<p>Try this:</p>

<pre class="lang-r prettyprint-override"><code>library(Seurat)
pbmc_small &lt;- RunUMAP(pbmc_small, dims = 1:10, reduction = "pca", n.components = 5)

names(pbmc_small[["umap"]])
#&gt; [1] "UMAP_1" "UMAP_2" "UMAP_3" "UMAP_4" "UMAP_5"

# plot
DimPlot(pbmc_small, reduction = "umap", dims = c(4, 5))
</code></pre>

<p><a href="https://i.sstatic.net/z3Vfd.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/z3Vfd.png" alt="enter image description here"></a></p>

<p>This should work with Seurat version 3.1.5</p>

<pre class="lang-r prettyprint-override"><code>packageVersion("Seurat")
#&gt; [1] '3.1.5'
</code></pre>

CC BY-SA 4.0
2020-05-14T12:34:17.913Z
2020-05-14T12:34:17.913Z
milanmlft
<p>Change <code>n.components</code> / <code>max.dims</code> (depending on your seurat version) to 5 when you call <code>runUMAP</code> and you should have dim 4 and 5 available.</p>

CC BY-SA 4.0
2019-12-24T15:48:41.070Z
Hi Pallie, i have tried to use "SAN <- RunUMAP(SAN, dims = 1:10, max.dim = 5L, dims.keep = 5L)"  and there still are no UMAP-4 and UMAP-5.
hua
CC BY-SA 4.0
2019-12-24T09:04:21.300Z
2019-12-24T09:04:21.300Z
Pallie
<p>I would like to know how to change the UMAP used in <code>Dimplot</code> and <code>FeaturePlot</code> from Seurat: how we can get the x-axis and the y-axis like UMAP-1 and UMAP-2 if I want to use UMAP-4 and UMAP-5. How to modify the code? It is easy to change the PC by using <code>DimPlot(object = pbmc_small, dims = c(4, 5), reduction = "PCA")</code> but if I changed to <code>reduction = "UMAP"</code>, I got the error </p>

<pre><code>"Error in Embeddings(object = object[[reduction]])[cells, dims] : subscript out of bounds Calls: DimPlot Execution halted". 
</code></pre>

<p>Does anyone have any idea how to solve this problem? </p>

CC BY-SA 4.0
2019-12-23T23:37:10.133Z
that is because UMAP-4 and UMAP-5 are not present in your object...head(object[['umap']]@cell.embeddings), or str(object[['umap']]@cell.embeddings)
Mack123456
CC BY-SA 4.0
2019-12-24T02:41:25.627Z
Yes, the UMAP-4 and UMAP-5 are not present in my project. So what should I do now?
hua
CC BY-SA 4.0
2020-05-14T13:42:23.090Z
What is the rationale for using UMAP-4 and UMAP-5? UMAP is different from PCA because you specify a dimension (usually) and it tries to put all information in those two dimensions.
Phoenix Mu
<seurat><single-cell>
how to change the UMAP use in the dimplot and feature plot
# how to change the UMAP use in the dimplot and feature plot

(Asked by: username_0 on 2019-12-23)

I would like to know how to change the UMAP used in Dimplot and FeaturePlot from Seurat: how we can get the x-axis and the y-axis like UMAP-1 and UMAP-2 if I want to use UMAP-4 and UMAP-5. How to modify the code? It is easy to change the PC by using DimPlot(object = pbmc_small, dims = c(4, 5), reduction = "PCA") but if I changed to reduction = "UMAP", I got the error 
"Error in Embeddings(object = object[[reduction]])[cells, dims] : subscript out of bounds Calls: DimPlot Execution halted". 

Does anyone have any idea how to solve this problem?

**Tags:** seurat, single-cell
> **Comments:**
> **username_1**: that is because UMAP-4 and UMAP-5 are not present in your object...head(object[['umap']]@cell.embeddings), or str(object[['umap']]@cell.embeddings)  
> **username_0**: Yes, the UMAP-4 and UMAP-5 are not present in my project. So what should I do now?  
> **username_2**: What is the rationale for using UMAP-4 and UMAP-5? UMAP is different from PCA because you specify a dimension (usually) and it tries to put all information in those two dimensions.  

---

## 2 answers

### Answer by username_3 on 2020-05-14. Score: 1

Try this:
library(Seurat)
pbmc_small <- RunUMAP(pbmc_small, dims = 1:10, reduction = "pca", n.components = 5)

names(pbmc_small[["umap"]])
#> [1] "UMAP_1" "UMAP_2" "UMAP_3" "UMAP_4" "UMAP_5"

# plot
DimPlot(pbmc_small, reduction = "umap", dims = c(4, 5))


This should work with Seurat version 3.1.5
packageVersion("Seurat")
#> [1] '3.1.5'


---

### Answer by username_4 on 2019-12-24. Score: 0

Change `n.components` / `max.dims` (depending on your seurat version) to 5 when you call `runUMAP` and you should have dim 4 and 5 available.

> **Comments:**
> **username_0**: Hi Pallie, i have tried to use "SAN <- RunUMAP(SAN, dims = 1:10, max.dim = 5L, dims.keep = 5L)"  and there still are no UMAP-4 and UMAP-5.  

---

