[Seqinr-commits] r1793 - www/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jun 6 18:44:13 CEST 2014
Author: jeanlobry
Date: 2014-06-06 18:44:13 +0200 (Fri, 06 Jun 2014)
New Revision: 1793
Modified:
www/src/mainmatter/getseqflat.rnw
www/src/mainmatter/getseqflat.tex
Log:
compil 3.0-11
Modified: www/src/mainmatter/getseqflat.rnw
===================================================================
--- www/src/mainmatter/getseqflat.rnw 2014-06-06 16:20:57 UTC (rev 1792)
+++ www/src/mainmatter/getseqflat.rnw 2014-06-06 16:44:13 UTC (rev 1793)
@@ -6,6 +6,7 @@
\author{Charif, D. \and Lobry, J.R.}
\begin{document}
+\SweaveOpts{concordance=TRUE}
\SweaveInput{../config/commonrnw.rnw}
\maketitle
\tableofcontents
@@ -195,8 +196,11 @@
which contains the sequences of 21,161 proteins.
<<readath,fig=F, eval=T>>=
-athfile <- system.file("sequences/ATH1_pep_cm_20040228.fasta", package = "seqinr")
-system.time(ath <- read.fasta(athfile, seqtype = "AA", as.string = TRUE, set.attributes = FALSE))
+athfile <- "ATH1_pep_cm_20040228.fasta"
+download.file(paste("http://seqinr.r-forge.r-project.org", athfile, sep = "/"),
+ athfile)
+system.time(ath <- read.fasta(athfile, seqtype = "AA", as.string = TRUE,
+ set.attributes = FALSE))
@
It's about 10 seconds here to read 21,161 protein sequences. We save them
Modified: www/src/mainmatter/getseqflat.tex
===================================================================
--- www/src/mainmatter/getseqflat.tex 2014-06-06 16:20:57 UTC (rev 1792)
+++ www/src/mainmatter/getseqflat.tex 2014-06-06 16:44:13 UTC (rev 1793)
@@ -7,6 +7,7 @@
\usepackage{Sweave}
\begin{document}
+\input{getseqflat-concordance}
%
% To change the R input/output style:
%
@@ -63,18 +64,14 @@
\begin{Schunk}
\begin{Sinput}
- list.files(path = system.file("sequences", package = "seqinr"),
- pattern = ".fasta")
+ list.files(path = system.file("sequences", package = "seqinr"), pattern = ".fasta")
\end{Sinput}
\begin{Soutput}
- [1] "Anouk.fasta" "ATH1_pep_cm_20040228.fasta"
- [3] "bb.fasta" "bordetella.fasta"
- [5] "ct.fasta" "DarrenObbard.fasta"
- [7] "ecolicgpe5.fasta" "gopher.fasta"
- [9] "humanMito.fasta" "legacy.fasta"
-[11] "louse.fasta" "malM.fasta"
-[13] "ortho.fasta" "seqAA.fasta"
-[15] "smallAA.fasta"
+ [1] "Anouk.fasta" "bb.fasta" "bordetella.fasta"
+ [4] "ct.fasta" "DarrenObbard.fasta" "ecolicgpe5.fasta"
+ [7] "gopher.fasta" "humanMito.fasta" "legacy.fasta"
+[10] "louse.fasta" "malM.fasta" "ortho.fasta"
+[13] "seqAA.fasta" "smallAA.fasta"
\end{Soutput}
\end{Schunk}
@@ -82,8 +79,7 @@
\begin{Schunk}
\begin{Sinput}
- cat(readLines(system.file("sequences/seqAA.fasta", package = "seqinr")),
- sep = "\n")
+ cat(readLines(system.file("sequences/seqAA.fasta", package = "seqinr")), sep = "\n")
\end{Sinput}
\begin{Soutput}
>A06852 183 residues
@@ -98,8 +94,7 @@
\begin{Schunk}
\begin{Sinput}
- cat(readLines(system.file("sequences/legacy.fasta", package = "seqinr")),
- sep = "\n")
+ cat(readLines(system.file("sequences/legacy.fasta", package = "seqinr")), sep = "\n")
\end{Sinput}
\begin{Soutput}
>LEGACY 921 bp
@@ -283,7 +278,7 @@
\begin{Schunk}
\begin{Sinput}
- aafile <- system.file("sequences/seqAA.fasta", package = "seqinr")
+ aafile <- system.file("sequences/seqAA.fasta", package = "seqinr")
cat(readLines(aafile), sep = "\n")
\end{Sinput}
\begin{Soutput}
@@ -342,8 +337,7 @@
\begin{Schunk}
\begin{Sinput}
- ortho <- read.fasta(file = system.file("sequences/ortho.fasta",
- package = "seqinr"))
+ ortho <- read.fasta(file = system.file("sequences/ortho.fasta", package = "seqinr"))
length(ortho)
\end{Sinput}
\begin{Soutput}
@@ -361,8 +355,7 @@
\begin{Schunk}
\begin{Sinput}
- ortho3 <- lapply(ortho, function(x) x[seq(from = 3, to = length(x),
- by = 3)])
+ ortho3 <- lapply(ortho, function(x) x[seq(from = 3, to = length(x), by = 3)])
ortho3[[1]][1:4]
\end{Sinput}
\begin{Soutput}
@@ -375,8 +368,7 @@
\begin{Schunk}
\begin{Sinput}
tmpf <- tempfile()
- write.fasta(sequences = ortho3, names = names(ortho3), nbchar = 80,
- file.out = tmpf)
+ write.fasta(sequences = ortho3, names = names(ortho3), nbchar = 80, file.out = tmpf)
\end{Sinput}
\end{Schunk}
@@ -403,12 +395,12 @@
\begin{Schunk}
\begin{Sinput}
- out <- oriloc(seq.fasta = system.file("sequences/ct.fasta",
- package = "seqinr"), g2.coord = system.file("sequences/ct.coord",
- package = "seqinr"), oldoriloc = TRUE)
- 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)
+ out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
+ g2.coord = system.file("sequences/ct.coord", package = "seqinr"),
+ oldoriloc = TRUE)
+ 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)
abline(h = 0, lty = 2)
text(400, -4, "Terminus")
text(850, 9, "Origin")
@@ -425,12 +417,11 @@
\begin{Schunk}
\begin{Sinput}
- out <- oriloc(seq.fasta = system.file("sequences/ct.fasta",
- package = "seqinr"), g2.coord = system.file("sequences/ct.coord",
- package = "seqinr"))
- 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)
+ out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
+ g2.coord = system.file("sequences/ct.coord", package = "seqinr"))
+ 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)
mtext("New version")
abline(h = 0, lty = 2)
text(400, -4, "Terminus")
@@ -473,14 +464,15 @@
\begin{Schunk}
\begin{Sinput}
- athfile <- system.file("sequences/ATH1_pep_cm_20040228.fasta",
- package = "seqinr")
+ athfile <- "ATH1_pep_cm_20040228.fasta"
+ download.file(paste("http://seqinr.r-forge.r-project.org", athfile, sep = "/"),
+ athfile)
system.time(ath <- read.fasta(athfile, seqtype = "AA", as.string = TRUE,
- set.attributes = FALSE))
+ set.attributes = FALSE))
\end{Sinput}
\begin{Soutput}
user system elapsed
- 6.753 0.129 7.143
+ 3.766 0.022 3.789
\end{Soutput}
\end{Schunk}
@@ -501,7 +493,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 0.331 0.009 0.343
+ 0.151 0.001 0.153
\end{Soutput}
\end{Schunk}
@@ -514,7 +506,7 @@
object.size(ath)/2^20
\end{Sinput}
\begin{Soutput}
-14.6553726196289 bytes
+16.2128143310547 bytes
\end{Soutput}
\begin{Sinput}
file.info(athfile)$size/2^20
@@ -535,9 +527,9 @@
\begin{Schunk}
\begin{Sinput}
nres <- nchar(ath) - 1
- hist(log10(nres), col = grey(0.7), xlab = "Protein size (log10 scale)",
- ylab = "Protein count", main = expression(italic(Arabidopsis ~
- ~thaliana)))
+ hist(log10(nres), col = grey(0.7), xlab = "Protein size (log10 scale)",
+ ylab = "Protein count",
+ main = expression(italic(Arabidopsis~~thaliana)))
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/getseqflat-athdistriprotsize}
@@ -588,10 +580,10 @@
\begin{Schunk}
\begin{Sinput}
- ngly <- function(data) {
- res <- sapply(data, function(x) sum(s2c(x) == "G"))
- names(res) <- NULL
- return(res)
+ ngly <- function(data){
+ res <- sapply(data, function(x) sum(s2c(x) == "G"))
+ names(res) <- NULL
+ return(res)
}
\end{Sinput}
\end{Schunk}
@@ -615,10 +607,10 @@
\begin{Schunk}
\begin{Sinput}
- hist(fgly, col = grey(0.7), main = "Distribution of Glycine frequency",
- xlab = "Glycine content", ylab = "Protein count")
+ hist(fgly, col = grey(0.7), main = "Distribution of Glycine frequency",
+ xlab = "Glycine content", ylab = "Protein count")
abline(v = 0.08, col = "red")
- legend("topright", inset = 0.01, lty = 1, col = "red", legend = "Threshold for hydrophilines")
+ legend("topright",inset=0.01,lty=1,col="red",legend="Threshold for hydrophilines")
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/getseqflat-histgly}
@@ -627,10 +619,10 @@
\begin{Schunk}
\begin{Sinput}
- boxplot(fgly, horizontal = TRUE, col = grey(0.7), main = "Distribution of Glycine frequency",
- xlab = "Glycine content", ylab = "Protein count")
+ boxplot(fgly, horizontal = TRUE, col = grey(0.7), main = "Distribution of Glycine frequency",
+ xlab = "Glycine content", ylab = "Protein count")
abline(v = 0.08, col = "red")
- legend("topright", inset = 0.01, lty = 1, col = "red", legend = "Threshold for hydrophilines")
+ legend("topright",inset=0.01,lty=1,col="red",legend="Threshold for hydrophilines")
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/getseqflat-boxplotgly}
@@ -696,7 +688,7 @@
\begin{Schunk}
\begin{Sinput}
- names(EXP$KD) <- sapply(words(), function(x) translate(s2c(x)))
+ names(EXP$KD) <- sapply(words(),function(x) translate(s2c(x)))
\end{Sinput}
\end{Schunk}
@@ -759,17 +751,17 @@
\begin{Schunk}
\begin{Sinput}
- linform <- function(data, coef) {
- f <- function(x) {
- aaseq <- s2c(x)
- freq <- table(factor(aaseq, levels = names(coef)))/length(aaseq)
- return(coef %*% freq)
- }
- res <- sapply(data, f)
- names(res) <- NULL
- return(res)
+ linform <- function(data, coef){
+ f <- function(x){
+ aaseq <- s2c(x)
+ freq <- table(factor(aaseq, levels = names(coef)))/length(aaseq)
+ return(coef %*% freq)
+ }
+ res <- sapply(data, f)
+ names(res) <- NULL
+ return(res)
}
- kdath <- linform(ath, kdc)
+ kdath <- linform(ath,kdc)
\end{Sinput}
\end{Schunk}
@@ -777,10 +769,11 @@
\begin{Schunk}
\begin{Sinput}
- boxplot(kdath, horizontal = TRUE, col = grey(0.7), main = "Distribution of Hydropathy index",
- xlab = "Kyte and Doolittle GRAVY score")
+ boxplot(kdath, horizontal = TRUE, col = grey(0.7),
+ main = "Distribution of Hydropathy index",
+ xlab = "Kyte and Doolittle GRAVY score")
abline(v = 1, col = "red")
- legend("topleft", inset = 0.01, lty = 1, col = "red", legend = "Threshold for hydrophilines")
+ legend("topleft",inset=0.01,lty=1,col="red",legend="Threshold for hydrophilines")
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/getseqflat-distriKD}
@@ -804,19 +797,19 @@
\begin{Schunk}
\begin{Sinput}
library(MASS)
- dst <- kde2d(kdath, fgly, n = 50)
- filled.contour(x = dst, color.palette = topo.colors, plot.axes = {
- axis(1)
- axis(2)
- title(xlab = "Kyte and Doolittle GRAVY score", ylab = "Glycine content",
- main = "Hydrophilines location")
- abline(v = 1, col = "yellow")
- abline(h = 0.08, col = "yellow")
- points(kdath[hydrophilines], fgly[hydrophilines], col = "white")
- legend("topleft", inset = 0.02, lty = 1, col = "yellow",
- bg = "white", legend = "Threshold for hydrophilines",
- cex = 0.8)
- })
+ dst <- kde2d(kdath,fgly, n = 50)
+ filled.contour(x = dst, color.palette = topo.colors,
+ plot.axes = {
+ axis(1)
+ axis(2)
+ title(xlab="Kyte and Doolittle GRAVY score", ylab = "Glycine content",
+ main = "Hydrophilines location")
+ abline(v=1, col = "yellow")
+ abline(h=0.08, col = "yellow")
+ points(kdath[hydrophilines], fgly[hydrophilines], col = "white")
+ legend("topleft",inset=0.02,lty=1,col="yellow", bg="white", legend="Threshold for hydrophilines", cex = 0.8)
+ }
+ )
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/getseqflat-chekhydro}
@@ -825,7 +818,8 @@
\begin{Schunk}
\begin{Sinput}
- athres <- data.frame(list(name = names(ath), KD = kdath, Gly = fgly))
+ data.frame(list("name"=names(ath),
+ "KD"=kdath, "Gly"=fgly)) -> athres
head(athres)
\end{Sinput}
\begin{Soutput}
@@ -864,8 +858,7 @@
\begin{Schunk}
\begin{Sinput}
- hannah <- read.table(system.file("sequences/hannah.txt", package = "seqinr"),
- sep = "\t", header = TRUE)
+ read.table(system.file("sequences/hannah.txt", package = "seqinr"), sep = "\t", header = TRUE)->hannah
head(hannah)
\end{Sinput}
\begin{Soutput}
@@ -907,13 +900,13 @@
head(join)
\end{Sinput}
\begin{Soutput}
- AGI Hydrophilicity Glycine KD Gly
-1 At1g01120.1 -0.10 0.06 0.10699433 0.05871212
-2 At1g01390.1 0.02 0.06 0.00914761 0.06458333
-3 At1g01390.1 0.02 0.06 0.00914761 0.06458333
-4 At1g01420.1 -0.05 0.07 0.06203320 0.07276507
-5 At1g01420.1 -0.05 0.07 0.06203320 0.07276507
-6 At1g01480.1 -0.20 0.07 0.20080483 0.06653226
+ AGI Hydrophilicity Glycine KD Gly
+1 At1g01120.1 -0.10 0.06 0.106994329 0.05871212
+2 At1g01390.1 0.02 0.06 0.009147609 0.06458333
+3 At1g01390.1 0.02 0.06 0.009147609 0.06458333
+4 At1g01420.1 -0.05 0.07 0.062033195 0.07276507
+5 At1g01420.1 -0.05 0.07 0.062033195 0.07276507
+6 At1g01480.1 -0.20 0.07 0.200804829 0.06653226
\end{Soutput}
\end{Schunk}
@@ -921,9 +914,9 @@
\begin{Schunk}
\begin{Sinput}
- plot(join$Glycine, join$Gly, xlab = "Glycine content in Hannah et al. (2005)",
- ylab = "Glycine content here", main = "Comparison of Glycine content results")
- abline(c(0, 1), col = "red")
+ plot(join$Glycine, join$Gly, xlab = "Glycine content in Hannah et al. (2005)",
+ ylab = "Glycine content here", main = "Comparison of Glycine content results")
+ abline(c(0,1), col = "red")
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/getseqflat-comparegly}
@@ -937,12 +930,11 @@
\begin{Schunk}
\begin{Sinput}
- plot(join$Hydrophilicity, join$KD, xlab = "GRAVY score in Hannah et al. (2005)",
- ylab = "GRAVY score here", main = "Comparison of hydropathy score results",
- las = 1)
- abline(c(0, -1), col = "red")
- abline(v = 0, lty = 2)
- abline(h = 0, lty = 2)
+ plot(join$Hydrophilicity, join$KD, xlab = "GRAVY score in Hannah et al. (2005)",
+ ylab = "GRAVY score here", main = "Comparison of hydropathy score results", las = 1)
+ abline(c(0,-1), col = "red")
+ abline(v=0, lty=2)
+ abline(h=0, lty=2)
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/getseqflat-comparekd}
@@ -1025,7 +1017,7 @@
\begin{Schunk}
\begin{Sinput}
- clustalf <- system.file("sequences/test.aln", package = "seqinr")
+ clustalf <-system.file("sequences/test.aln", package = "seqinr")
cat(readLines(clustalf), sep = "\n")
\end{Sinput}
\begin{Soutput}
@@ -1271,15 +1263,29 @@
example(read.alignment)
\end{Sinput}
\begin{Soutput}
-rd.lgn mase <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"), format = "mase")
+rd.lgn mase.res <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"), format = "mase")
-rd.lgn clustal <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"), format="clustal")
+rd.lgn clustal.res <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"), format="clustal")
-rd.lgn phylip <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
+rd.lgn phylip.res <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
-rd.lgn msf <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"), format = "msf")
+rd.lgn msf.res <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"), format = "msf")
-rd.lgn fasta <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
+rd.lgn fasta.res <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
+
+rd.lgn #
+rd.lgn # Quality control routine sanity checks:
+rd.lgn #
+rd.lgn
+rd.lgn data(mase); stopifnot(identical(mase, mase.res))
+
+rd.lgn data(clustal); stopifnot(identical(clustal, clustal.res))
+
+rd.lgn data(phylip); stopifnot(identical(phylip, phylip.res))
+
+rd.lgn data(msf); stopifnot(identical(msf, msf.res))
+
+rd.lgn data(fasta); stopifnot(identical(fasta, fasta.res))
\end{Soutput}
\end{Schunk}
@@ -1298,26 +1304,32 @@
\begin{Schunk}
\begin{Sinput}
- louse <- read.alignment(system.file("sequences/louse.fasta",
- package = "seqinr"), format = "fasta")
+ louse <- read.alignment(system.file("sequences/louse.fasta", package = "seqinr"), format = "fasta")
louse$nam
\end{Sinput}
\begin{Soutput}
-[1] "gi|548117|gb|L32667.1|GYDCYTOXIB" "gi|548119|gb|L32668.1|GYDCYTOXIC"
-[3] "gi|548121|gb|L32669.1|GYDCYTOXID" "gi|548125|gb|L32671.1|GYDCYTOXIF"
-[5] "gi|548127|gb|L32672.1|GYDCYTOXIG" "gi|548131|gb|L32675.1|GYDCYTOXII"
-[7] "gi|548133|gb|L32676.1|GYDCYTOXIJ" "gi|548137|gb|L32678.1|GYDCYTOXIL"
+[1] "gi|548117|gb|L32667.1|GYDCYTOXIB Geomydoecus chapini mitochondrial cytochrome oxidase I gene, partial cds"
+[2] "gi|548119|gb|L32668.1|GYDCYTOXIC Geomydoecus cherriei mitochondrial cytochrome oxidase I gene, partial cds"
+[3] "gi|548121|gb|L32669.1|GYDCYTOXID Geomydoecus costaricensis mitochondrial cytochrome oxidase I gene, partial cds"
+[4] "gi|548125|gb|L32671.1|GYDCYTOXIF Geomydoecus ewingi mitochondrial cytochrome oxidase I gene, partial cds"
+[5] "gi|548127|gb|L32672.1|GYDCYTOXIG Geomydoecus geomydis mitochondrial cytochrome oxidase I gene, partial cds"
+[6] "gi|548131|gb|L32675.1|GYDCYTOXII Geomydoecus oklahomensis mitochondrial cytochrome oxidase I gene, partial cds"
+[7] "gi|548133|gb|L32676.1|GYDCYTOXIJ Geomydoecus panamensis mitochondrial cytochrome oxidase I gene, partial cds"
+[8] "gi|548137|gb|L32678.1|GYDCYTOXIL Geomydoecus setzeri mitochondrial cytochrome oxidase I gene, partial cds"
\end{Soutput}
\begin{Sinput}
- gopher <- read.alignment(system.file("sequences/gopher.fasta",
- package = "seqinr"), format = "fasta")
+ gopher <- read.alignment(system.file("sequences/gopher.fasta", package = "seqinr"), format = "fasta")
gopher$nam
\end{Sinput}
\begin{Soutput}
-[1] "gi|548223|gb|L32683.1|PPGCYTOXIA" "gi|548197|gb|L32686.1|OGOCYTOXIA"
-[3] "gi|548199|gb|L32687.1|OGOCYTOXIB" "gi|548201|gb|L32691.1|OGOCYTOXIC"
-[5] "gi|548203|gb|L32692.1|OGOCYTOXID" "gi|548229|gb|L32693.1|PPGCYTOXID"
-[7] "gi|548231|gb|L32694.1|PPGCYTOXIE" "gi|548205|gb|L32696.1|OGOCYTOXIE"
+[1] "gi|548223|gb|L32683.1|PPGCYTOXIA Geomys breviceps mitochondrial cytochrome oxidase I gene, partial cds"
+[2] "gi|548197|gb|L32686.1|OGOCYTOXIA Orthogeomys cavator mitochondrial cytochrome oxidase I gene, partial cds"
+[3] "gi|548199|gb|L32687.1|OGOCYTOXIB Orthogeomys cherriei mitochondrial cytochrome oxidase I gene, partial cds"
+[4] "gi|548201|gb|L32691.1|OGOCYTOXIC Orthogeomys underwoodi mitochondrial cytochrome oxidase I gene, partial cds"
+[5] "gi|548203|gb|L32692.1|OGOCYTOXID Orthogeomys hispidus mitochondrial cytochrome oxidase I gene, partial cds"
+[6] "gi|548229|gb|L32693.1|PPGCYTOXID Geomys bursarius mitochondrial cytochrome oxidase I gene, partial cds"
+[7] "gi|548231|gb|L32694.1|PPGCYTOXIE Geomys bursarius mitochondrial cytochrome oxidase I gene, partial cds"
+[8] "gi|548205|gb|L32696.1|OGOCYTOXIE Orthogeomys heterodus mitochondrial cytochrome oxidase I gene, partial cds"
\end{Soutput}
\end{Schunk}
@@ -1343,8 +1355,7 @@
\begin{Schunk}
\begin{Sinput}
- l.names <- readLines(system.file("sequences/louse.names",
- package = "seqinr"))
+ l.names <- readLines(system.file("sequences/louse.names", package = "seqinr"))
l.names
\end{Sinput}
\begin{Soutput}
@@ -1352,8 +1363,7 @@
[6] "G.oklahome " "G.panamens " "G.setzeri "
\end{Soutput}
\begin{Sinput}
- g.names <- readLines(system.file("sequences/gopher.names",
- package = "seqinr"))
+ g.names <- readLines(system.file("sequences/gopher.names", package = "seqinr"))
g.names
\end{Sinput}
\begin{Soutput}
@@ -1409,13 +1419,12 @@
\begin{Sinput}
g$tip.label <- paste(1:8, g.names)
l$tip.label <- paste(1:8, l.names)
- layout(matrix(data = 1:2, nrow = 1, ncol = 2), width = c(1.4,
- 1))
- par(mar = c(2, 1, 2, 1))
- plot(g, adj = 0.8, cex = 1.4, use.edge.length = FALSE, main = "gopher (host)",
- cex.main = 2)
- plot(l, direction = "l", use.edge.length = FALSE, cex = 1.4,
- main = "louse (parasite)", cex.main = 2)
+ layout(matrix(data = 1:2, nrow = 1, ncol = 2), width=c(1.4, 1))
+ par(mar=c(2,1,2,1))
+ plot(g, adj = 0.8, cex = 1.4, use.edge.length=FALSE,
+ main = "gopher (host)", cex.main = 2)
+ plot(l,direction="l", use.edge.length=FALSE, cex = 1.4,
+ main = "louse (parasite)", cex.main = 2)
\end{Sinput}
\end{Schunk}
\includegraphics{../figs/getseqflat-face2face}
@@ -1504,20 +1513,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}\raggedright
- \item R version 2.10.0 (2009-10-26), \verb|i386-apple-darwin8.11.1|
- \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
+ \item R version 3.1.0 (2014-04-10), \verb|x86_64-apple-darwin13.1.0|
+ \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8|
\item Base packages: base, datasets, graphics, grDevices, grid,
methods, stats, utils
- \item Other packages: ade4~1.4-13, ape~2.4, grImport~0.4-4,
- MASS~7.3-3, quadprog~1.4-11, seqinr~2.0-7, tseries~0.10-21,
- XML~2.6-0, xtable~1.5-5, zoo~1.5-8
- \item Loaded via a namespace (and not attached): gee~4.13-14,
- lattice~0.17-26, nlme~3.1-96, tools~2.10.0
+ \item Other packages: ade4~1.6-2, ape~3.1-2, grImport~0.9-0,
+ MASS~7.3-31, seqinr~3.0-11, tseries~0.10-32, XML~3.98-1.1,
+ xtable~1.7-3
+ \item Loaded via a namespace (and not attached): lattice~0.20-29,
+ nlme~3.1-117, quadprog~1.5-5, tools~3.1.0, zoo~1.7-11
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Nov 5 11:19:19 2009
+ \item \Rlogo{} compilation time was: Fri Jun 6 18:34:24 2014
\item \LaTeX{} compilation time was: \today
\end{itemize}
More information about the Seqinr-commits
mailing list