I've written an Sweave document, but I'd like to know how to get Sweave() to format the R code chunks as I've written them in the *.Rnw file? For example, I'm using limma and have defined a contrast matrix as follows. I hope the lines format ok on the list! If not, each indented line has two tab stops, and I previously used "options(width=50)": <<contrastmatrix>>= cont.matrix<-makeContrasts( Helin_Acclimation = H.Y.N - H.N.N, Helin_Freezing = H.Y.Y - H.Y.N, Leitrim_Acclimation = L.Y.N - L.N.N, Leitrim_Freezing = L.Y.Y - L.Y.N, Acclimation = (H.Y.N + L.Y.N) - (H.N.N + L.N.N), Freezing = (H.Y.Y + L.Y.Y) - (H.Y.N + L.Y.N), Diff_Acclimation = (L.Y.N - L.N.N) - (H.Y.N - H.N.N), Diff_Freezing = (L.Y.Y - L.Y.N) - (H.Y.Y - H.Y.N), Population = (L.N.N + L.Y.N + L.Y.Y) - (H.N.N + H.Y.N + H.Y.Y), levels=design ) cont.matrix @ In the resulting *.tex file I get the following output for the above code block: > cont.matrix <- makeContrasts(Helin_Acclimation = H.Y.N - + H.N.N, Helin_Freezing = H.Y.Y - H.Y.N, + Leitrim_Acclimation = L.Y.N - L.N.N, + Leitrim_Freezing = L.Y.Y - L.Y.N, + Acclimation = (H.Y.N + L.Y.N) - (H.N.N + + L.N.N), Freezing = (H.Y.Y + L.Y.Y) - + (H.Y.N + L.Y.N), Diff_Acclimation = (L.Y.N - + L.N.N) - (H.Y.N - H.N.N), Diff_Freezing = (L.Y.Y - + L.Y.N) - (H.Y.Y - H.Y.N), Population = (L.N.N + + L.Y.N + L.Y.Y) - (H.N.N + H.Y.N + + H.Y.Y), levels = design) I'd like the formatting to remain the same for easy reading, such as: > cont.matrix <- makeContrasts(Helin_Acclimation = H.Y.N - + H.N.N, Helin_Freezing = H.Y.Y - H.Y.N, + Leitrim_Acclimation = L.Y.N - L.N.N, + Leitrim_Freezing = L.Y.Y - L.Y.N, + Acclimation = (H.Y.N + L.Y.N) - (H.N.N + L.N.N), + Freezing = (H.Y.Y + L.Y.Y) - (H.Y.N + L.Y.N), + Diff_Acclimation = (L.Y.N - L.N.N) - (H.Y.N - H.N.N), + Diff_Freezing = (L.Y.Y - L.Y.N) - (H.Y.Y - H.Y.N), + Population = (L.N.N + L.Y.N + L.Y.Y) - (H.N.N + H.Y.N + H.Y.Y), + levels = design) Any help much appreciated. ------------------------------------------------------------- Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) OCE Post Doctoral Fellow CSIRO Livestock Industries J M Rendel Laboratory Rockhampton QLD 4701 Tel: +61 (0)7 4923 8121 Australia Fax: +61 (0)7 4923 8222 ------------------------------------------------------------- [[alternative HTML version deleted]]

See ?RweaveLatex and the keep.source option; you can set this for a chunk <<my-chunk, keep.source="TRUE">>= @ or for the entire document using, in the preamble, \SweaveOpts(keep.source=TRUE} Martin Nathan.Watson-Haigh at csiro.au wrote: > I've written an Sweave document, but I'd like to know how to get > Sweave() to format the R code chunks as I've written them in the *.Rnw > file? For example, I'm using limma and have defined a contrast matrix as > follows. I hope the lines format ok on the list! If not, each indented > line has two tab stops, and I previously used "options(width=50)": > > <<contrastmatrix>>= > cont.matrix<-makeContrasts( > Helin_Acclimation = H.Y.N - H.N.N, > Helin_Freezing = H.Y.Y - H.Y.N, > > Leitrim_Acclimation = L.Y.N - L.N.N, > Leitrim_Freezing = L.Y.Y - L.Y.N, > > Acclimation = (H.Y.N + L.Y.N) - (H.N.N + L.N.N), > Freezing = (H.Y.Y + L.Y.Y) - (H.Y.N + L.Y.N), > > Diff_Acclimation = (L.Y.N - L.N.N) - (H.Y.N - H.N.N), > Diff_Freezing = (L.Y.Y - L.Y.N) - (H.Y.Y - H.Y.N), > Population = (L.N.N + L.Y.N + L.Y.Y) - (H.N.N + H.Y.N + H.Y.Y), > levels=design > ) > cont.matrix > @ > > In the resulting *.tex file I get the following output for the above > code block: > >> cont.matrix <- makeContrasts(Helin_Acclimation = H.Y.N - > + H.N.N, Helin_Freezing = H.Y.Y - H.Y.N, > + Leitrim_Acclimation = L.Y.N - L.N.N, > + Leitrim_Freezing = L.Y.Y - L.Y.N, > + Acclimation = (H.Y.N + L.Y.N) - (H.N.N + > + L.N.N), Freezing = (H.Y.Y + L.Y.Y) - > + (H.Y.N + L.Y.N), Diff_Acclimation = (L.Y.N - > + L.N.N) - (H.Y.N - H.N.N), Diff_Freezing = (L.Y.Y - > + L.Y.N) - (H.Y.Y - H.Y.N), Population = (L.N.N + > + L.Y.N + L.Y.Y) - (H.N.N + H.Y.N + > + H.Y.Y), levels = design) > > I'd like the formatting to remain the same for easy reading, such as: > >> cont.matrix <- makeContrasts(Helin_Acclimation = H.Y.N - > + H.N.N, Helin_Freezing = H.Y.Y - H.Y.N, > + Leitrim_Acclimation = L.Y.N - L.N.N, > + Leitrim_Freezing = L.Y.Y - L.Y.N, > + Acclimation = (H.Y.N + L.Y.N) - (H.N.N + L.N.N), > + Freezing = (H.Y.Y + L.Y.Y) - (H.Y.N + L.Y.N), > + Diff_Acclimation = (L.Y.N - L.N.N) - (H.Y.N - H.N.N), > + Diff_Freezing = (L.Y.Y - L.Y.N) - (H.Y.Y - H.Y.N), > + Population = (L.N.N + L.Y.N + L.Y.Y) - (H.N.N + H.Y.N + H.Y.Y), > + levels = design) > > Any help much appreciated. > > ------------------------------------------------------------- > Dr. Nathan S. Watson-Haigh (publish under Haigh, N.S.) > OCE Post Doctoral Fellow > CSIRO Livestock Industries > J M Rendel Laboratory > Rockhampton > QLD 4701 Tel: +61 (0)7 4923 8121 > Australia Fax: +61 (0)7 4923 8222 > ------------------------------------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793