celltype

[newone1988]

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?

[zhanghao-njmu]

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 ([email protected]) and use their names as the group.by parameter.

[kikokhalifa]

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?