[Seqinr-commits] r1970 - in pkg/man: . figures

[noreply at r-forge.r-project.org]

Author: jeanlobry
Date: 2016-06-30 19:44:29 +0200 (Thu, 30 Jun 2016)
New Revision: 1970

Added:
   pkg/man/figures/chargaff.png
Modified:
   pkg/man/chargaff.Rd
Log:
adding a figure in the chargaff dataset documentation

Modified: pkg/man/chargaff.Rd
===================================================================
--- pkg/man/chargaff.Rd	2016-06-30 17:08:16 UTC (rev 1969)
+++ pkg/man/chargaff.Rd	2016-06-30 17:44:29 UTC (rev 1970)
@@ -45,24 +45,34 @@
 of the AT type (Table 2, preps. 1-4). It cannot yet be said
 to be established for the DNA specimens from the equimolar
 and GC types (nos. 5-7)."
+
+Try \code{example(chargaff)} to mimic figure page 17 in Lobry
+(2000) :
+
+\if{html}{\figure{chargaff.png}{options: width=400}}
+\if{latex}{\figure{chargaff.png}{options: width=\textwidth}}
+
+
+Note that \code{example(chargaff)} gives more details:
+the red areas correspond to non-allowed values beause the sum
+of the four bases frequencies cannot exceed 100\%.
+The white areas correspond to possible values (more exactly
+to the projection from \code{R^4} to the corresponding \code{R^2} planes
+of the region of allowed values).
+The blue lines correspond to the very small subset of allowed
+values for which we have in addition PR2 state, that is
+\code{[A]=[T]} and \code{[C]=[G]}. Remember, these data are for ssDNA!
 }
+
 \source{
 Rudner, R., Karkas, J.D., Chargaff, E. (1968) Separation of
 \emph{B. subtilis} DNA into complementary strands, III. Direct
 Analysis. \emph{Proceedings of the National Academy of Sciences of the United States of America}, \bold{60}:921-922.\cr
-Rudner, R., Karkas, J.D., Chargaff, E. (1969) Separation of microbial deoxyribonucleic acids into complementary strands. \emph{Proceedings of the National Academy of Sciences of the United States of America}, \bold{63}:152-159.
+Rudner, R., Karkas, J.D., Chargaff, E. (1969) Separation of microbial deoxyribonucleic acids into complementary strands. \emph{Proceedings of the National Academy of Sciences of the United States of America}, \bold{63}:152-159.\cr
+
 }
 \references{
-Try \code{example(chargaff)} to mimic figure page 17 in
-\url{https://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf}.
-The red areas correspond to non-allowed values beause the sum
-of the four bases frequencies cannot exceed 100\%.
-The white areas correspond to possible values (more exactly
-to the projection from \code{R^4} to the corresponding \code{R^2} planes
-of the region of allowed values).
-The blue lines correspond to the very small subset of allowed
-values for which we have in addition PR2 state, that is
-\code{[A]=[T]} and \code{[C]=[G]}. Remember, these data are for ssDNA !
+Lobry, J.R. (2000) The black hole of symmetric molecular evolution. Habilitation thesis, Université Claude Bernard - Lyon 1. \url{https://pbil.univ-lyon1.fr/members/lobry/articles/HDR.pdf}.
 
 \code{citation("seqinr")}
 }

Added: pkg/man/figures/chargaff.png
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Property changes on: pkg/man/figures/chargaff.png
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