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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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DotPlot error in fetchdata #5273

Closed nayaracleite closed 2 years ago

nayaracleite commented 3 years ago

Hello,

I'm trying to do a DotPlot and I'm getting the following error: image

When I try to do a FeaturePlot, it works fine.

image

Idents(seurat_integrated) <- factor(Idents(seurat_integrated), levels = c("Ductal", "Beta ND",
    "Alpha", "Acinar", "Mesenchymal", "Beta T1D", "Immune", "Neuron"))
features <- c("INS", "NKX6-1", "GCG", "ARX", "CPA1", "COL1A1", "RAC2", "SPP1", "SOX10",
    "CHGA")
DotPlot(seurat_integrated, features = features, cols = c("blue", "red"), dot.scale = 8, split.by = "group") +
    RotatedAxis()
mhkowalski commented 3 years ago

Hi, do you have the integrated assay set as default? If so, it might be because the features you are looking to plot are not in the integrated assay (you can read more here #1198). We recommend using the RNA assay rather than the integrated assay for downstream analyses , so I would add assay = "RNA" to your DotPlot() command.

timoast commented 2 years ago

Closing this now, DotPlot() uses scaled data so those features may not have been scaled or may not be in the assay you're using.

WilliamMWei commented 2 years ago

Closing this now, DotPlot() uses scaled data so those features may not have been scaled or may not be in the assay you're using.

Hi excuse me for this but could I ask where could I find the information of which levels of the processed data do each visualizing function retrieve? Thank you so much