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plger / scDblFinder

Methods for detecting doublets in single-cell sequencing data

Home Page:https://plger.github.io/scDblFinder/

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why error ?

kdyoung100 opened this issue · comments

commented

bcmvn.MM482 <- find.pK(sweep.stats.MM482)
DimPlot(object = MM482.BM, reduction = 'umap', group.by = "RNA_snn_res.0.5", label = TRUE, repel = TRUE, raster=FALSE) + NoLegend()
FeaturePlot(MM482.BM, features = "scDblFinder.score", cols = c("yellow", "red"), reduction = 'umap', raster = FALSE) + DarkTheme()
FeaturePlot(MM482.BM, features = "pANN_0.25_0.005_555",cols = c("yellow", "red"), reduction = 'umap', raster=FALSE) + DarkTheme()
DimPlot(MM482.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_555")
DimPlot(MM482.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_483")
MM482.BM <- doubletFinder_v3(MM482.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM482, nExp = nExp_poi.adj.MM482, reuse.pANN = "pANN_0.25_0.005_555", sct = FALSE)
MM482.singlet <- subset(x = MM482.BM, subset = DF.classifications_0.25_0.005_483 == "Singlet")
MM482.singlet

FeaturePlot(MM482.BM, features = "scDblFinder.score", cols = c("yellow", "red"), reduction = 'umap', raster = FALSE) + DarkTheme()
Error: None of the requested features were found: scDblFinder.score in slot data
In addition: Warning message:
In FetchData(object = object, vars = c(dims, "ident", features), :
The following requested variables were not found: scDblFinder.score

commented

bcmvn.MM625 <- find.pK(sweep.stats.MM625)
DimPlot(object = MM625.BM, reduction = 'umap', group.by = "RNA_snn_res.0.5", label = TRUE, repel = TRUE, raster=FALSE) + NoLegend()
FeaturePlot(MM625.BM, features = "pANN_0.25_0.005_389",cols = c("yellow", "red"), reduction = 'umap', raster=FALSE) + DarkTheme()
MM625.BM <- doubletFinder_v3(MM625.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM625, nExp = nExp_poi.adj.MM625, reuse.pANN = "pANN_0.25_0.005_389", sct = FALSE)
DimPlot(MM625.BM, pt.size = 1, label = FALSE, label.size = 5, reduction = "umap", group.by = "scDblFinder.class")
DimPlot(MM625.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_389")
DimPlot(MM625.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_352")
MM625.singlet <- subset(x = MM625.BM, subset = DF.classifications_0.25_0.005_352 == "Singlet")
MM625.singlet
Error: Cannot find 'scDblFinder.class' in this Seurat object
why error?

commented

bcmvn.MM800 <- find.pK(sweep.stats.MM800)
DimPlot(object = MM800.BM, reduction = 'umap', group.by = "RNA_snn_res.0.5", label = TRUE, repel = TRUE, raster=FALSE) + NoLegend()
FeaturePlot(MM800.BM, features = "pANN_0.25_0.19_329",cols = c("yellow", "red"), reduction = 'umap', raster=FALSE) + DarkTheme()
MM800.BM <- doubletFinder_v3(MM800.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM800, nExp = nExp_poi.adj.MM800, reuse.pANN = "pANN_0.25_0.19_329", sct = FALSE)
DimPlot(MM800.BM, pt.size = 1, label = FALSE, label.size = 5, reduction = "umap", group.by = "scDblFinder.class")
DimPlot(MM800.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.19_329")
DimPlot(MM800.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.19_293")
MM800.singlet <- subset(x = MM800.BM, subset = DF.classifications_0.25_0.19_293 == "Singlet")
MM800.singlet
Error: None of the requested features were found: pANN_0.25_0.19_329 in slot data
In addition: Warning message:
In FetchData(object = object, vars = c(dims, "ident", features), :
The following requested variables were not found: pANN_0.25_0.19_329

MM800.BM <- doubletFinder_v3(MM800.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM800, nExp = nExp_poi.adj.MM800, reuse.pANN = "pANN_0.25_0.19_329", sct = FALSE)
Error in [.data.frame(seu@meta.data, , reuse.pANN) :
정의하지 않은 열들이 선택되었습니다
DimPlot(MM800.BM, pt.size = 1, label = FALSE, label.size = 5, reduction = "umap", group.by = "scDblFinder.class")
Error: Cannot find 'scDblFinder.class' in this Seurat object
DimPlot(MM800.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.19_329")
Error: Cannot find 'DF.classifications_0.25_0.19_329' in this Seurat object
DimPlot(MM800.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.19_293")
Error: Cannot find 'DF.classifications_0.25_0.19_293' in this Seurat object
MM800.singlet <- subset(x = MM800.BM, subset = DF.classifications_0.25_0.19_293 == "Singlet")
Error in FetchData(object = object, vars = unique(x = expr.char[vars.use]), :
None of the requested variables were found:
MM800.singlet
Error: object 'MM800.singlet' not found

why error??

commented

bcmvn.MM482 <- find.pK(sweep.stats.MM482)
DimPlot(object = MM482.BM, reduction = 'umap', group.by = "RNA_snn_res.0.5", label = TRUE, repel = TRUE, raster=FALSE) + NoLegend()
FeaturePlot(MM482.BM, features = "scDblFinder.score", cols = c("yellow", "red"), reduction = 'umap', raster = FALSE) + DarkTheme()
FeaturePlot(MM482.BM, features = "pANN_0.25_0.005_555",cols = c("yellow", "red"), reduction = 'umap', raster=FALSE) + DarkTheme()
DimPlot(MM482.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_555")
DimPlot(MM482.BM,pt.size = 1,label=FALSE, label.size = 5,reduction = "umap",group.by = "DF.classifications_0.25_0.005_483")
MM482.BM <- doubletFinder_v3(MM482.BM, PCs = use.pcs, pN = 0.25, pK = mpk.MM482, nExp = nExp_poi.adj.MM482, reuse.pANN = "pANN_0.25_0.005_555", sct = FALSE)
MM482.singlet <- subset(x = MM482.BM, subset = DF.classifications_0.25_0.005_483 == "Singlet")
MM482.singlet

FeaturePlot(MM482.BM, features = "scDblFinder.score", cols = c("yellow", "red"), reduction = 'umap', raster = FALSE) + DarkTheme()
Error: None of the requested features were found: scDblFinder.score in slot data
In addition: Warning message:
In FetchData(object = object, vars = c(dims, "ident", features), :
The following requested variables were not found: scDblFinder.score

commented

If you want help, you should try to make a minimum reproducible example rather than copy-pasting random chunks of mixed code and outputs. In this case the commands you run appear to be from the DoubletFinder package, so I'm not sure what you're doing here. If you want to run scDblFinder, please look at the documentation.