Nothing
Make4DPlots <-
function(GraphQuant){
message(paste("Constructing 4D", substr(GraphQuant$Name,15,18), "model"));
PlotTabs <- NULL;
if (!is.null(GraphQuant)){
## MAKE ALL THE NECESSARY PLOTS AND SAVE IN SUBDIRECTORIES.
## THREE SUBDIRECTORIES WILL BE CREATED ALONG WITH A SILHOUETTE PDF PLOT.
## TRUE MODEL(BLACK), ESTIMATED CLUSTER MODEL AND TRUE CLUSTER MODEL(OPTIONAL)
## DETERMINE IF IT IS A PCoA MODEL OR A MDS MODEL AND CREATE A DIRECTORY ACCORDINGLY.
ModType <- substr(GraphQuant$Name, 15, 18);
if (substr(ModType,4,4) == ""){
ModType <- substr(ModType,1,3);
}
DirName <- paste(ModType, "4DModel",sep="");
dir.create(DirName, showWarnings = FALSE);
# THE SILHOUETTE PLOT TAB
pdf(paste(DirName,"/Silhouette.pdf", sep=""));
plot(GraphQuant$PamClRange, GraphQuant$SilPlot,'o', pch=18, main="Silhouette plot", xlab="Number of cluster", ylab="Silhouette width")
dev.off()
## THE MODEL WITH ESTIMATED CLUSTERS TAB
## CREATE A SUBDIRECTORY FOR THE WEBPAGES
DirName_Clust <- paste(DirName, "/EstimatedClusters", sep="");
dir.create(DirName_Clust, showWarnings = FALSE);
Colors <- rainbow(GraphQuant$OptimClust);
## Tab$ClustModel TAB CONTAINS 4 TABS, EACH WITH PLOTS CONSTRUCTED BY REMOVING ONE DIMENSION AT A TIME.
open3d(useNULL = TRUE) #Estimated cluster MDS plot showing XYZ axis
plot3d(GraphQuant$Coords[,-4], col = Colors[GraphQuant$ClusMem], type='s',size=1,xlab="X",ylab="Y",zlab="Z",main="Cluster model");
writeWebGL(dir = DirName_Clust, filename = file.path(DirName_Clust, "Model_XYZ.html"), width=800, height=800, snapshot = FALSE)
rgl.close();
open3d(useNULL = TRUE) #Estimated cluster MDS plot showing YZW axis
plot3d(GraphQuant$Coords[,-1], col = Colors[GraphQuant$ClusMem], type='s',size=1,xlab="Y",ylab="Z",zlab="W",main="Cluster model");
writeWebGL(dir = DirName_Clust, filename = file.path(DirName_Clust, "Model_YZW.html"), width=800, height=800, snapshot = FALSE)
rgl.close();
open3d(useNULL = TRUE) #Estimated cluster MDS plot showing XZW axis
plot3d(GraphQuant$Coords[,-2], col = Colors[GraphQuant$ClusMem], type='s',size=1,xlab="X",ylab="Z",zlab="W",main="Cluster model");
writeWebGL(dir = DirName_Clust, filename = file.path(DirName_Clust, "Model_XZW.html"), width=800, height=800, snapshot = FALSE)
rgl.close();
open3d(useNULL = TRUE) #Estimated cluster MDS plot showing XYW axis
plot3d(GraphQuant$Coords[,-3], col = Colors[GraphQuant$ClusMem], type='s',size=1,xlab="X",ylab="Y",zlab="W",main="Cluster model");
writeWebGL(dir = DirName_Clust, filename = file.path(DirName_Clust, "Model_XYW.html"), width=800, height=800, snapshot = FALSE)
rgl.close();
## SAVE THE ESTIMATED CLUSTERS AS A TEXT FILE.
SaveClus <- matrix(as.vector(GraphQuant$ClusMem), nrow = length(GraphQuant$ClusMem), ncol = 1);
rownames(SaveClus) <- paste("Sample", as.character(seq(1, nrow(SaveClus))), sep="");
write.table(GraphQuant$ClusMem, file = paste(DirName,"/ClusterMembership.txt", sep = ""), sep = ",", row.names = TRUE);
# THE MODEL WITH THE TRUE CLUSTERS TAB
if (!is.null(GraphQuant$TrueMem)){
## CREATE A SUBDIRECTORY FOR THE WEBPAGES
DirName_True <- paste(DirName, "/TrueModel", sep="");
dir.create(DirName_True, showWarnings = FALSE);
NClust <- length(table(GraphQuant$TrueMem));
Colors <- rainbow(NClust);
open3d(useNULL = TRUE) #Estimated cluster MDS plot showing XYZ axis
plot3d(GraphQuant$Coords[,-4], col = Colors[GraphQuant$TrueMem], type='s',size=1,xlab="X",ylab="Y",zlab="Z",main="True Clusters");
writeWebGL(dir = DirName_True, filename = file.path(DirName_True, "Model_XYZ.html"), width=800, height=800, snapshot = FALSE)
rgl.close();
open3d(useNULL = TRUE) #Estimated cluster MDS plot showing YZW axis
plot3d(GraphQuant$Coords[,-1], col = Colors[GraphQuant$TrueMem], type='s',size=1,xlab="Y",ylab="Z",zlab="W",main="True Clusters");
writeWebGL(dir = DirName_True, filename = file.path(DirName_True, "Model_YZW.html"), width=800, height=800, snapshot = FALSE)
rgl.close();
open3d(useNULL = TRUE) #Estimated cluster MDS plot showing XZW axis
plot3d(GraphQuant$Coords[,-2], col = Colors[GraphQuant$TrueMem], type='s',size=1,xlab="X",ylab="Z",zlab="W",main="True Clusters");
writeWebGL(dir = DirName_True, filename = file.path(DirName_True, "Model_XZW.html"), width=800, height=800, snapshot = FALSE)
rgl.close();
open3d(useNULL = TRUE) #Estimated cluster MDS plot showing XYW axis
plot3d(GraphQuant$Coords[,-3], col = Colors[GraphQuant$TrueMem], type='s',size=1,xlab="X",ylab="Y",zlab="W",main="True Clusters");
writeWebGL(dir = DirName_True, filename = file.path(DirName_True, "Model_XYW.html"), width=800, height=800, snapshot = FALSE)
rgl.close();
}
}
}
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