Finalizing Part A

Schrick-Noah_CS-6643_Lab-2.R

@@ -19,10 +19,10 @@ a <- list()
 
 # each merged pair in a row  
 a$merge <- rbind(c(-1, -2),  # +1 (A-B)
-                 c(1,-3)  ,  # +2 (A-B)-C  
-                 _______  ,  # +3 (D-E) 
-                 _______  ,  # +4 ((A-B)-C)-(DE)
-                 _______)    # +5 (((A-B)-C)-(DE))-F
+                 c( 1, -3),  # +2 (A-B)-C  
+                 c(-4, -5),  # +3 (D-E) 
+                 c( 2,  3),  # +4 ((A-B)-C)-(DE)
+                 c( 4, -6))  # +5 (((A-B)-C)-(DE))-F
 
 a$height <- c(1, 2, 1.5, 3, 4) # merge heights
 a$order <- 1:6               # order of leaves
@@ -46,7 +46,7 @@ plot(hc1,hang=-1)
 
 ## 4 - install and run WGCNA
 # Install
-install.packages("BiocManager")
+if (!require("BiocManager")) install.packages("BiocManager")
 library(BiocManager)
 BiocManager::install("WGCNA")
 
@@ -83,6 +83,27 @@ plotDendroAndColors(hc1,
 ## 2 - no supporting code
 
 ## 3 - Plot the dendrogram
+# initialize an empty list that will contain fields of our hclust object
+a <- list()  
+#    encoding rules: 
+#    negative numbers are leaves (A,B,...,E) -> (-1,-2,...,-5) 
+#    positive are merged clusters (defined by row number in $merge)
+
+# each merged pair in a row  
+a$merge <- rbind(c(-1, -2),  # +1 (A-B)
+                 c(1,-3)  ,  # +2 (A-B)-C  
+                 _______  ,  # +3 (D-E) 
+                 _______  ,  # +4 ((A-B)-C)-(DE)
+                 _______)    # +5 (((A-B)-C)-(DE))-F
+
+a$height <- c(1, 2, 1.5, 3, 4) # merge heights
+a$order <- 1:6               # order of leaves
+a$labels <- LETTERS[1:6]     # labels of leaves as Letters
+class(a) <- "hclust"         # force a to be hclust object
+# plot the tree
+# plot knows that a is an hclust object and plots accordingly 
+plot(a,hang=-1) # or use plot(as.dendrogram(a))
+
 
 ## 4 - Verify results
 # create distance matrix