text: user4595: Seurat R package has some functions like FeaturePlot, DimPlot and DoHeatmap by which we can plot the expression of a list of genes on cell clusters. I am working with URD that likely does not have such options or I can not find that. URD has plotDot but would be clear only for a few number of genes (please look at the picture). Could somebody please help me in plotting the expression pattern of a list of genes in URD? As I am not good in R at all to write my own function or adopt Seurat functions to URD
  
  For example Seurat DoHeatmap gives such a picture by which we can see these set of genes are being expressed on which group of cells
  DoHeatmap(object ,genes.use=a vector of genes)
  
  
  Or we can plot a set of genes on seurat feature lot to they are being expressed more on which cluster
  FeaturePlot(object = pbmc_small, features.plot = 'PC1')
  
  
  In URD only by 
  plotDot(object.6s.mnn, genes = a vector of genes, clustering="Infomap-60")
  
  We can plot a set of genes but as you are being in the first picture that would not be clear much
  My question is how I can plot a vector of genes on URD object
  for example Seurat DimPlot function can visualise the expression pattern of a group of genes on cell clusters but when I am trying to do the same with URD, returns this error
  > plotDim(axial.6somite, c("DDB_G0291149","DDB_G0291029"), plot.title="SHHA (Notochord marker)")
  Error in names(data) <- cells.use : 
    invalid to use names()<- on an S4 object of class 'dgCMatrix'
  In addition: Warning messages:
  1: In if (label.type == "meta" | (label.type == "search" & label %in%  :
    the condition has length > 1 and only the first element will be used
  2: In if (label.type == "group" | (label.type == "search" & label %in%  :
    the condition has length > 1 and only the first element will be used
  3: In if (label.type == "sig" | (label.type == "search" & label %in%  :
    the condition has length > 1 and only the first element will be used
  4: In if (label.type == "gene" | (label.type == "search" & label %in%  :
    the condition has length > 1 and only the first element will be used
  > 
  >
  
  Actually only one gene can be visualised by this function on URD
  
  user4595: I just added URD clustering labels for each cel to seurat object and then I did DoHeatmap by using group.by="URD clustering labels"
  
original_text: 4595: <p>Seurat R package has some functions like <strong>FeaturePlot</strong>, <strong>DimPlot</strong> and <strong>DoHeatmap</strong> by which we can plot the expression of a list of genes on cell clusters. I am working with <strong>URD</strong> that likely does not have such options or I can not find that. URD has plotDot but would be clear only for a few number of genes (please look at the picture). Could somebody please help me in plotting the expression pattern of a list of genes in URD? As I am not good in R at all to write my own function or adopt Seurat functions to URD</p>
  
  <p><a href="https://i.stack.imgur.com/R7MRf.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/R7MRf.jpg" alt="enter image description here"></a></p>
  
  <p>For example Seurat DoHeatmap gives such a picture by which we can see these set of genes are being expressed on which group of cells</p>
  
  <pre><code>DoHeatmap(object ,genes.use=a vector of genes)
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/j0ACP.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/j0ACP.jpg" alt="enter image description here"></a></p>
  
  <p>Or we can plot a set of genes on seurat feature lot to they are being expressed more on which cluster</p>
  
  <pre><code>FeaturePlot(object = pbmc_small, features.plot = 'PC1')
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/jX0Ij.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/jX0Ij.png" alt="enter image description here"></a></p>
  
  <p>In URD only by </p>
  
  <pre><code>plotDot(object.6s.mnn, genes = a vector of genes, clustering="Infomap-60")
  </code></pre>
  
  <p>We can plot a set of genes but as you are being in the first picture that would not be clear much</p>
  
  <p>My question is how I can plot a vector of genes on URD object</p>
  
  <p>for example Seurat DimPlot function can visualise the expression pattern of a group of genes on cell clusters but when I am trying to do the same with URD, returns this error</p>
  
  <pre><code>&gt; plotDim(axial.6somite, c("DDB_G0291149","DDB_G0291029"), plot.title="SHHA (Notochord marker)")
  Error in names(data) &lt;- cells.use : 
    invalid to use names()&lt;- on an S4 object of class 'dgCMatrix'
  In addition: Warning messages:
  1: In if (label.type == "meta" | (label.type == "search" &amp; label %in%  :
    the condition has length &gt; 1 and only the first element will be used
  2: In if (label.type == "group" | (label.type == "search" &amp; label %in%  :
    the condition has length &gt; 1 and only the first element will be used
  3: In if (label.type == "sig" | (label.type == "search" &amp; label %in%  :
    the condition has length &gt; 1 and only the first element will be used
  4: In if (label.type == "gene" | (label.type == "search" &amp; label %in%  :
    the condition has length &gt; 1 and only the first element will be used
  &gt; 
  &gt;
  </code></pre>
  
  <p>Actually only one gene can be visualised by this function on URD</p>
   4595: <p>I just added URD clustering labels for each cel to seurat object and then I did DoHeatmap by using group.by="URD clustering labels"</p>
  