Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-29T23:15:46.260Z
Answers.LastActivityDate: 2021-07-29T23:15:46.260Z
Answers.UserDisplayName: gringer
Body: <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>
  
Tags: <scrnaseq><seurat><differential-expression><10x-genomics><heatmap>
Title: Seurat heatmap for two conditions
ThreadText: # 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" 
  > 
  
  ```
  
  [![enter image description here](https://i.sstatic.net/TbG8d.png)](https://i.sstatic.net/TbG8d.png)
  
  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>
  
  [![enter image description here](https://i.sstatic.net/ZVaJh.png)](https://i.sstatic.net/ZVaJh.png)
  
  Do you have any idea please how I can do that? I've looked at the [integration tutorial](https://satijalab.org/seurat/articles/integration_introduction.html), but can't find the heatmap in it.
  
  **Tags:** scrnaseq, seurat, differential-expression, 10x-genomics, heatmap
  
  
  ---
  
  ## 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")
  
  ```
  
  
  ---
  
  