Avoid dplyr loading

bbimber · bbimber · commit c83a8e94e35c · 2025-07-02T16:41:53.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SubsetSeurat.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SubsetSeurat.java
@@ -87,7 +87,7 @@ protected List<String> loadChunkFromFile() throws PipelineJobException
                     ret.add("\tprint(paste0('Subsetting dataset: ', datasetId, ' with the expression: " + subsetEscaped + "'))");
                     if (useDplyr)
                     {
-                        ret.add("\t\t\tcells <- rownames(seuratObj@meta.data %>% dplyr::filter( " + subset + " ))");
+                        ret.add("\t\t\tcells <- rownames(seuratObj@meta.data |> dplyr::filter( " + subset + " ))");
                     }
                     else
                     {

Original file line number	Diff line number	Diff line change
`@@ -87,7 +87,7 @@ protected List<String> loadChunkFromFile() throws PipelineJobException`
`87`	`87`	`ret.add("\tprint(paste0('Subsetting dataset: ', datasetId, ' with the expression: " + subsetEscaped + "'))");`
`88`	`88`	`if (useDplyr)`
`89`	`89`	`{`
`90`		`- ret.add("\t\t\tcells <- rownames(seuratObj@meta.data %>% dplyr::filter( " + subset + " ))");`
	`90`	`+ ret.add("\t\t\tcells <- rownames(seuratObj@meta.data \|> dplyr::filter( " + subset + " ))");`
`91`	`91`	`}`
`92`	`92`	`else`
`93`	`93`	`{`