[BioC] flowCore - cloud()

[Steve Lauriault]

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
dimension.

Regards,

Steve

---

Stevan Lauriault
Founder, President and C.E.O.
Lauritech Inc. 
steve at lauritech.com
www.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
flowFrame.

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)

Nishant

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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