NMDS in R

orders <- read.csv("condensed_order.csv", header = TRUE)

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head(orders)

# First load the vegan package

library(vegan)

nmds_results <- metaMDS(comm = orders[ , 4:11],  # Define the community data 

                        distance = "bray",       # Specify a bray-curtis distance

                        try = 100)               # Number of iterations 

nmds_results

## 

## Call:

## metaMDS(comm = orders[, 4:11], distance = "bray", try = 100) 

## 

## global Multidimensional Scaling using monoMDS

## 

## Data:     wisconsin(sqrt(orders[, 4:11])) 

## Distance: bray 

## 

## Dimensions: 2 

## Stress:     0.1756999 

## Stress type 1, weak ties

## Two convergent solutions found after 100 tries

## Scaling: centring, PC rotation, halfchange scaling 

## Species: expanded scores based on 'wisconsin(sqrt(orders[, 4:11]))'

#第二步， jump into plot

library(ggplot2)

library(viridis)

#First create a data frame of the scores from the individual sites.

# This data frame will contain x and y values for where sites are located.

data_scores=as.data.frame(scores(nmds_results, display = "sites"))

# Now add the extra aquaticSiteType column 

data_scores <- cbind(data_scores, orders[, 14])

colnames(data_scores)[3] <- "aquaticSiteType"  

# Next, we can add the scores for species data

species_scores <- as.data.frame(scores(nmds_results, "species"))

# Add a column equivalent to the row name to create species labels

species_scores$species <- rownames(species_scores)

# Now we can build the plot!

ggplot() +

  geom_text(data = species_scores, aes(x = NMDS1, y = NMDS2, label = species),

            alpha = 0.5, size = 8) + 

  geom_point(data = data_scores, aes(x = NMDS1, y = NMDS2, 

                                     color = aquaticSiteType), size = 3) +

  scale_color_manual(values = inferno(15)[c(3, 8, 11)],

                     name = "Aquatic System Type") +

  annotate(geom = "label", x = -1, y = 1.25, size = 6,

           label = paste("Stress: ", round(nmds_results$stress, digits = 3))) +

  theme_minimal() +

  theme(legend.position = "top",

        text = element_text(size = 16))

# 调整

ggplot() +

  geom_text(data = species_scores, aes(x = NMDS1, y = NMDS2, label = species),

            alpha = 0.6, size = 6) + #alpha字体颜色深度

  geom_point(data = data_scores, aes(x = NMDS1, y = NMDS2, 

                                     color = aquaticSiteType), size = 3) +

  scale_color_manual(values = inferno(15)[c(3, 8, 11)],

                     name = "Aquatic System Type") +

  annotate(geom = "label", x = -1, y = 1.25, size = 6,

           label = paste("Stress: ", round(nmds_results$stress, digits = 3))) +

  theme_minimal() +

  theme(legend.position = "top",

        text = element_text(size = 16))+

  scale_colour_manual(values = c("orange", "steelblue"))+

  xlim(-2,1)+ ylim(-1.5,1.5)

Code and data source: https://cougrstats.wordpress.com/2019/12/11/non-metric-multidimensional-scaling-nmds-in-r/