<p>See the <code>DoHeatmap</code> function in Seurat, which seems to be what that paper has used:</p>
<p><a href="https://satijalab.org/seurat/articles/pbmc3k_tutorial.html#cb50" rel="nofollow noreferrer">https://satijalab.org/seurat/articles/pbmc3k_tutorial.html#cb50</a></p>
<pre><code>&gt; DoHeatmap(pbmc, features = myGeneList, group.by=&quot;Condition&quot;)
</code></pre>

CC BY-SA 4.0
2021-07-29T23:15:46.260Z
2021-07-29T23:15:46.260Z
gringer
<p>I have a Seurat object of four cancers and four controls</p>
<pre><code>&gt; colnames(pbmc@meta.data)
 [1] &quot;orig.ident&quot;       &quot;nCount_RNA&quot;       &quot;nFeature_RNA&quot;     &quot;samples&quot;         
 [5] &quot;Condition&quot;        &quot;Gender&quot;           &quot;percent.mt&quot;       &quot;nCount_SCT&quot;      
 [9] &quot;nFeature_SCT&quot;     &quot;SCT_snn_res.0.75&quot; &quot;seurat_clusters&quot;  &quot;SCT_snn_res.0.5&quot; 
&gt; unique(pbmc@meta.data$Condition)
[1] &quot;control&quot; &quot;cancer&quot; 
&gt; 
</code></pre>
<p><a href="https://i.sstatic.net/TbG8d.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/TbG8d.png" alt="enter image description here" /></a></p>
<p>I want to have a heat map of differentially expressed between cancers and controls like <code>figure 3A</code> in this paper</p>
<p><a href="https://www.frontiersin.org/articles/10.3389/fgene.2020.610682/full" rel="nofollow noreferrer">https://www.frontiersin.org/articles/10.3389/fgene.2020.610682/full</a></p>
<p><a href="https://i.sstatic.net/ZVaJh.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ZVaJh.png" alt="enter image description here" /></a></p>
<p>Do you have any idea please how I can do that? I've looked at the <a href="https://satijalab.org/seurat/articles/integration_introduction.html" rel="nofollow noreferrer">integration tutorial</a>, but can't find the heatmap in it.</p>

<scrnaseq><seurat><differential-expression><10x-genomics><heatmap>
Seurat heatmap for two conditions
# Seurat heatmap for two conditions

(Asked by: username_0 on 2021-07-27)

I have a Seurat object of four cancers and four controls
> colnames(pbmc@meta.data)
 [1] "orig.ident"       "nCount_RNA"       "nFeature_RNA"     "samples"         
 [5] "Condition"        "Gender"           "percent.mt"       "nCount_SCT"      
 [9] "nFeature_SCT"     "SCT_snn_res.0.75" "seurat_clusters"  "SCT_snn_res.0.5" 
> unique(pbmc@meta.data$Condition)
[1] "control" "cancer" 
> 


I want to have a heat map of differentially expressed between cancers and controls like figure 3A in this paper
https://www.frontiersin.org/articles/10.3389/fgene.2020.610682/full

Do you have any idea please how I can do that? I've looked at the integration tutorial, but can't find the heatmap in it.

**Tags:** scrnaseq, seurat, differential-expression, 10x-genomics, heatmap

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## 1 answers

### Answer by username_1 on 2021-07-29. Score: 1 | Accepted answer

See the DoHeatmap function in Seurat, which seems to be what that paper has used:
https://satijalab.org/seurat/articles/pbmc3k_tutorial.html#cb50
> DoHeatmap(pbmc, features = myGeneList, group.by="Condition")


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