19 months ago by
Johannes Kepler University, Linz, Austria
Reply to question #1: The width is controlled by the global R option 'width' (in line with the print() methods in the 'Biostrings' package). So you can change the number of columns yourself. If you want to avoid this to have a global effect on your R session, you should save the current value and then, after running print(), revert to the previous value. Here is an example (the first lines are to be copied from above):
saveWidth <- getOption("width")
print(myAlignment, show="complete", halfNrow=-1)
Reply to question #2: Sorry, no. This is an implementation that is, to quite some extent, copied from or at least inspired by the methods in the '
Biostrings' package. You can influence the width of names by the '
nameWidth' argument, but that's all. If you want to tailor the print() methods to your very specific needs, you will have to make a copy of the relevant parts of the source file
msa/R/print-methods.R and customize the code of your local copy to your needs.