Readme

otutableNMDS

This package aims to assist the easy implementation of Nonmetric Multidimensional Scaling (NMDS) plots into ggplot.

The package includes an example dataset from Jauss et al. 2020, which is an OTU abundance table including sample metadata, and three functions:

• get_NMDS_ordination: The function takes the OTU table (with or without metadata) and performs the NMDS ordination. The resulting object is needed for the next step:
• get_hull_data: It returns a dataframe containing the coordinates for the convex hull data used for the drawing of polygons in the next function. The user can specify any sample type which the polygons should be drawn around
• plot_NMDS: This is a simple function pasting the hull data to ggplot2 and drawing polygons around the specified samples or habitats

Installation

You can easily install this package with devtools like this:

devtools::install_github('RJauss/otutableNMDS', ref = "HEAD")

Usage

Here is a simple example of how the package works. Let’s first have a look at the example data:

library(otutableNMDS)
data("OTU_Table")

tibble::as_tibble(OTU_Table[1:10, 1:10])

## # A tibble: 10 x 10
##    SampleID TreeID TreeSpecies Microhabitat Stratum X1_Peronosporal…
##    <fct>    <fct>  <fct>       <fct>        <fct>              <dbl>
##  1 K129_Bl… K129   Quercus ro… Fresh Leaves Canopy                 1
##  2 K129_Bor K129   Quercus ro… Bark         Canopy                 0
##  3 K129_Det K129   Quercus ro… Arboreal So… Canopy               121
##  4 K129_Hyp K129   Quercus ro… Hypnum       Canopy               382
##  5 K129_La… K129   Quercus ro… Leaf Litter  Ground             19129
##  6 K129_Oth K129   Quercus ro… Orthotrichum Canopy               354
##  7 K232_Bl… K232   Fraxinus e… Fresh Leaves Canopy                 0
##  8 K232_Bod K232   Fraxinus e… Soil         Ground             10264
##  9 K232_Bor K232   Fraxinus e… Bark         Canopy                32
## 10 K232_Det K232   Fraxinus e… Arboreal So… Canopy               348
## # … with 4 more variables:
## #   X2_Lagenidiales.Lagenidiales_Family_NoHit.Lagenidiales_Genus_NoHit.Lagenidiales_Species_NoHit <dbl>,
## #   X3_Peronosporales.Peronosporaceae.Hyaloperonospora.Hyaloperonospora_brassicae <dbl>,
## #   X4_Pythiales.Pythiaceae.Pythiaceae_Genus_NoHit.Pythiaceae_Species_NoHit <dbl>,
## #   X5_Peronosporales.Peronosporaceae.Peronospora.Peronospora_arborescens <dbl>

My data has the sample metadata included in columns 1-5, after that comes the species abundance matrix. So we need to specify which columns and which sample(-types) to use in the get_hull_data function. But first we run the get_NMDS_ordination function which uses the metaMDS function from vegan:

NMDS.data <- get_NMDS_ordination(OTU_Table = OTU_Table, 
                                 SampleMetadata = c(1, 5), 
                                 logtransform = T, 
                                 relative = T, 
                                 k = 3)
# Note that you can specify further arguments which will be passes
# to metaMDS(), for example "distance = 'jaccard'" etc

hull.data <- get_hull_data(NMDS_data = NMDS.data, 
                           SampleMetadata = OTU_Table[,1:5], 
                           NMDS = c("NMDS1", "NMDS2"), 
                           habitat = "Microhabitat", 
                           which = "all")

head(hull.data)

##          NMDS1      NMDS2      NMDS3 site  Microhabitat
## 10  0.52019236 -0.9101673 -0.2069323   10 Arboreal Soil
## 36  0.14206562 -0.6572729 -0.2794746   36 Arboreal Soil
## 23 -0.13023534 -0.4368888  0.8148968   23 Arboreal Soil
## 16 -0.38727621  0.1618064 -0.6832429   16 Arboreal Soil
## 3   0.46977397  0.3016228 -0.9926107    3 Arboreal Soil
## 49  0.02501816 -0.1959304  0.1791760   49          Bark

The function returns the dataframe with the coordinates neccessary for the polygons to draw around the microhabitats.

Plot NMDS

The dataframe will now be parsed into the third function, plot_NMDS:

g <- plot_NMDS(hull_data = hull.data, 
               NMDS_data = NMDS.data, 
               x = "NMDS1", y = "NMDS2", 
               habitat = "Microhabitat")

g

Plot additional NMDS on top

Let’s say we also want the hull data for the tree species, we can easily modify the code like this and plot a second ordination on top:

hull.data.TreeSpecies <- get_hull_data(NMDS_data = NMDS.data, 
                                       SampleMetadata = OTU_Table[,1:5],
                                       NMDS = c("NMDS1", "NMDS2"), 
                                       habitat = "TreeSpecies", 
                                       which = "all")

Now call the plot_NMDS again and specify both hull.datas. The second one will be plotted on top with non-filled polygons:

g <- plot_NMDS(hull_data = hull.data, 
               hull_data2 = hull.data.TreeSpecies, 
               NMDS_data = NMDS.data, 
               x = "NMDS1", y = "NMDS2", 
               habitat = "Microhabitat", 
               habitat2 = "TreeSpecies")

g

This is now a very basic ggplot NMDS which can be easily modified and appended with the ggplot syntax, e.g. “scale_fill_manual”