Friedman test with post-hoc using Bergmann-Hommel procedure

friedman.test.with.post.hoc.R

friedman.test.with.post.hoc <- function(data, alpha = 0.05)
{
  print("Check if you missing the packages 'graph' and 'Rgraphviz'. Try to install them using bioconductor")
  
  #source("http://bioconductor.org/biocLite.R")
  #biocLite(c("graph","Rgraphviz"))
  
  # Loading needed packages
  if(!require(ggplot2))
  {
    print("You are missing the package 'ggplot2', we will now try to install it...")
    install.packages("ggplot2")
    library(ggplot2)
  }
  
  if(!require(scmamp))
  {
    print("You are missing the package 'scmamp', we will now try to install it...")
    install.packages("scmamp")
    library(scmamp)
  }
  
  pre.results <- friedmanTest(data)
  imanDavenport.result <- imanDavenportTest(data)
  
  if(pre.results$p.value < alpha){
    post.results <- NULL
    
    if(length(colnames(my_data)) > 9){
      post.results <- postHocTest(data=data, test="friedman", correct="shaffer")
    }else{
      post.results <- postHocTest(data=data, test="friedman", correct="bergmann")
    }
    
    ## LaTeX formated: Significances highlighted in bold
    #avg.val <- post.results$summary
    
    #best.res <- avg.val == max(avg.val)
    #stat.diff <- post.results$corrected.pval < 0.05
    #stat.diff[is.na(stat.diff)] <- FALSE
    
    #writeTabular(table = avg.val, format = 'f', bold = best.res, mark = stat.diff, digits = 1)
    
    bold <- post.results$corrected.pval < alpha
    bold[is.na(bold)] <- FALSE
    writeTabular(table=post.results$corrected.pval, format='f', bold=bold, hrule=0, vrule=0)
    
    friedman.mc <- friedmanmc(data.matrix(data))
    
    plt <- plotPvalues(post.results$corrected.pval, alg.order=order(post.results$summary)) + labs(title=paste("Corrected p-values using Bergmann and Hommel procedure",sep="")) + xlab("Algorithm") + ylab("Algotithm") + scale_fill_gradientn("Corrected p-values" , colours = c("grey15" , "grey30"))
    list.to.return <- list(Friedman = pre.results, ImanDavenport = imanDavenport.result, PostHoc = post.results, FriedmanMC = friedman.mc, Plt = plt)
    return(list.to.return)
  }
  else{
    print("The results where not significant. There is no need for a post-hoc test.")
    list.to.return <- list(Friedman = pre.results, ImanDavenport = imanDavenport.result, PostHoc = NULL, FriedmanMC = NULL, Plt = NULL)
    return(list.to.return)
  }
}