Merge pull request #344 from OpenKnowledgeMaps/fix-336-maprotation

Fix 336 maprotation

Author: pkraker

server/preprocessing/other-scripts/cluster.R

@@ -97,7 +97,13 @@ get_ndms <- function(distance_matrix, mindim=2, maxdim=2, maxit=500) {
   # nm.nmin = nmds.min(nm)
   if (nrow(distance_matrix) <= 2) {
     points <- tryCatch({
-      ord <- metaMDS(distance_matrix, k = 2, parallel = 3)
+      ord <- metaMDS(distance_matrix, k = 2, parallel = 3, trymax=30,
+                     engine="monoMDS", distance='cao',
+                     threshold = 0.19, nthreshold=10,
+                     model = "linear",
+                     pc = TRUE,
+                     autotransform = FALSE, center = TRUE,
+                     halfchange = TRUE)
       points <- ord$points
     }, error=function(err){
       points <- cbind(runif(nrow(distance_matrix), min=-1, max=0),
@@ -107,20 +113,18 @@ get_ndms <- function(distance_matrix, mindim=2, maxdim=2, maxit=500) {
   } else if (nrow(distance_matrix) == 1) {
     points <- cbind(0, 0)
   } else {
-    ord <- metaMDS(distance_matrix, k = 2, parallel = 3)
+    ord <- metaMDS(distance_matrix, k = 2, parallel = 3, trymax=30,
+                   engine="monoMDS", distance='cao',
+                   threshold = 0.19, nthreshold=10,
+                   model = "linear",
+                   pc = TRUE,
+                   autotransform = FALSE, center = TRUE,
+                   halfchange = TRUE)
     points <- ord$points
     vclog$info(paste("NMDS-Stress:", min(ord$stress), sep=" "))
   }
 
-  # vclog$info(paste("NMDS-R2:", min(nm$r2), sep=" "))
 
-  # NEEDS FIX
-  # if(exists("DEBUG") && DEBUG == TRUE) {
-  #   # Plot results from multidimensional scaling, highlight clusters with symbols
-  #   pdf("mds.pdf")
-  #   plot(nm.nmin, pch=groups)
-  #   dev.off()
-  # }
   layout <- list(X1 = points[,1], X2 = points[,2])
   return(layout)
 }

server/preprocessing/other-scripts/postprocess.R

@@ -19,6 +19,19 @@ create_output <- function(clusters, layout, metadata) {
 
   output_json = toJSON(output)
 
+  if(exists("DEBUG") && DEBUG == TRUE) {
+    library(ggplot2)
+    # Plot results from multidimensional scaling, highlight clusters with symbols
+    temp <- fromJSON(output_json)
+    temp$x <- as.numeric(temp$x)
+    temp$y <- as.numeric(temp$y)
+    temp$title <- unlist(lapply(temp$title, substr, start=0, stop=15))
+    g <- ggplot(temp, aes(x, y, label=title)) +
+          geom_point(aes(colour=area_uri)) +
+          geom_text(size=2)
+    ggsave(file = "debug_nmds.svg", plot = g, width = 15, height = 15)
+  }
+
   # NEEDS FIX
   # if(exists("DEBUG") && DEBUG == TRUE) {
   #   # Write output to file

server/preprocessing/other-scripts/test/params_base.json

@@ -1,7 +1,7 @@
 {
   "document_types":["121"],
   "from":"1665-01-01",
-  "to":"2017-08-19",
-  "sorting":"most-recent",
+  "to":"2019-02-12",
+  "sorting":"most-relevant",
   "lang_id":"eng"
 }