[Seqinr-commits] r1475 - pkg/inst/doc/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 20 17:37:53 CEST 2008
Author: lobry
Date: 2008-10-20 17:37:52 +0200 (Mon, 20 Oct 2008)
New Revision: 1475
Modified:
pkg/inst/doc/src/mainmatter/risa.rnw
pkg/inst/doc/src/mainmatter/risa.tex
Log:
Modified: pkg/inst/doc/src/mainmatter/risa.rnw
===================================================================
--- pkg/inst/doc/src/mainmatter/risa.rnw 2008-10-12 08:29:25 UTC (rev 1474)
+++ pkg/inst/doc/src/mainmatter/risa.rnw 2008-10-20 15:37:52 UTC (rev 1475)
@@ -305,7 +305,8 @@
# Loop over all sequences:
#
for(i in seq_len(res3$nelem)){
- result[[i]] <- mn2risa(seqnames[i], amo1, amo2, verbose = verbose)
+ try.res <- try(result[[i]] <- mn2risa(seqnames[i], amo1, amo2, verbose = verbose))
+ if(inherits(try.res, "try-error")) result[[i]] <- -Inf
}
return(result)
}
@@ -372,7 +373,8 @@
i <- i + 1
next
}
- resultat[[i]] <- sp2risa(sp=sp,amo1, amo2, verbose = TRUE)
+ try.res <- try(resultat[[i]] <- sp2risa(sp=sp,amo1, amo2, verbose = TRUE))
+ if(inherits(try.res, "try-error")) resultat[[i]] <- -Inf
save(resultat, file = "resultat.RData")
print(paste("=>", resultat[[i]]))
i <- i + 1
@@ -400,6 +402,21 @@
table(unlist(lapply(resultat,length)))
@
+Show how many IGS of different size we have per species.
+
+<<ndIGSpsp,fig=T>>=
+igsdbysp <- unlist(lapply(resultat, function(x)length(unique(unlist(x)))))
+plot(table(igsdbysp),
+xlab = "Number of IGS of different size",
+ylab = "Number of species")
+@
+
+Which are the species with the most important number of IGS?
+
+<<igsdbysp,fig=F>>=
+tail(igsdbysp[order(igsdbysp)], n = 30)
+@
+
How many IGS do we have there:
<<brut,fig=F>>=
@@ -415,9 +432,9 @@
y <- tab
plot(x,y, type = "h", ylim = c(0, max(y)),
main = "Global distribution of IGS length",
-las = 1, ylab = "Count", xlab = "Size in bp")
+las = 1, ylab = "Count", xlab = "Size in bp", xlim = c(0,1500))
-dst <- density(brut2, adj = 0.1)
+dst <- density(brut2, adj = 0.2)
lines(dst$x, dst$y*max(y)/max(dst$y), col = "red", xpd=NA)
@
Modified: pkg/inst/doc/src/mainmatter/risa.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/risa.tex 2008-10-12 08:29:25 UTC (rev 1474)
+++ pkg/inst/doc/src/mainmatter/risa.tex 2008-10-20 15:37:52 UTC (rev 1475)
@@ -404,7 +404,8 @@
# Loop over all sequences:
#
for(i in seq_len(res3$nelem)){
- result[[i]] <- mn2risa(seqnames[i], amo1, amo2, verbose = verbose)
+ try.res <- try(result[[i]] <- mn2risa(seqnames[i], amo1, amo2, verbose = verbose))
+ if(inherits(try.res, "try-error")) result[[i]] <- -Inf
}
return(result)
}
@@ -475,7 +476,10 @@
i <- i + 1
next
}
- resultat[[i]] <- sp2risa(sp = sp, amo1, amo2, verbose = TRUE)
+ try.res <- try(resultat[[i]] <- sp2risa(sp = sp, amo1,
+ amo2, verbose = TRUE))
+ if (inherits(try.res, "try-error"))
+ resultat[[i]] <- -Inf
save(resultat, file = "resultat.RData")
print(paste("=>", resultat[[i]]))
i <- i + 1
@@ -500,7 +504,7 @@
(nnull <- sum(lesnull))
\end{Sinput}
\begin{Soutput}
-[1] 1901
+[1] 1
\end{Soutput}
\begin{Sinput}
resultat <- resultat[!lesnull]
@@ -514,11 +518,66 @@
table(unlist(lapply(resultat, length)))
\end{Sinput}
\begin{Soutput}
- 1 2 3 8 22 25 69 107
-236 10 1 1 1 1 1 1
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+1567 253 114 51 24 22 27 11 10 6 6 3 2 6 5
+ 16 17 18 19 20 21 22 23 24 25 26 29 31 35 37
+ 4 3 6 1 4 1 5 1 2 1 3 2 1 1 1
+ 39 45 64 69 71 72 80 107 139
+ 1 1 1 1 1 1 1 1 1
\end{Soutput}
\end{Schunk}
+Show how many IGS of different size we have per species.
+
+\begin{Schunk}
+\begin{Sinput}
+ igsdbysp <- unlist(lapply(resultat, function(x) length(unique(unlist(x)))))
+ plot(table(igsdbysp), xlab = "Number of IGS of different size",
+ ylab = "Number of species")
+\end{Sinput}
+\end{Schunk}
+\includegraphics{../figs/risa-ndIGSpsp}
+
+Which are the species with the most important number of IGS?
+
+\begin{Schunk}
+\begin{Sinput}
+ tail(igsdbysp[order(igsdbysp)], n = 30)
+\end{Sinput}
+\begin{Soutput}
+ KLEBSIELLA PNEUMONIAE 342 CAMPYLOBACTER JEJUNI
+ 6 7
+ PSEUDOMONAS PUTIDA SHEWANELLA WOODYI ATCC 51908
+ 7 7
+ SHEWANELLA SEDIMINIS HAW-EB3 ESCHERICHIA COLI CFT073
+ 7 7
+ VIBRIO CHOLERAE VIBRIO VULNIFICUS
+ 7 7
+VIBRIO PARAHAEMOLYTICUS RIMD 2210633 BACILLUS HALODURANS C-125
+ 7 7
+ HELIOBACTERIUM MODESTICALDUM ICE1 CUPRIAVIDUS NECATOR
+ 7 8
+ PSEUDOMONAS FLUORESCENS CANDIDATUS COMPETIBACTER PHOSPHATIS
+ 8 8
+ VIBRIO PARAHAEMOLYTICUS BACILLUS HALODURANS
+ 8 8
+ ALKALIPHILUS METALLIREDIGENS QYMF SORANGIUM CELLULOSUM
+ 8 9
+ BRADYRHIZOBIUM JAPONICUM PSYCHROMONAS INGRAHAMII 37
+ 9 9
+ GEOBACILLUS KAUSTOPHILUS HTA426 RHODOPSEUDOMONAS PALUSTRIS
+ 9 10
+ ESCHERICHIA COLI GEOBACILLUS KAUSTOPHILUS
+ 10 10
+ VIBRIO FISCHERI ES114 KLEBSIELLA PNEUMONIAE
+ 11 12
+ PHOTOBACTERIUM PROFUNDUM SS9 BACILLUS CEREUS
+ 12 13
+ STAPHYLOCOCCUS AUREUS UNCULTURED SYNECHOCOCCUS SP.
+ 24 29
+\end{Soutput}
+\end{Schunk}
+
How many IGS do we have there:
\begin{Schunk}
@@ -527,14 +586,14 @@
length(brut)
\end{Sinput}
\begin{Soutput}
-[1] 513
+[1] 7659
\end{Soutput}
\begin{Sinput}
brut2 <- brut[!is.na(brut)]
length(brut2)
\end{Sinput}
\begin{Soutput}
-[1] 172
+[1] 4373
\end{Soutput}
\end{Schunk}
@@ -544,8 +603,9 @@
x <- as.numeric(unlist(dimnames(tab)))
y <- tab
plot(x, y, type = "h", ylim = c(0, max(y)), main = "Global distribution of IGS length",
- las = 1, ylab = "Count", xlab = "Size in bp")
- dst <- density(brut2, adj = 0.1)
+ las = 1, ylab = "Count", xlab = "Size in bp", xlim = c(0,
+ 1500))
+ dst <- density(brut2, adj = 0.2)
lines(dst$x, dst$y * max(y)/max(dst$y), col = "red", xpd = NA)
\end{Sinput}
\end{Schunk}
@@ -570,7 +630,7 @@
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Sat Oct 11 18:42:20 2008
+ \item \Rlogo{} compilation time was: Thu Oct 16 11:18:43 2008
\item \LaTeX{} compilation time was: \today
\end{itemize}
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