comparison edgeR_Differential_Gene_Expression.xml @ 122:7bb87a6bc4d5 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc

121:6c90a67a13fa

  
  # hierarchical clustering makes use of the distance of the MDS
  if(output_MDSplot_logFC != "/dev/null" || output_MDSplot_logFC_coordinates != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
    write("Calculating MDS plot (logFC method)",stdout())
    n_dim <- nrow(dge\$samples)
    mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
    dev.off()# Kill it
    
    # Reset to primary dimensions
    mds_distance_logFC\$x = mds_distance_logFC\$cmdscale.out[,1]

122:7bb87a6bc4d5

  
  # hierarchical clustering makes use of the distance of the MDS
  if(output_MDSplot_logFC != "/dev/null" || output_MDSplot_logFC_coordinates != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
    write("Calculating MDS plot (logFC method)",stdout())
    n_dim <- nrow(dge\$samples)
    
    if(n_dim >= nrow(dge\$counts)) {
      n_dim <- 3
    }
    
    mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
    dev.off()# Kill it
    
    # Reset to primary dimensions
    mds_distance_logFC\$x = mds_distance_logFC\$cmdscale.out[,1]