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