Closed PKLiverpool closed 1 year ago
Not so much a CATALYST
-specific question, I suppose... But just to say: No, plotDR
does not do this. But you should be able to reproduce plots such as the ones above using ggplot
by i) extracting a data.frame
of the t-SNE coordinates (and, if needed, marker expression and cell metadata), and ii) using geom_density_2d()
or geom_density_2d_filled()
. Alternatively, there's also the schex
package, which might offer an interesting way of visualising.
Hi there,
Really appreciating this tool and the comment forum, very very useful.
Just wondering whether there's similar functionality to cytobank in terms of colouring a tSNE plot by contour/cell density?
Any ideas would be much appreciated.
Cheers Paul