You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
This is not a problem with your nice software rather my own problem.
I noticed by plotDRExpression function we can plot a list of genes very clean because you are using a sort of centring I guess (-2,2).
You please imagine that, I have made 3 clusters of cells (clusters 1, 2 and 3) . I expect if I plot a list of marker genes across these three clusters, only cluster 1 should be lighted up because these marker genes supposed to be specific to cluster 1. Is there any way to use your plotDRExpression function for a list of genes but not each of them individually rather something like mean of expression of them or whatever by which I could have such a nice featureplot showing the expression of these genes?
I tried seurat like below code but my way of centring another clusters also being lighted up that I don't want
mat=seurat_object@data[rownames(seurat_object@data)%in%rownames(gene_list),]
#I have converted expression matrix to a binary matrix by 2 as a threshold (arbitrarily)
mat[mat < 2] <- 0
mat[mat > 2] <- 1
exp=colSums(mat)
exp=as.matrix(exp)
colnames(exp)="value"
exp=as.data.frame(exp)
cc <- AddMetaData(object = surat_object, metadata = exp)
cc <- SetAllIdent(object = cc, id = "value")
TSNEPlot(object = cc, do.return= TRUE)
ggplot(as.data.frame(cc@meta.data), aes(x = cc@meta.data$CELL, y = cc@meta.data$res.0.7, colour =cc@meta.data$value)) +
geom_point(size = 9) +
scale_colour_gradient(low = "yellow", high = "blue")
Thanks a lot for any help
The text was updated successfully, but these errors were encountered:
Sorry,
This is not a problem with your nice software rather my own problem.
I noticed by
plotDRExpression
function we can plot a list of genes very clean because you are using a sort of centring I guess (-2,2).You please imagine that, I have made 3 clusters of cells (clusters 1, 2 and 3) . I expect if I plot a list of marker genes across these three clusters, only cluster 1 should be lighted up because these marker genes supposed to be specific to cluster 1. Is there any way to use your plotDRExpression function for a list of genes but not each of them individually rather something like mean of expression of them or whatever by which I could have such a nice featureplot showing the expression of these genes?
I tried seurat like below code but my way of centring another clusters also being lighted up that I don't want
Thanks a lot for any help
The text was updated successfully, but these errors were encountered: