I am doing practic like “Analysis of plant scRNA-Seq Data with Scanpy”, I want to find a way to make a dotplot that can split the shr and wt usin “Plot with scanpy”, but I can not do it. Is anybody can let me know how can I do it.
I mean make a similar graph like above using “Plot with scanpy”
Tutorials that include Scanpy and related scRNA tools are here. These reproduce published analysis translated for Galaxy and serve as examples of how to map the various line command options onto the tool forms. Search GTN Materials (query=scanpy, and you could try others or navigate by analysis domain)
If a tutorial doesn’t cover your exact manipulation, the tool forms have most of the command line options added in and annotated with the –flags, so the original tool documentation is also a good reference.
For the graph shown, it looks like the AnnData object was manipulated to add in extra annotation to the labels (A_STIM and A_CTRL), probably done before merging the cell types, to avoid the variables clustering together in the graphic. Clever, and easy to interpret! If you decide to do that, remember that you’ll need to use the modified names in any other filters, too, or you won’t get a match when choosing the variables to plot.
Hope this helps!
Thanks for your kind replying.