SUMMARIZEplot was developed by Umer Zeeshan Ijaz in the following hackathon:

Event Title: From signals to environmentally tagged sequences III
Location: Hellenic Centre for Marine Research, Crete, Greece
Dates: from 22-09-2014 to 25-09-2014

This work was sponsored by European Union's Earth System Science and Environmental Management ES1103 COST Action ("Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools").
Source code: [summarize_v0.2.zip]
You can run the following R code (provided as generatedata.R) to generate data.js from your abundance table that you can place in your current directory, and then click on summarize.html to load the plot:
library(vegan)
 
#Load the abundance table
x<- read.csv("abundance_table.csv",header=TRUE,row.names=1)
x<-t(x)
 
#Perform non-metric distance scaling
MDS<-metaMDS(x, distance = "bray", k = 2, trymax = 50)
 
#Normalize the data
x<-x/rowSums(x)
x<-x[,order(colSums(x),decreasing=TRUE)]
 
#Extract list of top N Taxa
N<-21
taxa_list<-colnames(x)[1:N]
 
#Remove "Unknown" and add it to others
taxa_list<-taxa_list[!grepl("Unknown",taxa_list)]
N<-length(taxa_list)
 
#Generate data for SUMMARIZEplot
new_x<-data.frame(x[,colnames(x) %in% taxa_list],Others=rowSums(x[,!colnames(x) %in% taxa_list]))
names<-gsub("\\.","_",gsub(" ","_",colnames(new_x)))
sink("data.js")
cat("var freqData=[\n")
for (i in (1:dim(new_x)[1])){  
  cat(paste("{Samples:\'",rownames(new_x)[i],"\',",sep=""))
  cat(paste("freq:{",paste(paste(names,":",new_x[i,],sep=""),collapse=","),"},",sep=""))
  cat(paste("MDS:{",paste(paste(colnames(MDS$points),MDS$points[rownames(new_x)[i],],sep=":"),collapse=","),"}}\n",sep=""))
  if(i!=dim(new_x)[1]){cat(",")}
}
cat("];")
sink()

Working example

Hint: Clicking on the bars loads proportion of terms for a particular sample on the pie chart, selects that sample on the MDS plot and maintains the history for selection, where as clicking on the pie chart slices loads distribution of particular term on the bar plot. Double-clicking on the pie chart displays the stacked bar plot and removes all the selected samples from the MDS plot.