Open newone1988 opened 10 months ago
group.by = c("CellType", "SubCellType")
means using the CellType
and SubCellType
variables from the pancreas_sub
dataset to plot the graph. In your dataset, you need to check the grouping variables available for plotting in your data (GSM6784571_object@meta.data
) and use their names as the group.by
parameter.
I used a downloaded data to try SCP,but it always reminder me the data lack the celltype.
CellDimPlot(
* srt = GSM6784571_object, group.by = c("CellType", "SubCellType"), * reduction = "StandardUMAP2D", theme_use = "theme_blank" * ) Error in CellDimPlot(srt = GSM6784571_object, group.by = c("CellType", : CellType is not in the meta.data of srt object.
Do I need to annotate cell types myself before conducting subsequent analysis using SCP?
I had the same problem, may I ask what was the final solution?
I used a downloaded data to try SCP,but it always reminder me the data lack the celltype.
Do I need to annotate cell types myself before conducting subsequent analysis using SCP?