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

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. Florian 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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 206-667-3148 fhahne at fhcrc.org