https://github.com/jfq3/ggordiplots

Make ggplot Versions of Vegan's Ordiplots
https://github.com/jfq3/ggordiplots

Last synced: 3 days ago
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Make ggplot Versions of Vegan's Ordiplots

• Host: GitHub
• URL: https://github.com/jfq3/ggordiplots
• Owner: jfq3
• License: gpl-2.0
• Created: 2017-04-05T12:52:13.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-10-23T20:49:20.000Z (24 days ago)
• Last Synced: 2024-10-25T16:21:50.771Z (22 days ago)
• Language: R
• Size: 282 KB
• Stars: 6
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE.md

Awesome Lists containing this project

README

        
---

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

  

```