05162024: SeuratObjectFunctions.R changed.

vizapp/shinyapp/functions/SeuratObjectFunctions.R

@@ -213,18 +213,22 @@ getAvgExp=function(seuratObject,cells,colID,geneDescriptions,features) {
 		colID='Altogether'
 		cells$Altogether='all'
 	}
-	Idents(seuratObject)=cells[,colID]
 	features=unique(features)
-	expressions=AverageExpression(seuratObject,assays='RNA',features=features)	#By default this uses non-scaled values.
-	if (length(features)==1)
-		rownames(expressions[['RNA']])=features
-	expressions[['RNA']]=expressions[['RNA']][,mixedsort(colnames(expressions[['RNA']])),drop=F]
 	stats=cells%>%count(!!as.name(colID))
 	rownames(stats)=stats[,1]
-	stats=stats[colnames(expressions[['RNA']]),]
-	colnames(expressions[['RNA']])=paste0(colnames(expressions[['RNA']]),'(n=',stats$n,')')
+	ids=1:(dim(stats)[1])
+	names(ids)=rownames(stats)
+	if (colID=='Altogether')
+		Idents(seuratObject)='all'
+	else
+		Idents(seuratObject)=paste0('ID',ids[cells[,colID]],'@',cells[,colID])
+	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
+	expressions[['RNA']]=data.frame(expressions[['RNA']][,mixedsort(colnames(expressions[['RNA']])),drop=F],check.names=F)
+	colnames(expressions[['RNA']])=paste0(rownames(stats),'(n=',stats$n,')')
 	if (!is.null(geneDescriptions))
-		expressions[['RNA']]=cbind(name=paste0('"',left_join(data.frame(gene=rownames(expressions[['RNA']])),geneDescriptions,by=c('gene'='SYMBOL'))$name,'"'),expressions[['RNA']])
+		expressions[['RNA']]=cbind2(name=paste0('"',left_join(data.frame(gene=rownames(expressions[['RNA']])),geneDescriptions,by=c('gene'='SYMBOL'))$name,'"'),expressions[['RNA']])
 	return(expressions)
 }
 
@@ -238,11 +242,10 @@ getPercentExp=function(seuratObject,cells,colID,geneDescriptions,features) {
 	else
 		data=t(GetAssayData(seuratObject,assay='RNA')[features,,drop=F]>0)
 	percent=aggregate.Matrix(data,cells[,colID])
-	tempNames=rownames(percent)
 	stats=cells%>%count(!!as.name(colID))
-	percent=data.frame(t(percent*100/stats$n))
-	colnames(percent)=paste0(tempNames,'(n=',stats$n,')')
-	percent=percent[,mixedsort(colnames(percent)),drop=F]
+	rownames(stats)=stats[,1]
+	percent=data.frame(t(percent[rownames(stats),,drop=F]*100/stats$n),check.names=F)
+	colnames(percent)=paste0(rownames(stats),'(n=',stats$n,')')
 	if (!is.null(geneDescriptions))
 		percent=cbind(name=paste0('"',left_join(data.frame(gene=rownames(percent)),geneDescriptions,by=c('gene'='SYMBOL'))$name,'"'),percent)
 	return(percent)
@@ -442,7 +445,7 @@ saveDimPlots=function(seuratObject,fileName,format='png',split.by=NULL,shape.by=
 			if (is.null(split.by))
 				ggsave(paste0(fileName,'.',i),plot=p,height=20,width=20)
 			else
-				ggsave(paste0(fileName,'.',i),plot=p,height=10,width=30)
+#				ggsave(paste0(fileName,'.',i),plot=p,height=10,width=30)
 				ggsave(paste0(fileName,'.',i),plot=p,height=min(48,max(4,ceiling(infoList$nClusters/12)*4)),width=min(48,max(4,infoList$nClusters*4)))
 	}
 }