text: user2482: 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
  
  user2388: I am not totally sure what you are trying to do, but I think you want FeaturePlot, not DimPlot
  
  user73: As @swbarnes2 has suggested, you can plot gene expression over the top of a dimensional reduction using the FeaturePlot function, using the features parameter for gene names:
  p <- FeaturePlot(DG.combined, reduction = "umap", features = c("Fos", "Inhba"))
  
  See the 3k tutorial here:
  https://satijalab.org/seurat/articles/pbmc3k_tutorial.html#cb49
  
original_text: 2482: <p>I saw in the extensive Seurat documentation for Dimplot (dimensional reduction plot), <a href="https://satijalab.org/seurat/reference/dimplot" rel="nofollow noreferrer">here</a>, you can plot a gene by specifying it with group.by = &quot;gene&quot; but this does not work in practice.</p>
  <pre><code>&gt; p &lt;- DimPlot(DG.combined, reduction = &quot;umap&quot;, group.by = &quot;Fos&quot;)
  Error: Cannot find 'Fos' in this Seurat object
  &gt; p &lt;- DimPlot(DG.combined, reduction = &quot;umap&quot;, group.by = &quot;Inhba&quot;)
  Error: Cannot find 'Inhba' in this Seurat object
  </code></pre>
  <p>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?</p>
  <p>References
  <a href="https://satijalab.org/seurat/reference/dimplot" rel="nofollow noreferrer">https://satijalab.org/seurat/reference/dimplot</a></p>
   2388: <p>I am not totally sure what you are trying to do, but I think you want FeaturePlot, not DimPlot</p>
   73: <p>As @swbarnes2 has suggested, you can plot gene expression over the top of a dimensional reduction using the <code>FeaturePlot</code> function, using the <code>features</code> parameter for gene names:</p>
  <pre><code>p &lt;- FeaturePlot(DG.combined, reduction = &quot;umap&quot;, features = c(&quot;Fos&quot;, &quot;Inhba&quot;))
  </code></pre>
  <p>See the 3k tutorial here:</p>
  <p><a href="https://satijalab.org/seurat/articles/pbmc3k_tutorial.html#cb49" rel="nofollow noreferrer">https://satijalab.org/seurat/articles/pbmc3k_tutorial.html#cb49</a></p>
  