Option not to plot the points in violin plots about scater HOT 5 CLOSED

Try this on master:

library("scater")
example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
colData(example_sce) <- cbind(colData(example_sce), perCellQCMetrics(example_sce))
plotColData(example_sce, y = "detected", x = "Cell_Cycle", colour_by = "Mutation_Status", point_fun = function(...) list())

from scater.

Hi, thanks for fixing this. But it would still be nice to be able to fill the violins with colors to indicate clusters, as in Seurat. However, there's no fill_by argument. Also, I feel like point_fun = function(...) list() is kind of cumbersome and confusing to users who aren't very fluent in R. It would be nice to have an argument like plot_points = FALSE.

from scater.

I don't know how common it is for people to not want points, and point_fun is a more flexible option than plot_points, so I'm going to leave it as is for now.

I'm slightly dubious about fill_by here as in the case that it's not the same as x you then have to start specifying positions and complexity may balloon slightly

from scater.

Hey,

First thanks a lot for developing and maintaining this package.

I agree that the fill_by argument would be also very good in these cases where you don't want to plot each individual point but just want to see the shape. I have seen that you have it in your code. The problem is that if I combine both options fill_by and point_fun = function(...) list() I have not been able to modify the colors of the violin plots and all my violins have the same color.

plotColData(all_sce, x="ident",y="sum" ,point_fun = function(...) list(), fill_by = "ident")

Is there an option to just plot the shape of the violin and fill it according to your particular interest?

Thanks for any help you might be able to provide,

Kike

from scater.

I'm going to open a separate issue (#175) as this is unrelated to the original topic.

Please submit any suggestions or feedback there instead

from scater.