[BioC] flowCore - cloud()

Steve Lauriault stevan at lauriault.com
Thu Jan 29 15:19:19 CET 2009

Thank you Nishant,

Not to be nit-picky, but is there a function that would allow one to rotate
and/or zoom-in on the cube?  If not, there is a plot developed in MatLab by
Laszlo Balkay (sp?) that allows one to do this (rotate, zoom-in, etc) with
3-D FCS dataframes.  Not sure how congruent the two languages are, or if
this is any help at all, but I thought I'd relay the info.  I thought it was
a cool function, but it would be cooler if one could add colour to represent
fluorescence intensity, offspring or subset populations in the 4th




Stevan Lauriault
Founder, President and C.E.O.
Lauritech Inc. 
steve at lauritech.com
t/f: (416)283-4066


-----Original Message-----
From: Nishant Gopalakrishnan [mailto:ngopalak at fhcrc.org] 
Sent: Wednesday, January 28, 2009 8:47 PM
To: stevan at lauriault.com
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] flowCore - cloud() and lapply

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
> or "/Data/FMO.fcs", and I would like to include FSC-H, SSC-H, and FL1-H
> 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
> 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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