Hello, I would like to do a violin plot from my fcs files. Is there a way to do it similar to ggplot-geom_violin()? Thank you for your help!

First read your FCS file into a flowCore object, and then extract the values via the exprs() function:

require(flowCore)
x <- read.FCS('FCS/20181121-07 HeB PB Kings HD_02_0_Live_cells_viSNE.fcs')
x <- exprs(x)
x[1:5,1:5]
         Time Event_length   Y89Di Rh103Di Sn120Di
[1,] 2493.802           21 200.266   0.000   0.000
[2,] 2497.904           34 163.380   0.000   0.000
[3,] 2502.721           18 130.506   0.000   0.000
[4,] 2504.961           21 154.235   0.000   0.000
[5,] 2518.802           28  32.545   0.773   0.257

Then you can make any visualisation that you want.

For what it is worth, I am currently developing a single cell Bioconductor package that is focussed on CyTOF data, here: https://github.com/kevinblighe/scToolkit

Kevin