Entering edit mode
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:
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?
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
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.