[R] BA.plot with logarithmic axes (MethComp)

[Thorsten Raff]

Dear R-helpers,

I am trying to plot a Bland-Altman-Plot using the BA.plot function from the 
package MethComp. While there is a function to transform the values for 
analysis as shown in the snippet below, I would like to have logarithmic axes 
for display as well. The usual log = 'xy' does not work because of the 
properties of the y-asxis (positive and negative values). I am sure that there 
is a way but I haven't found it. Any suggestions?

Best regards an many thanks in advance

Thorsten


---- begin code snippet ----

example <- data.frame(meth = c('Marker 1', 'Marker 2', 'Marker 1', 'Marker 2', 
'Marker 1', 'Marker 2', 'Marker 1', 'Marker 2', 'Marker 1', 'Marker 2', 
'Marker 1', 'Marker 2', 'Marker 1', 'Marker 2', 'Marker 1', 'Marker 2', 
'Marker 1', 'Marker 2', 'Marker 1', 'Marker 2'), item = c('QC12_2_TP1', 
'QC12_2_TP1', 'QC12_2_TP1', 'QC12_2_TP1', 'QC12_2_TP1', 'QC12_2_TP1', 
'QC12_2_TP1', 'QC12_2_TP1', 'QC12_2_TP1', 'QC12_2_TP1', 'QC12_2_TP2', 
'QC12_2_TP2', 'QC12_2_TP2', 'QC12_2_TP2', 'QC12_2_TP2', 'QC12_2_TP2', 
'QC12_2_TP2', 'QC12_2_TP2', 'QC12_2_TP2', 'QC12_2_TP2'), repl = c('BER', 
'BER', 'BRI', 'BRI', 'BRU', 'BRU', 'COP', 'COP', 'FRA', 'FRA', 'BER', 'BER', 
'BRI', 'BRI', 'BRU', 'BRU', 'COP', 'COP', 'FRA', 'FRA'), y = c(7e-04, 9e-04, 
4e-04, 4e-04, 8e-04, 7e-04, 5e-04, 7e-04, 5e-04, 6e-04, 0.0049, 0.0048, 
0.0054, 0.0052, 0.00508, 0.00462, 0.0049, 0.0043, 0.0048, 0.0045))
	
example <- Meth(example)
	
BA.plot(example, col.points = rainbow(12), main = 'Bland-Altman analysis', 
Transform = 'log')
	
rm(example)

---- end code snippet ----

-- 
Thorsten Raff
2nd Medical Department,
University Hospital Schleswig-Holstein, Campus Kiel
Chemnitzstraße 33
24116 Kiel
GERMANY

phone: +49 431 1697-5234
fax:   +49 431 1697-1264

email: t.raff<at>med2.uni-kiel.de
web:   www.uk-sh.de