[Seqinr-commits] r1898 - www/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 2 14:43:37 CEST 2016
Author: jeanlobry
Date: 2016-06-02 14:43:37 +0200 (Thu, 02 Jun 2016)
New Revision: 1898
Modified:
www/src/mainmatter/getseqflat.rnw
www/src/mainmatter/getseqflat.tex
Log:
Two new figures
Modified: www/src/mainmatter/getseqflat.rnw
===================================================================
--- www/src/mainmatter/getseqflat.rnw 2016-06-02 12:30:31 UTC (rev 1897)
+++ www/src/mainmatter/getseqflat.rnw 2016-06-02 12:43:37 UTC (rev 1898)
@@ -133,10 +133,30 @@
\subsubsection{Oriloc example (\textit{Chlamydia trachomatis} complete genome)}
+\begin{figure}[ht!]
+\fbox{\begin{minipage}{0.98\textwidth}
+ \begin{center}\includegraphics[width=0.98\textwidth]{../figs/fig1oriloc}
+ \caption{\label{fig1oriloc}. Screenshot copy of figure 1 from \cite{oriloc}.
+ The complete genome sequence of \textit{Chlamydia trachomatis}
+ (accession number: \texttt{AE001273}) was used to illustrate
+ the method used by oriloc. (\textbf{a}) A DNA-walk is performed
+ by reading the sequence in the third
+ codon positions predicted by glimmer and walking into the plane according to the four
+ directions defined by the four bases as indicated on the bottom left of the figure.
+ The resulting DNA-walk is then summarized by projection onto the orthogonal
+ regression line pointing out at about 11 o’clock in the figure.
+ (\textbf{b}) The projected values are used as a composite skew index
+ plotted versus map position on the chromosome. The origin is predicted at
+ the maximum skew value while the terminus is predicted at the minimum.
+ }
+ \end{center}
+\end{minipage}}
+\end{figure}
+
A more consequent example is given in the fasta file \texttt{ct.fasta.gz} which
contains the complete genome of \textit{Chlamydia trachomatis} that was
used in \cite{oriloc}. You should be able to reproduce figure 1b from this
-paper with the following code:
+paper (\textit{cf.} screenshot in figure \ref{fig1oriloc}) with the following code:
<<oriloc, fig=TRUE, results = hide, eval=T>>=
out <- oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package ="seqinr"),
@@ -155,11 +175,10 @@
if you are interested in the prediction of origins and terminus of
replication from base composition biases (more on this at
\url{http://pbil.univ-lyon1.fr/software/oriloc.html}). See also \cite{smorfland}
-for a recent review on this topic.
+for a review on this topic. Here is the improved version:
<<oriloc2, fig=TRUE, results = hide, eval=T>>=
-out <- oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package ="seqinr"),
- g2.coord = system.file("sequences/ct.predict", package = "seqinr"))
+out <- oriloc()
plot(out$st, out$sk/1000, type="l", xlab = "Map position in Kb",
ylab = "Cumulated composite skew in Kb",
main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome), las = 1)
@@ -169,6 +188,19 @@
text(850, 9, "Origin")
@
+You can also call the \texttt{draw.oriloc()} function for the simultaneous
+representation of the CDS, AT and GC skew along with the combined skew
+of the previous plots:
+
+<<oriloc3, fig=TRUE,eval=TRUE>>=
+draw.oriloc(out,
+ main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome),
+ ta.mtext = "TA skew", ta.col = "red",
+ cg.mtext = "CG skew", cg.col = "blue",
+ cds.mtext = "CDS skew", cds.col = "seagreen",
+ add.grid = FALSE)
+@
+
\subsubsection{Example with 21,161 proteins from \textit{Arabidobpsis thaliana}}
As from \seqinr{} 1.0-5 the automatic conversion of sequences into vector
Modified: www/src/mainmatter/getseqflat.tex
===================================================================
--- www/src/mainmatter/getseqflat.tex 2016-06-02 12:30:31 UTC (rev 1897)
+++ www/src/mainmatter/getseqflat.tex 2016-06-02 12:43:37 UTC (rev 1898)
@@ -388,10 +388,30 @@
\subsubsection{Oriloc example (\textit{Chlamydia trachomatis} complete genome)}
+\begin{figure}[ht!]
+\fbox{\begin{minipage}{0.98\textwidth}
+ \begin{center}\includegraphics[width=0.98\textwidth]{../figs/fig1oriloc}
+ \caption{\label{fig1oriloc}. Screenshot copy of figure 1 from \cite{oriloc}.
+ The complete genome sequence of \textit{Chlamydia trachomatis}
+ (accession number: \texttt{AE001273}) was used to illustrate
+ the method used by oriloc. (\textbf{a}) A DNA-walk is performed
+ by reading the sequence in the third
+ codon positions predicted by glimmer and walking into the plane according to the four
+ directions defined by the four bases as indicated on the bottom left of the figure.
+ The resulting DNA-walk is then summarized by projection onto the orthogonal
+ regression line pointing out at about 11 o’clock in the figure.
+ (\textbf{b}) The projected values are used as a composite skew index
+ plotted versus map position on the chromosome. The origin is predicted at
+ the maximum skew value while the terminus is predicted at the minimum.
+ }
+ \end{center}
+\end{minipage}}
+\end{figure}
+
A more consequent example is given in the fasta file \texttt{ct.fasta.gz} which
contains the complete genome of \textit{Chlamydia trachomatis} that was
used in \cite{oriloc}. You should be able to reproduce figure 1b from this
-paper with the following code:
+paper (\textit{cf.} screenshot in figure \ref{fig1oriloc}) with the following code:
\begin{Schunk}
\begin{Sinput}
@@ -413,12 +433,11 @@
if you are interested in the prediction of origins and terminus of
replication from base composition biases (more on this at
\url{http://pbil.univ-lyon1.fr/software/oriloc.html}). See also \cite{smorfland}
-for a recent review on this topic.
+for a review on this topic. Here is the improved version:
\begin{Schunk}
\begin{Sinput}
- out <- oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package ="seqinr"),
- g2.coord = system.file("sequences/ct.predict", package = "seqinr"))
+ out <- oriloc()
plot(out$st, out$sk/1000, type="l", xlab = "Map position in Kb",
ylab = "Cumulated composite skew in Kb",
main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome), las = 1)
@@ -430,6 +449,22 @@
\end{Schunk}
\includegraphics{../figs/getseqflat-oriloc2}
+You can also call the \texttt{draw.oriloc()} function for the simultaneous
+representation of the CDS, AT and GC skew along with the combined skew
+of the previous plots:
+
+\begin{Schunk}
+\begin{Sinput}
+ draw.oriloc(out,
+ main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome),
+ ta.mtext = "TA skew", ta.col = "red",
+ cg.mtext = "CG skew", cg.col = "blue",
+ cds.mtext = "CDS skew", cds.col = "seagreen",
+ add.grid = FALSE)
+\end{Sinput}
+\end{Schunk}
+\includegraphics{../figs/getseqflat-oriloc3}
+
\subsubsection{Example with 21,161 proteins from \textit{Arabidobpsis thaliana}}
As from \seqinr{} 1.0-5 the automatic conversion of sequences into vector
@@ -472,7 +507,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 3.822 0.031 3.851
+ 3.908 0.035 3.948
\end{Soutput}
\end{Schunk}
@@ -493,7 +528,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 0.158 0.002 0.159
+ 0.164 0.002 0.167
\end{Soutput}
\end{Schunk}
@@ -1531,7 +1566,7 @@
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Jun 2 13:57:06 2016
+ \item \Rlogo{} compilation time was: Thu Jun 2 14:42:23 2016
\item \LaTeX{} compilation time was: \today
\end{itemize}
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