Question: Plotting flow cytometry data
gravatar for gori73
3.5 years ago by
United States
gori730 wrote:




 I am  new  to R and would appreciate your help.


I am using flowcore package to load my FCS files to R but then extract the relevant data to a regular dataframe

as I am not familiar with the manipulation of S4 type data.


I am currently using smoothscatter function to display my data but would like to produce non-smoothed  image more similar to FlowJo.

I like the images produced by the examples in  FlowViz vignette but don’t know how to use on my simple dataframe.

When I use the code below I get just a one color plot instead of different colors representing cell densities.



colramp <- colorRampPalette(IDPcolorRamp(21))

xyplot(DNAA~YFP, data, nbin = 100, smooth=FALSE, colramp=colramp)


In this case DNAA and YFP are two columns in the dataframe “data”.


How should I modify my code to get a plot similar to the one in FlowViz vignette? (use on simple dataframes)


Thank you very much,



flowcore flowviz • 691 views
ADD COMMENTlink modified 3.5 years ago by Jiang, Mike1.2k • written 3.5 years ago by gori730
Answer: Plotting flow cytometry data
gravatar for Jiang, Mike
3.5 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

You must use flowSet/flowFrame in order to take advantage of all the features provided by flowViz package.  If you convert it to a data.frame,  then it is simply a generic visualization question of 'lattice' or 'ggplot2' which is beyond the scope of flowViz or flow cytometry. But I can help you with this particular one, 


cols <- densCols(x = data[["DNAA"]], y = data[["YFP"]], colramp=colramp)

xyplot(`SSC-H`~`FSC-H`, data,  col = cols)



Again, this is not an idea way of using flowCore. What kind of data manipulation are you talking about?I would say at least you can assign the data back to flowSet/flowFrame object before plotting them. See

ADD COMMENTlink written 3.5 years ago by Jiang, Mike1.2k
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