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Question: Plotting flow cytometry data
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2.5 years ago by
gori730
United States
gori730 wrote:

Hello,

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.

library(flowViz)
require(IDPmisc)

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,

Igor

modified 2.5 years ago by Jiang, Mike1.1k • written 2.5 years ago by gori730
0
2.5 years ago by
Jiang, Mike1.1k
Jiang, Mike1.1k 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

?exprs<-