<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>

CC BY-SA 4.0
2022-02-17T21:09:27.950Z
2022-02-17T21:09:27.950Z
gringer
<p>I am not totally sure what you are trying to do, but I think you want FeaturePlot, not DimPlot</p>

CC BY-SA 4.0
2022-02-17T21:04:33.537Z
2022-02-17T21:04:33.537Z
swbarnes2
<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>

<r><rna-seq><scrnaseq><seurat><visualization>
Plotting a gene in Seurat
# Plotting a gene in Seurat

(Asked by: username_0 on 2022-02-17)

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

**Tags:** r, rna-seq, scrnaseq, seurat, visualization

---

## 2 answers

### Answer by username_1 on 2022-02-17. Score: 2 | Accepted answer

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


---

### Answer by username_2 on 2022-02-17. Score: 2

I am not totally sure what you are trying to do, but I think you want FeaturePlot, not DimPlot


---

