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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

enter image description here

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)

enter image description here

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')

enter image description here

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

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  • $\begingroup$ 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? $\endgroup$
    – llrs
    Sep 28, 2018 at 8:26
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    $\begingroup$ Please edit your question and give us a minimal, complete, verifiable example 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. $\endgroup$
    – terdon on strike ♦
    Sep 28, 2018 at 9:33
  • $\begingroup$ Sorry, I know something in R but not as good as to be able write a function in a deadline $\endgroup$
    – Exhausted
    Sep 28, 2018 at 9:50

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

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