noah/CS-6643-Bioinformatics-Lab-2
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This commit is contained in:
Noah L. Schrick 2022-09-15 17:48:15 -05:00
parent 26e4e4fe97
commit 798191249d
1 changed files with 15 additions and 11 deletions
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Schrick-Noah_CS-6643_Lab-2.R
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@ -38,8 +38,10 @@ my.dist1 <- read.table("distance_matrix.txt",sep="\t", header=T)
rownames(my.dist1) = colnames(my.dist1) rownames(my.dist1) = colnames(my.dist1)
my.dist1[lower.tri(my.dist1)] = t(my.dist1)[lower.tri(my.dist1)] my.dist1[lower.tri(my.dist1)] = t(my.dist1)[lower.tri(my.dist1)]
hc1 <- hclust(as.dist(my.dist1), method="average") hc1 <- hclust(as.dist(my.dist1), method="average")
hc1
plot(hc1,hang=-1) plot(hc1,hang=-1)
## 2 - Paste the distance matrix in the report. Use header=T ## 2 - Paste the distance matrix in the report. Use header=T
## 3 - no supporting code ## 3 - no supporting code
@ -48,6 +50,7 @@ plot(hc1,hang=-1)
# Install # Install
if (!require("BiocManager")) install.packages("BiocManager") if (!require("BiocManager")) install.packages("BiocManager")
library(BiocManager) library(BiocManager)
if (!require("WGCNA"))
BiocManager::install("WGCNA") BiocManager::install("WGCNA")
# load WGCNA and run on the hc1 dendrogram # load WGCNA and run on the hc1 dendrogram
@ -61,7 +64,9 @@ dynamicMods = cutreeDynamic(
minClusterSize = 2) minClusterSize = 2)
names(dynamicMods) <- colnames(my.dist1) names(dynamicMods) <- colnames(my.dist1)
## 5 - no supporting code ## 5 - identify clusters
dynamicMods
## 6 - show clustered data ## 6 - show clustered data
dynamicColors = labels2colors(dynamicMods) # colors might not work dynamicColors = labels2colors(dynamicMods) # colors might not work
@ -91,18 +96,17 @@ a <- list()
# each merged pair in a row # each merged pair in a row
a$merge <- rbind(c(-1, -2), # +1 (A-B) a$merge <- rbind(c(-1, -2), # +1 (A-B)
c(1,-3) , # +2 (A-B)-C c(1, -4), # +2 (A-B)-D
_______ , # +3 (D-E) c(2, -3)) # +3 ((A-B)-D)-C
_______ , # +4 ((A-B)-C)-(DE)
_______) # +5 (((A-B)-C)-(DE))-F
a$height <- c(1, 2, 1.5, 3, 4) # merge heights a$height <- c(0.14, 0.305, 0.51) # merge heights
a$order <- 1:6 # order of leaves a$order <- 1:4 # order of leaves
a$labels <- LETTERS[1:6] # labels of leaves as Letters a$labels <- LETTERS[1:4] # labels of leaves as Letters
class(a) <- "hclust" # force a to be hclust object class(a) <- "hclust" # force a to be hclust object
# plot the tree # plot the tree
# plot knows that a is an hclust object and plots accordingly # 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 ## 4 - Verify results
@ -121,7 +125,7 @@ test$merge
test$height test$height
test$order test$order
test$labels<-LETTERS[1:4] test$labels<-LETTERS[1:4]
plot(test,hang=-1) plot(test)
#### Part D - MDS #### Part D - MDS
## 1 - Show the 2D MDS ## 1 - Show the 2D MDS
@ -134,4 +138,4 @@ plot(x,y,main="Multi-dimensional Scaling",
xlab="MDS dimension-1", ylab="MDS dimension-2", pch=NA,asp=1) xlab="MDS dimension-1", ylab="MDS dimension-2", pch=NA,asp=1)
# pch specifies plot symbol; we want null because we are using letter next # pch specifies plot symbol; we want null because we are using letter next
# plot the text labels instead of symbols: # plot the text labels instead of symbols:
text(x,y,test$labels,cex=1) text(x,y,test$labels,cex=1)