Lab2_GitHubRMarkdown.rmd

---
title: "Lab2_GitHubRMarkdown"
author: "Sal Jahromi"
date: "`r Sys.Date()`"
output: html_document
---

# Lab2: Dune Data Set MDS Ggplot ScatterPlots

Loading the vegan and ape packages.
```{r adding_vegan_ape_packages, warning=FALSE, message = FALSE}
library("vegan")
library("ape")
```


loading the dune data set and log transforming it.
```{r dune_dataset}
data("dune")
dune2 <- dune

#log transform dune
dune2 <- log1p(dune2)
```



Performing nmds on dune2 and assigning the point element to 'dpoints'.
```{r nmds_dune2, message = FALSE}

dune2_ndms <- metaMDS(dune2)
dpoint <- dune2_ndms$point
```


Creating a ggplot scatterplot of mds and saving it as a pdf.
```{r ggplot_scatterplot , message = FALSE}
library(ggplot2)
ggplot(dpoint,aes(x=MDS1, y=MDS2)) + 
  geom_point() + 
  theme_bw() + 
  ggtitle("Scatterplot of MDS: MDS2 vs MDS1")

ggsave("MDS_Scatterplot.pdf")
```