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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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celltype #195

Open newone1988 opened 10 months ago

newone1988 commented 10 months ago

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 commented 9 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.

kikokhalifa commented 7 months ago

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?