text: user4858: I have a list of genes that I'd like to visualize using the DoHeatmap function in Seurat. However, the output of the heatmap does not result in hierarchical clustering and therefore makes it very difficult to interpret. My code is,
   DoHeatmap(object = obj, genes.use = genes), 
            slim.col.label = TRUE, remove.key = T,group.label.rot = F, use.scaled = T)
  
   
  Is there a way to adjust the DoHeatmap command to rank the cells by the intensity of gene expression? Here's an example output:
  
  
  user3631: You need to order the marker matrix (e.g. by avg_logFC) before calling DoHeatMap.
  library(dplyr)
  all.markers <- FindAllMarkers(object = obj)
  top20 <- all.markers %>% group_by(cluster) %>% top_n(20, avg_logFC)
  DoHeatmap(object = obj, genes.use = top20$gene, slim.col.label = TRUE, remove.key = TRUE)
  
  
original_text: 4858: <p>I have a list of genes that I'd like to visualize using the DoHeatmap function in Seurat. However, the output of the heatmap does not result in hierarchical clustering and therefore makes it very difficult to interpret. My code is,</p>
  
  <pre><code> DoHeatmap(object = obj, genes.use = genes), 
            slim.col.label = TRUE, remove.key = T,group.label.rot = F, use.scaled = T)
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/x85hy.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/x85hy.png" alt="Seurat"></a> </p>
  
  <p>Is there a way to adjust the <code>DoHeatmap</code> command to rank the cells by the intensity of gene expression? Here's an example output:</p>
  
  <p><a href="https://i.stack.imgur.com/Jy8Xs.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Jy8Xs.png" alt="enter image description here"></a></p>
   3631: <p>You need to order the marker matrix (e.g. by <code>avg_logFC</code>) before calling <code>DoHeatMap</code>.</p>
  
  <pre><code>library(dplyr)
  all.markers &lt;- FindAllMarkers(object = obj)
  top20 &lt;- all.markers %&gt;% group_by(cluster) %&gt;% top_n(20, avg_logFC)
  DoHeatmap(object = obj, genes.use = top20$gene, slim.col.label = TRUE, remove.key = TRUE)
  </code></pre>
  