Optional 3 and report

.~lock.Schrick-Noah_CS-6643_Lab-4.docx#

@@ -1 +0,0 @@
-,noah,NovaArchSys,30.09.2022 13:06,file:///home/noah/.config/libreoffice/4;

Schrick-Noah_CS-6643_Lab-4.R

@@ -171,3 +171,45 @@ colors = rep("black",nrow(SxG.df))
 colors[startsWith(rownames(SxG.df),"MDD")] <- "red"
 plot(obs_umap$layout, col=colors, 
      main="umap of observations", xlab="umap dim1", ylab="umap dim2")
+
+#### Optional 3: WGCNA and UMAP of Genes
+if (!require("BiocManager")) install.packages("BiocManager")
+library(BiocManager)
+if (!require("WGCNA")) BiocManager::install("WGCNA")
+library(WGCNA)
+
+# change umap config parameters
+custom.config = umap.defaults
+custom.config$random_state = 123
+custom.config$n_epochs = 50
+custom.config$n_neighbors=30
+custom.config$metric = "pearson"
+custom.config$input = "dist"
+custom.config$a = 9.5
+custom.config$b = 0.5
+
+GxS.df <- data.frame(GxS.covfilter)
+
+obs_umap = umap(GxS.df, config=custom.config)
+#add colors for MDD/HC
+colors = rep("black",nrow(GxS.df))
+colors[startsWith(colnames(GxS.df),"MDD")] <- "red"
+plot(obs_umap$layout, col=colors, 
+     main="umap of observations", xlab="umap dim1", ylab="umap dim2")
+
+# Plot the dendrogram and colors underneath
+num.clust <- 2
+mddCuts <- cutree(mddTree,k=num.clust)
+
+sizeGrWindow(8,6)
+dynamicMods = cutreeDynamic(dendro = mddTree, distM = d,
+                            deepSplit = 2, pamRespectsDendro = FALSE,
+                            minClusterSize = 2, method = "hybrid")
+mddColors = labels2colors(dynamicMods)
+table(mddColors)
+mddColorstable <- table(mddColors,names(mddCuts))
+prop.table(mddColorstable, margin = 1)
+plotDendroAndColors(mddTree, mddColors, "Dynamic Clusters",
+                    dendroLabels = NULL, # hang = -1,
+                    addGuide = TRUE, #guideHang = 0.05,
+                    main = "Clustering with WGCNA")