--- a
+++ b/common_scripts/visualisation/oncoprint_memo.R
@@ -0,0 +1,56 @@
+# This function sorts the matrix for better visualization of mutual exclusivity across genes
+memoSort <- function(M) {
+  geneOrder <- sort(rowSums(M), decreasing=TRUE, index.return=TRUE)$ix;
+  scoreCol <- function(x) {
+    score <- 0;
+    for(i in 1:length(x)) {
+      if(x[i]) {
+        score <- score + 2^(length(x)-i);
+      }
+    }
+    return(score);
+  }
+  scores <- apply(M[geneOrder, ], 2, scoreCol);
+  sampleOrder <- sort(scores, decreasing=TRUE, index.return=TRUE)$ix;
+  return(M[geneOrder, sampleOrder]);
+}
+
+# This is the plotting function
+oncoPrint <- function(M, sort=TRUE) {
+  if(sort) {
+    alts <- memoSort(M);		
+  } else {
+    alts <- M;
+  }
+  
+  ngenes <- nrow(alts);
+  nsamples <- ncol(alts);
+  coverage <- sum(rowSums(alts) > 0);
+  
+  ### OncoPrint
+  numOfOncos <- ngenes*nsamples;
+  oncoCords <- matrix( rep(0, numOfOncos * 5), nrow=numOfOncos );
+  colnames(oncoCords) <- c("xleft", "ybottom", "xright", "ytop", "altered");
+  
+  xpadding <- .01;
+  ypadding <- .01;
+  cnt <- 1;
+  for(i in 1:ngenes) {
+    for(j in 1:nsamples) {
+      xleft <- j-1 + xpadding;
+      ybottom <- ((ngenes-i+1) -1) + ypadding;
+      xright <- j - xpadding;
+      ytop <- (ngenes-i+1) -ypadding;
+      altered <- alts[i, j];
+      
+      oncoCords[cnt, ] <- c(xleft, ybottom, xright, ytop, altered);
+      cnt <- cnt+1;
+    }
+  }
+  
+  colors <- rep("lightgray", cnt);
+  colors[ which(oncoCords[, "altered"] == 1) ] <- "black";
+  plot(c(0, nsamples), c(0, ngenes), type="n", main=sprintf("Gene set altered in %.2f%%: %d of %d cases", coverage/nsamples*100, coverage, nsamples), xlab="Samples", ylab="", yaxt="n");
+  rect(oncoCords[, "xleft"], oncoCords[, "ybottom"],oncoCords[, "xright"], oncoCords[, "ytop"], col=colors, border="white");
+  axis(2, at=(ngenes:1)-.5, labels=rownames(alts), las=2);
+}