issue #49 : fixed handling of datasets with missing error; corrected …

…terminology in tooltip; distinguish between se and sd

R/mavevis.R

@@ -230,10 +230,14 @@ dashboard <- function(ssid,uniprotId=NULL,pdbs=NULL,mainChains=NULL,
 	errColIdx <- which(colnames(data) %in% c("se","SE","stderr","sem","SEM","sd","SD","stdev","std","STD"))
 	if (length(errColIdx) == 0) {
 		errCol <- NULL
+		errName <- NULL
 	} else {
 		errCol <- as.numeric(data[,errColIdx[[1]]])
+		errName <- colnames(data)[errColIdx]
 	}
 
+
+
 	cat("Filtering for single mutant variants...\n")
 	#Reduce to single mutants
 	#TODO: Add option to average over multi-mutants
@@ -337,6 +341,7 @@ dashboard <- function(ssid,uniprotId=NULL,pdbs=NULL,mainChains=NULL,
 			score=sm.data$score,error=sm.errCol,syn.med=syn.med,stop.med=stop.med,
 			grayBack=TRUE,img.width=img.width,tracks=td,pixelMap=pixelMap)
 		if (pixelMap && !is.null(pxMap)) {
+			pxMap$errName <- errName
 			mapFile <- getCacheFile(paste0("result_",outID,"_pxmap_",outFormat,".Rdata"))
 			save(pxMap,file=mapFile)
 		}

docker/cgi/getMap.R

@@ -54,23 +54,31 @@ if (!file.exists(mapfile)) {
 #load the pxMap object from the data file
 tryCatch({
 	load(mapfile)
-	mainMap <- na.omit(pxMap$main)
-	summaryMap <- na.omit(pxMap$summary)
+	mainMap <- pxMap$main
+	summaryMap <- pxMap$summary
+
+	errName <- "uncertainty"
+	if ("errName" %in% names(pxMap)) {
+		errName <- pxMap$errName
+	}
 
 	#translate main map into HTML areas
 	mainAreas <- paste(do.call(c,lapply(1:nrow(mainMap),function(i) with(mainMap[i,],{
 		paste0("<area shape=\"rect\" coords=\"",
-			paste(x0,y1,x1,y0,sep=","),"\" ",
-			"title=\"",sprintf("%s%d%s fitness=%.2f error=%.2f",wt,pos,aa,score,error),"\"",
-			"/>"
+			paste(x0,y1,x1,y0,sep=","),
+			"\" ","title=\"",
+			sprintf(
+				"Variant: %s%d%s; score = %.2f; %s = %.2f",
+				wt,pos,aa,score,errName,error
+			),"\"/>"
 		)
 	}))),collapse="\n")
 
 	#translate summary map into HTML areas
 	summaryAreas <- paste(do.call(c,lapply(1:nrow(summaryMap),function(i) with(summaryMap[i,],{
 		paste0("<area shape=\"rect\" coords=\"",
 			paste(x0,y1,x1,y0,sep=","),"\" ",
-			"title=\"",sprintf("%s%d median=%.2f",wt,pos,Median),"\"",
+			"title=\"",sprintf("Residue: %s%d; median=%.2f",wt,pos,Median),"\"",
 			"/>"
 		)
 	}))),collapse="\n")