added log option to avgExp

vizapp/shinyapp/functions/my_ui.R

@@ -354,7 +354,7 @@ getPercentExpressions=function(seuratObject,geneDescriptions,features=NULL) {
 }
 ####################
 ####################
-getAvgExp=function(seuratObject,cells,colID,geneDescriptions,features) {
+getAvgExp=function(seuratObject,cells,colID,geneDescriptions,features,log) {
 	if (is.null(colID)) {
 		colID='Altogether'
 		cells$Altogether='all'
@@ -371,6 +371,9 @@ getAvgExp=function(seuratObject,cells,colID,geneDescriptions,features) {
 	expressions=AverageExpression(seuratObject,assays='RNA',features=features)	#By default this uses non-scaled values.	#This function doesn't preserve column names of expressions. a 'g' can be added as prefix.
 	if (length(features)==1)
 		rownames(expressions[['RNA']])=features
+	if (log==T){
+		expressions[['RNA']]=log2(expressions[['RNA']]+1) #Added by BC 
+	}
 	expressions[['RNA']]=data.frame(expressions[['RNA']][,mixedsort(colnames(expressions[['RNA']])),drop=F],check.names=F)
 	colnames(expressions[['RNA']])=paste0(rownames(stats),'(n=',stats$n,')')
 	if (!is.null(geneDescriptions))