[BioC] flowCore - cloud() and lapply

Nishant Gopalakrishnan ngopalak at fhcrc.org
Thu Jan 29 02:46:46 CET 2009

Hi Steve

The cloud function from lattice takes a data frame as the argument and
will not directly
work with a flowFrame . You can use the exprs function to obtain a
matrix from the

Perhaps this example might help

file.name <- system.file("extdata", "0877408774.B08", package = "flowCore")
x <- read.FCS(file.name, transformation = FALSE)
data<-data.frame(exprs(x), check.names=F)
cloud(`FSC-H`~ `SSC-H` * `FL1-H`,data)


Steve Lauriault wrote:
> I noticed the cloud function, and have tried to apply my flowFrame, but to
> no avail.  Any hints on the annotation?  The FCS file can be named MyData[1]
> or “/Data/FMO.fcs”, and I would like to include FSC-H, SSC-H, and FL1-H into
> cloud().  FSC-H and SSC-H would be in linear, and FL1-H in log (10^0 to
> 10^4) scale.
> I think it would be cool to add a fourth colour-based dimension to a cloud
> plot.  Let's say FL2-H is on scale[0,1].  Any relative fluorescence
> intensity of 0 would correspond to a yellow event, and a relative
> fluorescence intensity of 1 would correspond to red.  0.5 would be orange.
> Any value ascending from zero would become more-red and less-yellow.  The
> light wavelength (colour) of the “dot” wold be directly related to the
> fluorescence intensity of the corresponding event.  The user would have the
> option to have the fourth dimension enabled or disabled (in the case of
> colours representing offspring gates, this function would complicate
> things).    
> It would also be cool to “cycle-through” FCS file visualizations within a
> 4-D cloud-based GUI.  Is there a function or package like this currently
> available in R?
> These are just some thoughts.  I hope you guys don't mind.  Now back to
> figuring out how to use lapply to create a new flowSet out of separate
> directories located in "/Data" (HowTo-flowCore 2.2.1).
> Thanks,
> Stevan
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