[BioC] Axis Scales & Components After Logicle Transformation (flowViz)

Florian Hahne fhahne at fhcrc.org
Thu Mar 12 20:13:30 CET 2009

Hi Aric,
as far as I understand, you want to plot your Logicle transformed data 
using a logarithmic axis. I am not quite sure if this is in the spirit 
of R's plotting scheme, since the data you are plotting and the axis 
will no longer match, i.e., a user might assume from the plot that a 
certain point is (100, 1000), while in the underlying data it actually 
is (Logicle(100), Logicle(1000)).
If you really want to go down this path, you basically need to get the 
tick marks in the original scale and transform them using the same 
transformation function that was applied to the data. For Logicle this 
could be a bit tricky, since it is data driven and it is somewhat hard 
to get to the parameters that completely define the transformation. 
There is no easy short cut that I know of.

Aric Gregson wrote:
> Hello,
> Following a transformation of the flowSet data with Logicle, the axis
> labels remain whole numbers within the axis limit range. This is
> perfect for any necessary gating procedures, as it is very easy to add
> more tick marks to assist with gate placement (trying to place a grid
> for this as well). 
> However, for display to others who prefer a more traditional look, it
> appears to get complicated quickly to place the linear:log scales
> necessary. I have tried a few ideas from pages 138-150 of Sarkar's
> 'Lattice', but have singularly failed. I was wondering if there is a
> simple shortcut that I am missing, or how one would suggest I go about
> this. 
> Thanks very much. 
> Aric
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Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
fhahne at fhcrc.org

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