2`. In addition, `gg_ordibubble()` sizes points relative to the value of an environmental variable.

The functions are written so that features from each can be combined in customized ordination plots.  

The functions `ord_labels()` and `scale_arrow()` (used to ensure vector arrows fit within a plot) are exported to make it easier to generate custom ordination plots.  

## Installation

You can install the development version of ggordiplots from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("jfq3/ggordiplots")
```
You can install the latest release from CRAN with:  

``` r
install.packages("ggordiplots")
```

## Examples

Plot an ordination with ellipses around treatment group centroids (at distances of one standard deviation) with `gg_ordiplot()`.  

```{r}
library(ggordiplots)
data("dune")
data("dune.env")
dune_bray <- vegdist(dune, method = "bray")
ord <- cmdscale(dune_bray, k = (nrow(dune) - 1), eig = TRUE, add = TRUE)
plt1 <- gg_ordiplot(ord, groups = dune.env$Management, plot = FALSE)
```
`plt1` is list with items named:
```{r}
names(plt1)
```
The first 5 items are data frames for making plots. The last item is a ggplot:  
```{r}
plt1$plot
```
Fit a vector of Al concentrations to the ordination with `gg_envfit()`.  
```{r}
Al <- as.data.frame(dune.env$A1)
colnames(Al) <- "Al"
plt2 <- gg_envfit(ord, env = Al, groups = dune.env$Management, plot = FALSE)
plt2$plot
```
Add ellipses from the first plot to the second plot. The resulting plot can be further customized using usual `ggplot2` methods. For example, change the legend title.  
```{r}
plt2$plot +
  geom_path(data = plt1$df_ellipse, aes(x=x, y=y, color=Group)) +
  guides(color=guide_legend(title="Management")) # Change legend title
  
```

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