@sjcrh/proteinpaint-server 2.53.0 → 2.55.0

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Files changed (7) hide show
  1. package/package.json +2 -2
  2. package/routes/gdc.maf.js +5 -2
  3. package/routes/gdc.topMutatedGenes.js +10 -5
  4. package/routes/termdb.cluster.js +6 -0
  5. package/routes/termdb.config.js +11 -2
  6. package/src/app.js +428 -336
  7. package/utils/hclust.R +6 -6
package/utils/hclust.R CHANGED
@@ -42,10 +42,10 @@ input <- fromJSON(json)
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  #print (dim(normalized_matrix))
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  # For Rows (i.e genes)
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- RowDist <- dist(input$matrix, method = "euclidean") # Transposing the matrix
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+ RowDist <- dist(input$matrix, method = tolower(input$distance_method)) # Transposing the matrix
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  # Hierarchical clustering
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- RowDend <- hclust(RowDist, method = tolower(input$cluster_method))
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- #RowDend <- flashClust(RowDist, method = tolower(input$cluster_method))
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+ RowDend <- hclust(RowDist, method = input$cluster_method)
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+ #RowDend <- flashClust(RowDist, method = input$cluster_method)
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  RowDendMergeDf <- as.data.frame(RowDend$merge)
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  colnames(RowDendMergeDf) <- c("n1","n2")
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  #print ("merge")
@@ -57,12 +57,12 @@ colnames(RowDendOrderHeight) <- "height"
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  #print (RowDendOrderHeight)
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  # For columns (i.e samples)
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- ColumnDist <- dist(t(input$matrix), method = "euclidean") # Transposing the matrix
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+ ColumnDist <- dist(t(input$matrix), method = tolower(input$distance_method)) # Transposing the matrix
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  # Hierarchical clustering
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- ColumnDend <- hclust(ColumnDist, method = tolower(input$cluster_method))
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- #ColumnDend <- flashClust(ColumnDist,method = tolower(input$cluster_method))
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+ ColumnDend <- hclust(ColumnDist, method = input$cluster_method)
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+ #ColumnDend <- flashClust(ColumnDist,method = input$cluster_method)
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  ColumnDendMergeDf <- as.data.frame(ColumnDend$merge)
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  colnames(ColumnDendMergeDf) <- c("n1","n2")