2
$\begingroup$

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

$\endgroup$
  • $\begingroup$ 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 '18 at 8:26
  • 1
    $\begingroup$ 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 Sep 28 '18 at 9:33
  • $\begingroup$ Sorry, I know something in R but not as good as to be able write a function in a deadline $\endgroup$ – Angel Sep 28 '18 at 9:50
1
$\begingroup$

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

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.