[Rflptools-commits] r3 - in pkg/RFLPtools: . R inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Mar 17 11:40:04 CET 2010
Author: stamats
Date: 2010-03-17 11:40:04 +0100 (Wed, 17 Mar 2010)
New Revision: 3
Modified:
pkg/RFLPtools/DESCRIPTION
pkg/RFLPtools/NEWS
pkg/RFLPtools/R/RFLPplot.R
pkg/RFLPtools/R/RFLPrefplot.R
pkg/RFLPtools/inst/doc/RFLPtools.pdf
pkg/RFLPtools/man/0RFLP-package.Rd
pkg/RFLPtools/man/RFLPplot.Rd
pkg/RFLPtools/man/RFLPrefplot.Rd
Log:
increased version number to 1.2 and added argument "colBands" to functions RFLPplot and RFLPrefplot. Now it's possible for the user to specify her/his own color(s) for the bands.
Modified: pkg/RFLPtools/DESCRIPTION
===================================================================
--- pkg/RFLPtools/DESCRIPTION 2010-02-24 18:50:56 UTC (rev 2)
+++ pkg/RFLPtools/DESCRIPTION 2010-03-17 10:40:04 UTC (rev 3)
@@ -1,13 +1,13 @@
Package: RFLPtools
Type: Package
Title: Tools to analyse RFLP data
-Version: 1.1
-Date: 2010-02-21
+Version: 1.2
+Date: 2010-03-17
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(>= 2.9.0), stats, utils, graphics, grDevices, RColorBrewer
+Depends: R(>= 2.10.0), stats, utils, graphics, grDevices, RColorBrewer
Suggests: lattice, MKmisc
License: LGPL-3
Modified: pkg/RFLPtools/NEWS
===================================================================
--- pkg/RFLPtools/NEWS 2010-02-24 18:50:56 UTC (rev 2)
+++ pkg/RFLPtools/NEWS 2010-03-17 10:40:04 UTC (rev 3)
@@ -16,3 +16,8 @@
which do not occur as query.ids
- extended vignette and package Rd-file by RFLPplot and RFLPrefplot examples
+###########################################################
+## Version 1.2
+###########################################################
+- RFLPplot and RFLPrefplot gained argument "colBands" to specify color(s) for
+ the plotted bands.
Modified: pkg/RFLPtools/R/RFLPplot.R
===================================================================
--- pkg/RFLPtools/R/RFLPplot.R 2010-02-24 18:50:56 UTC (rev 2)
+++ pkg/RFLPtools/R/RFLPplot.R 2010-03-17 10:40:04 UTC (rev 3)
@@ -4,8 +4,10 @@
## x: data.frame with RFLP data
## distfun: function to compute distance (cf. ?dist)
-RFLPplot <- function(x, nrBands, nrMissing, distfun = dist, hclust.method = "complete",
- mar.bottom = 5, cex.axis = 0.5){
+RFLPplot <- function(x, nrBands, nrMissing, distfun = dist,
+ hclust.method = "complete",
+ mar.bottom = 5, cex.axis = 0.5,
+ colBands){
stopifnot(is.data.frame(x))
stopifnot(is.function(dist))
if(missing(nrBands))
@@ -54,11 +56,21 @@
}
}
rm(temp1)
- if(length(temp) <= 9){
- mycol <- brewer.pal(max(3, length(temp)), "Set1")
+ if(missing(colBands)){
+ if(length(temp) <= 9){
+ mycol <- brewer.pal(max(3, length(temp)), "Set1")
+ }else{
+ mycol1 <- brewer.pal(9, "Set1")
+ mycol <- colorRampPalette(mycol1)(length(temp))
+ }
}else{
- mycol1 <- brewer.pal(9, "Set1")
- mycol <- colorRampPalette(mycol1)(length(temp))
+ if((length(colBands) != 1) && (length(colBands) != length(temp)))
+ stop("Length of 'colBands' is", length(colBands), "and should be 1 or", length(temp))
+ if(length(colBands) == 1){
+ mycol <- rep(colBands, length(temp))
+ }else{
+ mycol <- colBands
+ }
}
temp.o <- temp[dend.ord]
Modified: pkg/RFLPtools/R/RFLPrefplot.R
===================================================================
--- pkg/RFLPtools/R/RFLPrefplot.R 2010-02-24 18:50:56 UTC (rev 2)
+++ pkg/RFLPtools/R/RFLPrefplot.R 2010-03-17 10:40:04 UTC (rev 3)
@@ -5,7 +5,8 @@
## x: data.frame with RFLP data
## distfun: function to compute distance (cf. ?dist)
RFLPrefplot <- function(x, ref, distfun = dist, nrBands, mar.bottom = 5,
- cex.main = 1.2, cex.axis = 0.5, devNew = FALSE){
+ cex.main = 1.2, cex.axis = 0.5, devNew = FALSE,
+ colBands){
res <- RFLPdist2ref(x, ref, distfun, nrBands)
x1 <- split(x, x$Sample)
@@ -47,11 +48,21 @@
abline(h = temp.mw, col = "black", lty = 1)
box()
title(paste("Reference sample:", colnames(res)[i]), cex.main = cex.main)
- if(length(temp) <= 9){
- mycol <- brewer.pal(max(3, length(temp)), "Set1")
+ if(missing(colBands)){
+ if(length(temp) <= 9){
+ mycol <- brewer.pal(max(3, length(temp)), "Set1")
+ }else{
+ mycol1 <- brewer.pal(9, "Set1")
+ mycol <- colorRampPalette(mycol1)(length(temp))
+ }
}else{
- mycol1 <- brewer.pal(9, "Set1")
- mycol <- colorRampPalette(mycol1)(length(temp))
+ if((length(colBands) != 1) && (length(colBands) != length(temp)))
+ stop("Length of 'colBands' is", length(colBands), "and should be 1 or", length(temp))
+ if(length(colBands) == 1){
+ mycol <- rep(colBands, length(temp))
+ }else{
+ mycol <- colBands
+ }
}
matlines(rbind(rep(0.75, reps), rep(1.25, reps)),
Modified: pkg/RFLPtools/inst/doc/RFLPtools.pdf
===================================================================
(Binary files differ)
Modified: pkg/RFLPtools/man/0RFLP-package.Rd
===================================================================
--- pkg/RFLPtools/man/0RFLP-package.Rd 2010-02-24 18:50:56 UTC (rev 2)
+++ pkg/RFLPtools/man/0RFLP-package.Rd 2010-03-17 10:40:04 UTC (rev 3)
@@ -14,9 +14,9 @@
\details{
\tabular{ll}{
Package: \tab RFLPtools\cr
-Version: \tab 1.0 \cr
-Date: \tab 2010-02-21 \cr
-Depends: \tab R(>= 2.9.0), stats, utils, grDevices, RColorBrewer\cr
+Version: \tab 1.2 \cr
+Date: \tab 2010-03-17 \cr
+Depends: \tab R(>= 2.10.0), stats, utils, grDevices, RColorBrewer\cr
Suggests: \tab lattice, MKmisc\cr
License: \tab LGPL-3\cr
}}
Modified: pkg/RFLPtools/man/RFLPplot.Rd
===================================================================
--- pkg/RFLPtools/man/RFLPplot.Rd 2010-02-24 18:50:56 UTC (rev 2)
+++ pkg/RFLPtools/man/RFLPplot.Rd 2010-03-17 10:40:04 UTC (rev 3)
@@ -9,7 +9,8 @@
}
\usage{
RFLPplot(x, nrBands, nrMissing, distfun = dist,
- hclust.method = "complete", mar.bottom = 5, cex.axis = 0.5)
+ hclust.method = "complete", mar.bottom = 5,
+ cex.axis = 0.5, colBands)
}
\arguments{
\item{x}{ data.frame with RFLP data; see \code{\link{RFLPdata}}.}
@@ -24,6 +25,9 @@
see \code{\link[stats]{hclust}}.}
\item{mar.bottom}{ bottom margin of the plot; see \code{\link[graphics]{par}}. }
\item{cex.axis}{ size of the x-axis annotation. }
+ \item{colBands}{ color for the bands. Has to be of length 1 or number of samples.
+ If missing, \code{"Set1"} of \pkg{RColorBrewer} is used; see
+ \code{\link[RColorBrewer]{brewer.pal}}. }
}
\details{
RFLP data is plotted. The samples are sorted according to the corresponding
Modified: pkg/RFLPtools/man/RFLPrefplot.Rd
===================================================================
--- pkg/RFLPtools/man/RFLPrefplot.Rd 2010-02-24 18:50:56 UTC (rev 2)
+++ pkg/RFLPtools/man/RFLPrefplot.Rd 2010-03-17 10:40:04 UTC (rev 3)
@@ -9,7 +9,8 @@
}
\usage{
RFLPrefplot(x, ref, distfun = dist, nrBands, mar.bottom = 5,
- cex.main = 1.2, cex.axis = 0.5, devNew = FALSE)
+ cex.main = 1.2, cex.axis = 0.5, devNew = FALSE,
+ colBands)
}
\arguments{
\item{x}{ data.frame with RFLP data; e.g. \code{\link{RFLPdata}}.}
@@ -22,6 +23,9 @@
\item{cex.main}{ size of the plot title. }
\item{cex.axis}{ size of the x-axis annotation. }
\item{devNew}{ logical. Open new graphics device for each plot. }
+ \item{colBands}{ color for the bands. Has to be of length 1 or number of samples.
+ If missing, \code{"Set1"} of \pkg{RColorBrewer} is used; see
+ \code{\link[RColorBrewer]{brewer.pal}}. }
}
\details{
Given RFLP samples are plotted together with reference samples and
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