Microbiome beta-diversity 3D plot in R (mds, pcoa)

Hello,

Beta-diversity is one of the mostly used analysis method in microbiome community composition study.

Diversity has three kind of scale; Alpha-, Beta-, Gamma-.

What is the difference?

Simply, The group size are getting bigger from Alpha to Gamma.

 

Alpha diversity is the diversity within a particular area or ecosystem; usually expressed by the number of species (i.e., species richness) in that ecosystem 

Beta diversity is a comparison of of diversity between ecosystems, usually measured as the amount of species change between the ecosystems

Gamma diversity is a measure of the overall diversity within a large region. Geographic-scale species diversity according to Hunter (2002: 448)

 

 

This is the method the Beta diversity analysis and visualization to 3D plot.

The "rgl" and "car" packages are used in R program.

 

Let's follow-up the 8 steps below, then you are the professional 3D plot of diversity analysis.

 

 

1. Install Packages

 

############ Packages Install ###########

 

install.packages("rgl")

install.packages("car")

 

######################################

 

 

2. Launch Packages

 

############ Launch packages ###########

 

library("rgl")

library("car")

 

#######################################

 

3. Input Dataframe

 

############## Input Dataframe ###############

 

data <- read.delim("clipboard", row.names=1) #Copy dataframe from excel and launch command

 

########################################

 

4. Calculate Distance

 

################ Calculate Dist ################

 

data.dist <- dist(data[,3:359]) # [,3:999] = row from 3 to 999 (bacteria data)

 

#########################################

 

5. Calculate Metric Multidimensional Scaling (MDS) 

 

############### Calaulte MDS #################

 

data.mds <- cmdscale(data.dist, k=3)

 

#########################################

 

6. Make x, y, z axis from created data

 

############## Create x,y,z ################

 

data.x <- data.mds[,1]

data.y <- data.mds[,2]

data.z <- data.mds[,3]

 

#########################################

 

7. Visualization

 

################### Plot ##################

 

### i) Observe by monotonic color

 

scatter3d(data.x,data.y,data.z,

          col = "blue", 

          grid = TRUE,)

 

 

### ii) Observe flat surface

 

scatter3d(data.x,data.y,data.z,

          groups = as.factor(data$weight), 

          grid = TRUE,

          

         )

        #data$weight = group named weight in column

 

### iii) Observe boundary

scatter3d(x = data.x, y = data.y, z = data.z,

          groups = as.factor(data$species),

          surface=FALSE, ellipsoid = TRUE, grid = FALSE

          )

        #data$species = group named species in column

 

############################################

 

8. Run 3D with video

 

############## Launch 3D Video ###############

 

play3d(spin3d(axis=c(0,1,1), rpm=3), duration=30)

 

############################################

 

This was the posting about microbiome data to 3D plot visualization with beta diversity analysis.

If you run all command without any error, i give you clap!! 

If you are wondering something or error, reply below. I will give you hands.