Final edits

Schrick-Noah_CS-6643_Lab-2.R

@@ -38,8 +38,10 @@ my.dist1 <- read.table("distance_matrix.txt",sep="\t", header=T)
 rownames(my.dist1) = colnames(my.dist1)
 my.dist1[lower.tri(my.dist1)] = t(my.dist1)[lower.tri(my.dist1)]
 hc1 <- hclust(as.dist(my.dist1), method="average")
+hc1
 plot(hc1,hang=-1)
 
+
 ## 2 - Paste the distance matrix in the report. Use header=T
 
 ## 3 - no supporting code
@@ -48,6 +50,7 @@ plot(hc1,hang=-1)
 # Install
 if (!require("BiocManager")) install.packages("BiocManager")
 library(BiocManager)
+if (!require("WGCNA"))
 BiocManager::install("WGCNA")
 
 # load WGCNA and run on the hc1 dendrogram
@@ -61,7 +64,9 @@ dynamicMods = cutreeDynamic(
   minClusterSize = 2)
 names(dynamicMods) <- colnames(my.dist1)
 
-## 5 - no supporting code
+## 5 - identify clusters
+dynamicMods
+
 
 ## 6 - show clustered data
 dynamicColors = labels2colors(dynamicMods) # colors might not work
@@ -91,18 +96,17 @@ 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, -4),   # +2 (A-B)-D  
+                 c(2, -3))   # +3 ((A-B)-D)-C 
  
-a$height <- c(1, 2, 1.5, 3, 4) # merge heights
-a$order <- 1:6               # order of leaves
-a$labels <- LETTERS[1:6]     # labels of leaves as Letters
+
+a$height <- c(0.14, 0.305, 0.51) # merge heights
+a$order <- 1:4               # order of leaves
+a$labels <- LETTERS[1:4]     # 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))
+plot(a) # or use plot(as.dendrogram(a))
 
 
 ## 4 - Verify results
@@ -121,7 +125,7 @@ test$merge
 test$height
 test$order
 test$labels<-LETTERS[1:4]
-plot(test,hang=-1)
+plot(test)
 
 #### Part D - MDS
 ## 1 - Show the 2D MDS