<p>It's possible that the original identities are encoded in the Seurat object under the name <code>orig.ident</code>.</p>
<pre><code>old.cluster.ids &lt;- pbmc$orig.ident
</code></pre>
<p>I prefer explicitly creating a new named metadata value in the Seurat object for each new feature I want to add, including the initial clusters:</p>
<pre><code>pbmc<span class="math-container">$seurat.clusterID &lt;- Idents(pbmc)
pbmc$</span>cluster.names &lt;- new.cluster.ids
</code></pre>
<p>More details about identity modifications can be found here:</p>
<p><a href="https://satijalab.org/seurat/articles/essential_commands.html" rel="nofollow noreferrer">https://satijalab.org/seurat/articles/essential_commands.html</a></p>
<p>Most Seurat functions allow you to specify the identity using the <code>ident</code> parameter, which means you can often create workflows that don't need to ever explicitly change the default identity.</p>

CC BY-SA 4.0
2024-04-26T21:50:09.270Z
2024-04-26T21:50:09.270Z
gringer
<p>I am analysing the scRNA-seq data using Seurat, in the annotation step, I change the idents of cell manually using the function <code>RenameIdents</code>:</p>
<pre class="lang-r prettyprint-override"><code>new.cluster.ids &lt;- c(&quot;Naive CD4 T&quot;, &quot;CD14+ Mono&quot;, &quot;Memory CD4 T&quot;, &quot;B&quot;, &quot;CD8 T&quot;, &quot;FCGR3A+ Mono&quot;,
    &quot;NK&quot;, &quot;DC&quot;, &quot;Platelet&quot;)
names(new.cluster.ids) &lt;- levels(pbmc)
pbmc &lt;- RenameIdents(pbmc, new.cluster.ids)
</code></pre>
<p>Now I want to get back to the original indent which uses number such as 0 1 2 3...</p>

<scrnaseq><seurat>
After changing the idents of cells in seurat, how can I get back to original ident?
# After changing the idents of cells in seurat, how can I get back to original ident?

(Asked by: username_0 on 2024-04-25)

I am analysing the scRNA-seq data using Seurat, in the annotation step, I change the idents of cell manually using the function RenameIdents:
new.cluster.ids <- c("Naive CD4 T", "CD14+ Mono", "Memory CD4 T", "B", "CD8 T", "FCGR3A+ Mono",
    "NK", "DC", "Platelet")
names(new.cluster.ids) <- levels(pbmc)
pbmc <- RenameIdents(pbmc, new.cluster.ids)

Now I want to get back to the original indent which uses number such as 0 1 2 3...

**Tags:** scrnaseq, seurat

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## 1 answers

### Answer by username_1 on 2024-04-26. Score: 3 | Accepted answer

It's possible that the original identities are encoded in the Seurat object under the name orig.ident.
old.cluster.ids <- pbmc$orig.ident

I prefer explicitly creating a new named metadata value in the Seurat object for each new feature I want to add, including the initial clusters:
pbmc$seurat.clusterID <- Idents(pbmc)
pbmc$cluster.names <- new.cluster.ids

More details about identity modifications can be found here:
https://satijalab.org/seurat/articles/essential_commands.html
Most Seurat functions allow you to specify the identity using the ident parameter, which means you can often create workflows that don't need to ever explicitly change the default identity.


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