[BioC] cannot adjust legend in diffreport output

[FRANKLIN JOHNSON [guest]]

Dear Maintainer,
Thanks for this package. It is great and very useful.

I am (6) Analyzing and Visualizing Results, however,
I cannot seem to adjust the legend in the EIC plot. 
I tried using the logical, legend=FALSE, as well as alternatives, but my approaches did not work. 
Is there not an argument used by diffreport function to not print the legend? The legend that does print is too large as I have 95 files, and covers a large area of the EIC plot.

Additionally, if my arguments in diffreport are such that class1 = levels(sampclass(object))[1], class2 = level(sampclass(object)[2], the diffreport reads and prints the appropriate samples in each sampclass(object), 3 samples per class  [06041319.mzdata 06041320.mzdata 06071324.mzdata <-class[1] samples; 06041303.mzdata 06071321.mzdata 06071322.mzdata <- class[2] sample],  
although the output file has all 95 samples. 
1) How is it the intensity is being adjusted in the other 93 samples, when in diffreport function, I compare 2 different classes? 
2) How can I use these intensity values in the output file of only a single two way comparison to help me understand the dataset?  

3) If possible, what is the best way to obtain intensity values for each class (total 29 classes, total 95 samples) in xset3, such that I could do multiple comparisons using limma?; 
as this is a time course experiment with 3 different class levels, and comparing two different years. 

> xset3
An "xcmsSet" object with 95 samples

Time range: 77.9-2095.8 seconds (1.3-34.9 minutes)
Mass range: 93.0698-1235.9832 m/z
Peaks: 240836 (about 2535 per sample)
Peak Groups: 2490 
Sample classes: Y2011Peel.Y11CA12WK, Y2012Peel.Y11CA12WK, Y2011Peel.Y11CA2WK, Y2012Peel.Y11CA2WK, Y2011Peel.Y11CA4WK, Y2012Peel.Y11CA4WK, Y2011Peel.Y11CA8WK, Y2012Peel.Y11CA8WK, Y2011Peel.Y11CAp12WK, Y2012Peel.Y11CAp12WK, Y2011Peel.Y11CAp2WK, Y2012Peel.Y11CAp2WK, Y2011Peel.Y11CAp4WK, Y2012Peel.Y11CAp4WK, Y2011Peel.Y11CAp8WK, Y2012Peel.Y11CAp8WK, Y2011Peel.Y11HARVEST, Y2012Peel.Y11HARVEST, Y2011Peel.Y11RA12WK, Y2012Peel.Y11RA12WK, Y2011Peel.Y11RA2WK, Y2012Peel.Y11RA2WK, Y2011Peel.Y11RA4WK, Y2012Peel.Y11RA4WK, Y2011Peel.Y11RA8WK, Y2012Peel.Y11RA8WK, Y2011Peel.Y12CA1WK, Y2012Peel.Y12CA1WK, Y2011Peel.Y12CA24HR, Y2012Peel.Y12CA24HR, Y2011Peel.Y12CA2WK, Y2012Peel.Y12CA2WK, Y2011Peel.Y12CA4WK, Y2012Peel.Y12CA4WK, Y2011Peel.Y12CA72HR, Y2012Peel.Y12CA72HR, Y2011Peel.Y12CAp1WK, Y2012Peel.Y12CAp1WK, Y2011Peel.Y12CAp24HR, Y2012Peel.Y12CAp24HR, Y2011Peel.Y12CAp2WK, Y2012Peel.Y12CAp2WK, Y2011Peel.Y12CAp4WK, Y2012Peel.Y12CAp4WK, Y2011Peel.Y12CAp72HR, Y2012Peel.Y12CAp72HR, Y2011Peel.Y12HARVE
 ST, Y2012Peel.Y12HARVEST, Y2011Peel.Y12RA1WK, Y2012Peel.Y12RA1WK, Y2011Peel.Y12RA24HR, Y2012Peel.Y12RA24HR, Y2011Peel.Y12RA2WK, Y2012Peel.Y12RA2WK, Y2011Peel.Y12RA4WK, Y2012Peel.Y12RA4WK, Y2011Peel.Y12RA72HR, Y2012Peel.Y12RA72HR 

Profile settings: method = bin
                  step = 0.1

Memory usage: 28.5 MB


Sorry if this is hard to understand. 
Hope to hear from you soon.    
Franklin
 

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] multtest_2.16.0    xcms_1.36.0        Biobase_2.20.0     BiocGenerics_0.6.0 mzR_1.6.0          Rcpp_0.10.3       

loaded via a namespace (and not attached):
[1] codetools_0.2-8 MASS_7.3-26     splines_3.0.1   stats4_3.0.1    survival_2.37-4


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