[BioC] flowCore - cloud() and lapply

[Steve Lauriault]

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