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]]

