Generation of Heatmaps from Microarray Data (KEGG2heatmap or GO2heatmap)

From Bioconductor mailing list (Saurin D. Jani" <saurin_jani@yahoo.com>)

1. Input: expression matrix, chip environments
2. output: heatmaps of all the pathways for all the genes in expression matrix

1. About Pathway to HEATMAP

1. Variable explanation:

1. esetSub2 = expression matirx
2. esetSub2X = exprs(esetSub2)
3. chiptype = annotation found from GeneChip, here 'hgu95a'
4. envPath2Probes = Environment
5. e.g.
6. envGeneNames <- hgu95aGENENAME;
7. envPath2Probes <- hgu95aPATH2PROBE;

1. Generate Pathway Heatmap

? All_DE_Pathway <- aafPathway(featureNames(esetSub2), chiptype); ? unique(sapply(All_DE_Pathway, length)); ? pathlist <- do.call("c", All_DE_Pathway); ? pathL <- length(pathlist); ? pathmatrix <- sapply(pathlist, attributes); ? pathnamesX <- unique(t(pathmatrix)); ? kegg <- as.list(envPath2Probes); ? pathRow <-? as.numeric(nrow(pathnamesX)); ? if(pathL >=1) ? { ??? for(i in 1:pathRow) ??? { ????? pathID <- pathnamesX[,"id"][i]; ????? pathID <- as.character(unlist(pathID));

????? pathName <- as.character(unlist(pathnamesX[,"name"][i])); ????? pathName <- trimWhiteSpace(pathName); ????? pathName <- sub("/", "_", pathName); ????? pathName <- sub(" ", "_", pathName); ????? pathName <- sub("? ", "_", pathName); ????? pathName <- sub("?? ", "_", pathName); ????? pathName <- sub(" ", "_", pathName); ????? pathName <- sub("-", "_", pathName); ????? pathFile <- paste("Pathway",pathName,".jpeg",sep = "_"); ????? pathSub <- paste(pathName,"Legend: Red = High, Blue = Low, White = Medium",sep = "? "); ????? pathSub <- paste("Date of Analysis:",date(),pathSub,sep = "? ");

????? Pathway2Heatmap(pathID,pathFile,pathSub); # check out the function below ??? }

? } # if ends here

Pathway2Heatmap <- function(pathway,file,Hsub) {

? kegg <- as.list(envPath2Probes); ? pathProbes <- as.matrix(keggpathway); # genes extracted from pathway ? esetSub2Genes <- as.matrix(featureNames(esetSub2));

? temp <- as.matrix(rbind(unique(esetSub2Genes),unique(pathProbes))); ? temp1 <- as.matrix(temp[ as.matrix(duplicated(temp,))]);

? exp2 <- esetSub2[temp1]; ? exp2X <-? exprs(exp2);

? pathDEGenes <- as.matrix(featureNames(exp2)); ? pathDEGeneNames <- mget(unique(pathDEGenes),env = envGeneNames,ifnotfound="No Annotation For this Probe");

? row.names(exp2X) <- pathDEGeneNames; ? colnames(exp2X) <- samples;

? if (nrow(exp2X) > 1) ? { ??? jpeg(filename= file,width=2000,height=2000); ??? row.dist <- as.dist(1 - cor(t(exp2X))); ??? Hsub <- c("Generated by EXAMPLE"); ??? gmpalette <- bluered(64);

heatmap.2(exp2X,col=gmpalette,Colv= FALSE,Rowv = as.dendrogram(hclust(row.dist,method="centroid")),scale="row",key=TRUE,keysize=0.60,symkey=FALSE,density.info="none",trace="none",margins=c(5,85),cexRow=1,cexCol=1, sub=Hsub,cex.sub=1);

dev.off(which = dev.cur());

??? print("Pathway Heat map done"); ? }#if

?if(nrow(exp2X) == 1) ? {

? dotchart(exp2X); ? p_t <- paste(Hsub,"Gene:",pathDEGeneNames,sep = " "); ? title(sub = p_t,cex.sub = 1); ? dev.off(); ?}

}#pathway2heatmap