Plot UCell/Gene correlations

bbimber · bbimber · commit c4dc67c4371b · 2024-03-11T19:43:19.000-07:00
diff --git a/singlecell/resources/chunks/CustomUCell.R b/singlecell/resources/chunks/CustomUCell.R
@@ -13,6 +13,9 @@ for (datasetId in names(seuratObjects)) {
   }
 
   seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate, storeRanks = storeRanks, assay = assayName)
+  corData <- RIRA::PlotUcellCorrelation(seuratObj, toCalculate)
+  saveRDS(corData, file = paste0(datasetId, '.ucellcorr.rds'))
+
   for (n in names(toCalculate)) {
     print(Seurat::FeaturePlot(seuratObj, features = paste0(n, '_UCell'), min.cutoff = 'q02', max.cutoff = 'q98'))
   }

Original file line number	Diff line number	Diff line change
`@@ -13,6 +13,9 @@ for (datasetId in names(seuratObjects)) {`
`13`	`13`	`}`
`14`	`14`
`15`	`15`	`seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate, storeRanks = storeRanks, assay = assayName)`
	`16`	`+ corData <- RIRA::PlotUcellCorrelation(seuratObj, toCalculate)`
	`17`	`+ saveRDS(corData, file = paste0(datasetId, '.ucellcorr.rds'))`
	`18`	`+`
`16`	`19`	`for (n in names(toCalculate)) {`
`17`	`20`	`print(Seurat::FeaturePlot(seuratObj, features = paste0(n, '_UCell'), min.cutoff = 'q02', max.cutoff = 'q98'))`
`18`	`21`	`}`