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

Aric Gregson a.gregson at ucla.edu
Thu Mar 12 21:52:04 CET 2009

On Thu, 12 Mar 2009 12:13:30 -0700
Florian Hahne <fhahne at fhcrc.org> wrote:

> 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.

This is what I suspected. I would of course want the plot to reflect
the underlying Logicle(100), Logicle(1000), not just look like it does. 

Thanks, Aric

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