How to create a violin plot
1
0
Entering edit mode
vasildmb • 0
@vasildmb-22029
Last seen 24 months ago

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!

plot ggcyte • 266 views
ADD COMMENT
0
Entering edit mode
@kevin
Last seen 55 minutes ago
Republic of Ireland

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

ADD COMMENT

Login before adding your answer.

Traffic: 336 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6