[Rflptools-commits] r4 - in pkg/RFLPtools: . inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 9 10:41:29 CEST 2010
Author: stamats
Date: 2010-06-09 10:41:28 +0200 (Wed, 09 Jun 2010)
New Revision: 4
Added:
pkg/RFLPtools/inst/doc/PaulMartini.png
Modified:
pkg/RFLPtools/DESCRIPTION
pkg/RFLPtools/NEWS
pkg/RFLPtools/inst/doc/RFLPtools.Rnw
pkg/RFLPtools/inst/doc/RFLPtools.pdf
pkg/RFLPtools/man/0RFLP-package.Rd
pkg/RFLPtools/man/RFLPdist.Rd
pkg/RFLPtools/man/RFLPdist2.Rd
pkg/RFLPtools/man/sim2dist.Rd
pkg/RFLPtools/man/simMatrix.Rd
Log:
modifications: reference to recent article, switched to simPlot (MKmisc version 0.8), updated vignette
Modified: pkg/RFLPtools/DESCRIPTION
===================================================================
--- pkg/RFLPtools/DESCRIPTION 2010-03-17 10:40:04 UTC (rev 3)
+++ pkg/RFLPtools/DESCRIPTION 2010-06-09 08:41:28 UTC (rev 4)
@@ -2,12 +2,12 @@
Type: Package
Title: Tools to analyse RFLP data
Version: 1.2
-Date: 2010-03-17
+Date: 2010-06-09
Author: Fabienne Flessa, Alexandra Kehl, Matthias Kohl
Maintainer: Matthias Kohl <Matthias.Kohl at stamats.de>
Description: RFLPtools provides functions to analyse DNA fragment samples
(i.e. derived from RFLP-analysis) and standalone BLAST report files
(i.e. DNA sequence analysis).
Depends: R(>= 2.10.0), stats, utils, graphics, grDevices, RColorBrewer
-Suggests: lattice, MKmisc
+Suggests: lattice, MKmisc(>= 0.8)
License: LGPL-3
Modified: pkg/RFLPtools/NEWS
===================================================================
--- pkg/RFLPtools/NEWS 2010-03-17 10:40:04 UTC (rev 3)
+++ pkg/RFLPtools/NEWS 2010-06-09 08:41:28 UTC (rev 4)
@@ -21,3 +21,6 @@
###########################################################
- RFLPplot and RFLPrefplot gained argument "colBands" to specify color(s) for
the plotted bands.
+- added reference to recent article
+- in examples now use of simPlot instead of corPlot, hence requires package
+ MKmisc version 0.8
Added: pkg/RFLPtools/inst/doc/PaulMartini.png
===================================================================
(Binary files differ)
Property changes on: pkg/RFLPtools/inst/doc/PaulMartini.png
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Modified: pkg/RFLPtools/inst/doc/RFLPtools.Rnw
===================================================================
--- pkg/RFLPtools/inst/doc/RFLPtools.Rnw 2010-03-17 10:40:04 UTC (rev 3)
+++ pkg/RFLPtools/inst/doc/RFLPtools.Rnw 2010-06-09 08:41:28 UTC (rev 4)
@@ -35,8 +35,14 @@
%-------------------------------------------------------------------------------
\title{RFLPtools: Analysis of DNA fragment samples and standalone BLAST report files}
%-------------------------------------------------------------------------------
-\author{F. Flessa, A. Kehl and M. Kohl\\ \\
+\author{F. Flessa\thanks{Chair for Plant Systematics, Section Mycology,
+University of Bayreuth, 95440 Bayreuth, Germany, Fabienne.Flessa at uni-bayreuth.de},
+A. Kehl\thanks{Chair for Plant Systematics, Section Mycology,
+University of Bayreuth, 95440 Bayreuth, Germany, Alexandra.Kehl at uni-bayreuth.de} and
+M. Kohl\thanks{Department of Anesthesiology and Intensive Care Medicine,
+Friedrich-Schiller-University Jena, 07747 Jena, Germany, Matthias.Kohl at stamats.de}\\ \\
\includegraphics[width = 3cm]{logoUBT.png}
+\includegraphics[width = 3cm]{PaulMartini.png}
}
\maketitle
\tableofcontents
@@ -101,7 +107,7 @@
myCol <- colorRampPalette(brewer.pal(8, "RdYlGn"))(128)
ord <- order.dendrogram(as.dendrogram(hclust(res[[1]])))
temp <- as.matrix(res[[1]])
-corPlot(temp[ord,ord], col = rev(myCol), minCor = 0,
+simPlot(temp[ord,ord], col = rev(myCol), minVal = 0,
labels = colnames(temp), title = "(Dis-)Similarity Plot")
@
\myinfig{1}{RFLPtools-sim1.pdf}
@@ -192,7 +198,7 @@
We visualize the similarity matrix ...
<<blast2, fig = TRUE>>=
library(MKmisc)
-corPlot(res2, col = myCol, minCor = 0, cex.axis = 0.5,
+simPlot(res2, col = myCol, minVal = 0, cex.axis = 0.5,
labels = colnames(res2), title = "(Dis-)Similarity Plot")
@
\myinfig{1}{RFLPtools-blast2.pdf}
Modified: pkg/RFLPtools/inst/doc/RFLPtools.pdf
===================================================================
(Binary files differ)
Modified: pkg/RFLPtools/man/0RFLP-package.Rd
===================================================================
--- pkg/RFLPtools/man/0RFLP-package.Rd 2010-03-17 10:40:04 UTC (rev 3)
+++ pkg/RFLPtools/man/0RFLP-package.Rd 2010-06-09 08:41:28 UTC (rev 4)
@@ -15,9 +15,9 @@
\tabular{ll}{
Package: \tab RFLPtools\cr
Version: \tab 1.2 \cr
-Date: \tab 2010-03-17 \cr
+Date: \tab 2010-06-09 \cr
Depends: \tab R(>= 2.10.0), stats, utils, grDevices, RColorBrewer\cr
-Suggests: \tab lattice, MKmisc\cr
+Suggests: \tab lattice, MKmisc(>= 0.8)\cr
License: \tab LGPL-3\cr
}}
@@ -43,6 +43,10 @@
Matsumoto, Masaru; Furuya, Naruto; Takanami, Yoichi; Matsuyama, Nobuaki.
RFLP analysis of the PCR-amplified 28S rDNA in Rhizoctonia solani.
Mycoscience 1996 37:351 - 356
+
+ Persoh, D., Melcher, M., Flessa, F., Rambold, G.:
+ First fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum
+ and itshost Pinus sylvestris. Fungal Biology 2010, in press.
}
\examples{
data(RFLPdata)
@@ -57,12 +61,11 @@
RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
+library(MKmisc)
data(BLASTdata)
res <- simMatrix(BLASTdata, sequence.range = TRUE, Min = 500)
-library(RColorBrewer)
-library(MKmisc)
myCol <- colorRampPalette(brewer.pal(8, "RdYlGn"))(128)
-corPlot(res, col = myCol, minCor = 0,
+simPlot(res, col = myCol, minVal = 0,
labels = colnames(res), title = "(Dis-)Similarity Plot")
}
\keyword{package}
Modified: pkg/RFLPtools/man/RFLPdist.Rd
===================================================================
--- pkg/RFLPtools/man/RFLPdist.Rd 2010-03-17 10:40:04 UTC (rev 3)
+++ pkg/RFLPtools/man/RFLPdist.Rd 2010-06-09 08:41:28 UTC (rev 4)
@@ -81,13 +81,11 @@
## Similarity matrix
-library(RColorBrewer)
library(MKmisc)
-
myCol <- colorRampPalette(brewer.pal(8, "RdYlGn"))(128)
ord <- order.dendrogram(as.dendrogram(hclust(res[[1]])))
temp <- as.matrix(res[[1]])
-corPlot(temp[ord,ord], col = rev(myCol), minCor = 0,
+simPlot(temp[ord,ord], col = rev(myCol), minVal = 0,
labels = colnames(temp), title = "(Dis-)Similarity Plot")
Modified: pkg/RFLPtools/man/RFLPdist2.Rd
===================================================================
--- pkg/RFLPtools/man/RFLPdist2.Rd 2010-03-17 10:40:04 UTC (rev 3)
+++ pkg/RFLPtools/man/RFLPdist2.Rd 2010-06-09 08:41:28 UTC (rev 4)
@@ -71,13 +71,11 @@
plot(hclust(res3), main = "3 bands missing")
## Similarity matrix
-library(RColorBrewer)
library(MKmisc)
-
myCol <- colorRampPalette(brewer.pal(8, "RdYlGn"))(128)
ord <- order.dendrogram(as.dendrogram(hclust(res1)))
temp <- as.matrix(res1)
-corPlot(temp[ord,ord], col = rev(myCol), minCor = 0,
+simPlot(temp[ord,ord], col = rev(myCol), minVal = 0,
labels = colnames(temp), title = "(Dis-)Similarity Plot")
@@ -94,7 +92,6 @@
## Other distances
res11 <- RFLPdist2(RFLPdata, distfun = function(x) dist(x, method = "manhattan"),
nrBands = 9, nrMissing = 1)
-library(MKmisc)
res12 <- RFLPdist2(RFLPdata, distfun = corDist, nrBands = 9, nrMissing = 1)
res1
res11
Modified: pkg/RFLPtools/man/sim2dist.Rd
===================================================================
--- pkg/RFLPtools/man/sim2dist.Rd 2010-03-17 10:40:04 UTC (rev 3)
+++ pkg/RFLPtools/man/sim2dist.Rd 2010-06-09 08:41:28 UTC (rev 4)
@@ -44,7 +44,7 @@
## visualize similarity matrix
library(MKmisc)
-corPlot(res2, minCor = 0,
+simPlot(res2, minVal = 0,
labels = colnames(res2), title = "(Dis-)Similarity Plot")
Modified: pkg/RFLPtools/man/simMatrix.Rd
===================================================================
--- pkg/RFLPtools/man/simMatrix.Rd 2010-03-17 10:40:04 UTC (rev 3)
+++ pkg/RFLPtools/man/simMatrix.Rd 2010-06-09 08:41:28 UTC (rev 4)
@@ -39,6 +39,10 @@
Blast News: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
BioEdit v7.0.9: Tom Hall, Ibis Biosciences; http://www.mbio.ncsu.edu/BioEdit/bioedit.html
+
+ Persoh, D., Melcher, M., Flessa, F., Rambold, G.:
+ First fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum
+ and itshost Pinus sylvestris. Fungal Biology 2010, in press.
}
\author{
Fabienne Flessa \email{Fabienne.Flessa at uni-bayreuth.de},\cr
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