Converting to functions and adding matrix heatmap support

Schrick-Noah_CS-6643_Lab-9.R

@@ -83,7 +83,83 @@ while( (n+m)!=2 ){
     m <- m-1
   }           
 } # end while
-
 seq_align
 
 
+#### Part D: Convert to functions
+make.alignment.matrices <- function(x_str, y_str, match_score, mismatch_score, 
+                                    gap_penalty){
+  ## Substitution Matrix
+  dna.letters<-c("A","C","G","T")
+  num.letters <- length(dna.letters)
+  S<-data.frame(matrix(0,nrow=num.letters,ncol=num.letters))  # data frame
+  rownames(S)<-dna.letters; colnames(S)<-dna.letters
+  for (i in 1:4){
+    for (j in 1:4){
+      if(dna.letters[i]==dna.letters[j]){ 
+        S[i,j]<- match_score
+      }
+      else{ 
+        S[i,j]<- mismatch_score
+      }
+    }
+  }
+  
+  ## F Matrix and T Matrix
+  x <- unlist(strsplit(x_str, ""))
+  y <- unlist(strsplit(y_str, ""))
+  x.len <- length(x) 
+  y.len <- length(y) 
+  
+  Fmat<-matrix(0,nrow=x.len+1,ncol=y.len+1) 
+  Tmat<-Fmat # 0's to start
+  
+  rownames(Fmat)<-c("-",x); colnames(Fmat)<-c("-",y)
+  rownames(Tmat)<-c("-",x); colnames(Tmat)<-c("-",y)
+  
+  # create first row and column
+  Fmat[,1]<- seq(from=0,len=x.len+1,by=-abs(gap_penalty))  
+  Fmat[1,]<- seq(from=0,len=y.len+1,by=-abs(gap_penalty))
+  Tmat[,1]<- rep(2,x.len+1)  # 2 means align with a gap in the upper seq
+  Tmat[1,]<- rep(3,y.len+1)  # 3 means align with a gap in the side seq
+  
+  ## Building Fmat and Tmat
+  for (i in 2:nrow(Fmat)){
+    for (j in 2:ncol(Fmat)){    # use F recursive rules 
+      test_three_cases <- c(Fmat[i-1, j-1] + S[rownames(Fmat)[i], colnames(Fmat)[j]],   # 1 mis/match
+                            Fmat[i-1, j] + gap_penalty,    # 2 up-gap
+                            Fmat[i, j-1] + gap_penalty)  # 3 left-gap
+      Fmat[i,j]=max(test_three_cases)
+      Tmat[i,j]=which.max(test_three_cases)
+    }
+  }
+  final_score <- Fmat[nrow(Fmat),ncol(Fmat)]
+  return(list(Fmat=Fmat, Tmat=Tmat, score_out=final_score))
+}
+
+# load new input
+x_str2 <- "GATTA"  # side sequence
+y_str2 <- "GAATTC" # top sequence
+match_score <- 2
+mismatch_score <- -1
+gap_penalty <- -2
+
+align.list2 <- make.alignment.matrices(x_str2, y_str2, match_score,
+                                       mismatch_score, gap_penalty)
+align.list2$Fmat
+align.list2$Tmat
+align.list2$score_out  
+  
+if (!require("gplots")) install.packages("gplots")
+library(gplots)
+Fmat2 <- align.list2$Fmat
+col = c("black","blue","red","yellow","green")
+breaks = seq(min(Fmat2),max(Fmat2),len=length(col)+1)
+
+heatmap.2(Fmat2[-1,-1], dendrogram='none', density.info="none", 
+          Rowv=FALSE, Colv=FALSE, trace='none', 
+          breaks = breaks, col = col,
+          sepwidth=c(0.01,0.01),
+          sepcolor="black",
+          colsep=1:ncol(Fmat2),
+          rowsep=1:nrow(Fmat2))