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I inserted the link to Dimplot, it is a good manual, also a brief description and an "R" tag. Good question
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M__ ♦
M__ ♦
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I saw in the extensive Seurat documentation for Dimplot (dimensional reduction plot), here, you can plot a gene by specifying it with group.by = "gene" but this does not work in practice.

> p <- DimPlot(DG.combined, reduction = "umap", group.by = "Fos")
Error: Cannot find 'Fos' in this Seurat object
> p <- DimPlot(DG.combined, reduction = "umap", group.by = "Inhba")
Error: Cannot find 'Inhba' in this Seurat object

Am I mistaken? Do I need to add a metadata column containing expression of the gene? How can I access individual cells gene expression data in seurat so I can create a metadata label based on binned expression levels? Also how would I tell seurat to use a color gradient to label them?

References https://satijalab.org/seurat/reference/dimplot

I saw in the Seurat documentation for Dimplot you can plot a gene by specifying it with group.by = "gene" but this does not work in practice.

> p <- DimPlot(DG.combined, reduction = "umap", group.by = "Fos")
Error: Cannot find 'Fos' in this Seurat object
> p <- DimPlot(DG.combined, reduction = "umap", group.by = "Inhba")
Error: Cannot find 'Inhba' in this Seurat object

Am I mistaken? Do I need to add a metadata column containing expression of the gene? How can I access individual cells gene expression data in seurat so I can create a metadata label based on binned expression levels? Also how would I tell seurat to use a color gradient to label them?

I saw in the extensive Seurat documentation for Dimplot (dimensional reduction plot), here, you can plot a gene by specifying it with group.by = "gene" but this does not work in practice.

> p <- DimPlot(DG.combined, reduction = "umap", group.by = "Fos")
Error: Cannot find 'Fos' in this Seurat object
> p <- DimPlot(DG.combined, reduction = "umap", group.by = "Inhba")
Error: Cannot find 'Inhba' in this Seurat object

Am I mistaken? Do I need to add a metadata column containing expression of the gene? How can I access individual cells gene expression data in seurat so I can create a metadata label based on binned expression levels? Also how would I tell seurat to use a color gradient to label them?

References https://satijalab.org/seurat/reference/dimplot

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Angus Campbell
Angus Campbell
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Plotting a gene in Seurat

I saw in the Seurat documentation for Dimplot you can plot a gene by specifying it with group.by = "gene" but this does not work in practice.

> p <- DimPlot(DG.combined, reduction = "umap", group.by = "Fos")
Error: Cannot find 'Fos' in this Seurat object
> p <- DimPlot(DG.combined, reduction = "umap", group.by = "Inhba")
Error: Cannot find 'Inhba' in this Seurat object

Am I mistaken? Do I need to add a metadata column containing expression of the gene? How can I access individual cells gene expression data in seurat so I can create a metadata label based on binned expression levels? Also how would I tell seurat to use a color gradient to label them?