<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>

CC BY-SA 4.0
2018-09-30T11:18:34.387Z
2018-09-30T11:18:34.387Z
Zizogolu
<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.sstatic.net/R7MRf.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/j0ACP.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/jX0Ij.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>

CC BY-SA 4.0
2018-09-28T08:26:54.427Z
Which plot do you want? Could you post an example from the similar function from Seurat? You say you are not good at R, did you try learning with a bootcamp or with online books (such as [this one](http://r4ds.had.co.nz/)?
llrs
CC BY-SA 4.0
2018-09-28T09:33:08.607Z
Please [edit] your question and give us a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve) that we can use on our machines to reproduce your code. Those users who can answer will need to have access to a test dataset they can use to test their answers. Not your entire data, just a small part of it, or a similar dataset that we can play with.
terdon
CC BY-SA 4.0
2018-09-28T09:50:13.633Z
Sorry, I know something in R but not as good as to be able write a function in a deadline
Zizogolu
<r><scrnaseq><seurat>
The visualisation of a list of genes on URD object
# The visualisation of a list of genes on URD object

(Asked by: username_0 on 2018-09-27)

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

**Tags:** r, scrnaseq, seurat
> **Comments:**
> **username_1**: Which plot do you want? Could you post an example from the similar function from Seurat? You say you are not good at R, did you try learning with a bootcamp or with online books (such as [this one](http://r4ds.had.co.nz/)?  
> **username_2**: Please [edit] your question and give us a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve) that we can use on our machines to reproduce your code. Those users who can answer will need to have access to a test dataset they can use to test their answers. Not your entire data, just a small part of it, or a similar dataset that we can play with.  
> **username_0**: Sorry, I know something in R but not as good as to be able write a function in a deadline  

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## 1 answers

### Answer by username_0 on 2018-09-30. Score: 1 | Accepted answer

I just added URD clustering labels for each cel to seurat object and then I did DoHeatmap by using group.by="URD clustering labels"


---

