Seurat DimPlot generates a weird data frame together with the scatter plot
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25 days ago
solo.albif • 0

Hi all, for some reason that I can not figure out, this code:

 # View UMAP with macrophages and patient clusters
macrophage_cells_patient_id_plot <- DimPlot(
  breast_cancer_patients_macrophage_cells,
  reduction = "umap",
  group.by = "Patient.ID",
)
macrophage_cells_patient_id_plot

which makes use of the Seurat function DimPlot, generates not only the scatter plot but also a data.frame:

Unusual data frame generated by Seurat DimPlot

I have used the DimPlot function in many other R scripts/Quarto documents and this never happened. Has anyone experienced this? Why is this happening? Is it connected to the reductions in the Seurat object? How can I get rid of the data frame?

R Seurat • 470 views
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It seems that the issue is related to the following discussion. Can you just run the DimPlot() code without assigning it to an object?

https://github.com/rstudio/rstudio/issues/13470

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Yes, if I run DimPlot() without assigning to an object it works fine.

Thank you for the link to the RStudio issue! It did not come up during my searches.

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