[Phylobase-commits] r284 - in branches/pdcgsoc: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 20 07:02:58 CEST 2008
Author: pdc
Date: 2008-08-20 07:02:58 +0200 (Wed, 20 Aug 2008)
New Revision: 284
Added:
branches/pdcgsoc/man/reorder-methods.Rd
branches/pdcgsoc/man/treePlot-methods.Rd
Removed:
branches/pdcgsoc/man/treePlot.Rd
Modified:
branches/pdcgsoc/DESCRIPTION
branches/pdcgsoc/man/phyloXXYY.Rd
branches/pdcgsoc/man/phylobubbles.Rd
branches/pdcgsoc/man/segs.Rd
branches/pdcgsoc/man/tree.plot.Rd
Log:
Update several plotting related docs and the description file
Modified: branches/pdcgsoc/DESCRIPTION
===================================================================
--- branches/pdcgsoc/DESCRIPTION 2008-08-18 20:39:58 UTC (rev 283)
+++ branches/pdcgsoc/DESCRIPTION 2008-08-20 05:02:58 UTC (rev 284)
@@ -4,7 +4,7 @@
Version: 0.3
Date: 2007-12-18
Depends: methods, grid, ape(>= 2.1)
-Suggests: ade4, MASS
+Suggests: ade4, MASS, gridBase
Author: R Hackathon (Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Thibaut Jombart, Steve Kembel, David Orme, Emmanuel Paradis, Derrick Zwickl)
Maintainer: Ben Bolker <bolker at ufl.edu>
Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data
Modified: branches/pdcgsoc/man/phyloXXYY.Rd
===================================================================
--- branches/pdcgsoc/man/phyloXXYY.Rd 2008-08-18 20:39:58 UTC (rev 283)
+++ branches/pdcgsoc/man/phyloXXYY.Rd 2008-08-20 05:02:58 UTC (rev 284)
@@ -16,7 +16,9 @@
The y coordinates of the tips are evenly spaced from 0 to 1 in pruningwise order. Ancestor y nodes are given the mean value of immediate descendants. The root is given the x coordinate 0 and descendant nodes are placed according to the cumulative branch length from the root, with a maximum x value of 1.
}
\value{
- \item{xxyy}{A list with three items: \code{yy}, the y locations, \code{xx}, the x locations, \code{traverse}, the tree traversal order}
+ \item{yy}{Internal node and tip y coordinates}
+ \item{xx}{Internal node and tip x coordinates}
+ \item{traverse}{The tree traversal order}
\item{phy}{A \code{phylo4} or \code{phylo4d} object}
\item{phy.orig}{The original \code{phylo4} or \code{phylo4d} object}
}
@@ -24,10 +26,12 @@
% \references{ ~put references to the literature/web site here ~ }
\author{Peter Cowan \email{pdc at berkeley.edu}}
-\seealso{\code{\link{segs}}, \code{\link{treePlot}}, \code{\link{tree.plot}}}
+\seealso{\code{\link{segs}}, \code{treePlot}, \code{\link{tree.plot}}}
\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==> Define data, use random,
-##-- or do help(data=index) for the standard data sets.
+
+data(geospiza)
+coor <- phyloXXYY(geospiza)
+plot(coor$xx, coor$yy, pch = 20)
+
}
\keyword{methods}
Modified: branches/pdcgsoc/man/phylobubbles.Rd
===================================================================
--- branches/pdcgsoc/man/phylobubbles.Rd 2008-08-18 20:39:58 UTC (rev 283)
+++ branches/pdcgsoc/man/phylobubbles.Rd 2008-08-20 05:02:58 UTC (rev 284)
@@ -22,7 +22,7 @@
\author{Peter Cowan \email{pdc at berkeley.edu}}
-\seealso{ \code{\link{phyloXXYY}}, \code{\link{treePlot}} }
+\seealso{ \code{\link{phyloXXYY}}, \code{treePlot} }
\examples{
##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
Added: branches/pdcgsoc/man/reorder-methods.Rd
===================================================================
--- branches/pdcgsoc/man/reorder-methods.Rd (rev 0)
+++ branches/pdcgsoc/man/reorder-methods.Rd 2008-08-20 05:02:58 UTC (rev 284)
@@ -0,0 +1,49 @@
+\name{reorder-methods}
+\docType{methods}
+\alias{reorder-methods}
+\alias{reorder,phylo-method}
+\alias{reorder,phylo4-method}
+\alias{reorder,phylo4d-method}
+\title{ ~~ Methods for Function reorder in Package `stats' ~~}
+\description{
+ ~~ Methods for function \code{reorder} in Package `stats' ~~
+}
+\section{Methods}{
+ \describe{
+ \item{phylo = "phylo"}{reorders a \code{phylo} object}
+ \item{phylo = "phylo4"}{reorders a \linkS4class{phylo4} object}
+ \item{phylo = "phylo4d"}{reorders a \linkS4class{phylo4d} object}
+ }
+}
+
+\usage{
+\S4method{reorder}{phylo}(x, ...)
+\S4method{reorder}{phylo4}(x, ...)
+\S4method{reorder}{phylo4d}(x, ...)
+}
+
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{x}{ ~~Describe \code{x} here~~ }
+ \item{\dots}{ ~~Describe \code{\dots} here~~ }
+}
+\details{
+ ~~ If necessary, more details than the description above ~~
+}
+\value{
+ ~Describe the value returned
+ If it is a LIST, use
+ \item{comp1 }{Description of 'comp1'}
+ \item{comp2 }{Description of 'comp2'}
+ ...
+}
+\references{ ~put references to the literature/web site here ~ }
+\author{ ~~who you are~~ }
+\note{ ~~further notes~~
+
+ ~Make other sections like Warning with \section{Warning }{....} ~
+}
+\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{methods}
Modified: branches/pdcgsoc/man/segs.Rd
===================================================================
--- branches/pdcgsoc/man/segs.Rd 2008-08-18 20:39:58 UTC (rev 283)
+++ branches/pdcgsoc/man/segs.Rd 2008-08-20 05:02:58 UTC (rev 284)
@@ -5,7 +5,7 @@
\description{
Calculates the line segments necessary to draw a phylogenetic tree.
}
-\usage
+\usage{
segs(XXYY)
}
%- maybe also 'usage' for other objects documented here.
@@ -25,7 +25,7 @@
}
\author{Peter Cowan \email{pdc at berkeley.edu}}
-\seealso{ \code{\line{phyloXXYY}}, \code{\line{treePlot}}, \code{\line{tree.plot}} }
+\seealso{ \code{\link{phyloXXYY}}, \code{treePlot}, \code{\link{tree.plot}} }
\examples{
##---- Should be DIRECTLY executable !! ----
Modified: branches/pdcgsoc/man/tree.plot.Rd
===================================================================
--- branches/pdcgsoc/man/tree.plot.Rd 2008-08-18 20:39:58 UTC (rev 283)
+++ branches/pdcgsoc/man/tree.plot.Rd 2008-08-20 05:02:58 UTC (rev 284)
@@ -29,11 +29,26 @@
\author{Peter Cowan \email{pdc at berkeley.edu}}
-\seealso{ \code{\link{treePlot}}, \code{\link{phyloXXYY}} }
+\seealso{ \code{treePlot}, \code{\link{phyloXXYY}} }
\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==> Define data, use random,
-##-- or do help(data=index) for the standard data sets.
+
+data(geospiza)
+xxyy <- phyloXXYY(geospiza)
+tree.plot(xxyy, type = 'phylogram',
+ show.tip.label = TRUE, show.node.label = TRUE,
+ edge.color = 'black', node.color = 'orange', tip.color = 'blue',
+ edge.width = 1, rot = 0
+)
+
+grid.newpage()
+pushViewport(viewport(w = 0.8, h = 0.8))
+tree.plot(xxyy, type = 'phylogram',
+ show.tip.label = TRUE, show.node.label = TRUE,
+ edge.color = 'black', node.color = 'orange', tip.color = 'blue',
+ edge.width = 1, rot = 0
+)
+popViewport()
+
}
\keyword{methods}
Added: branches/pdcgsoc/man/treePlot-methods.Rd
===================================================================
--- branches/pdcgsoc/man/treePlot-methods.Rd (rev 0)
+++ branches/pdcgsoc/man/treePlot-methods.Rd 2008-08-20 05:02:58 UTC (rev 284)
@@ -0,0 +1,48 @@
+\name{treePlot-methods}
+\docType{methods}
+\alias{treePlot-method}
+\alias{treePlot,phylo4,phylo4d-method}
+\title{ Phylogeny plotting }
+\description{
+ Plot \code{phylo4} or \code{phylo4d} objects, including associated data.
+}
+\section{Methods}{
+ \describe{
+ \item{phy = "phylo4"}{plots a tree of class \linkS4class{phylo4}}
+ \item{phy = "phylo4d"}{plots a tree with one or more
+ quantitative traits contained in a \linkS4class{phylo4d} object.}
+ }
+}
+\usage{
+ \S4method{treePlot}{phylo4,phylo4d}(phy, type = c("phylogram", "cladogram", "fan"), show.tip.label = TRUE,
+ show.node.label = FALSE, tip.order = NULL, plot.data = is(phy, "phylo4d"),
+ rot = 0, tip.plot.fun = "bubbles", plot_by_tip = TRUE, edge.color = "black",
+ node.color = "black", tip.color = "black", edge.width = 1, newpage = TRUE, \dots)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{phy}{ A \code{phylo4} or \code{phylo4d} object }
+ \item{type}{ A character string indicating the shape of plotted tree }
+ \item{show.tip.label}{ Logical, indicating whether tip labels should be shown }
+ \item{show.node.label}{ Logical, indicating whether node labels should be shown }
+ \item{tip.order}{ Unused, a character vector of tip labels, indicating they're order along the y axis }
+ \item{plot.data}{ Logical indicating whether \code{phylo4d} data should be plotted }
+ \item{rot}{ Numeric indicating the rotation of the plot in degrees }
+ \item{tip.plot.fun}{ A function used to generate plot at the each tip of the phylogenetic trees }
+ \item{plot_by_tip} {TODO} % TODO what does the plot_by_tip argument do
+ \item{edge.color}{ A vector of colors in the order of \code{edges(phy)} }
+ \item{node.color}{ A vector of colors indicating the colors of the node labels }
+ \item{tip.color}{ A vector of colors indicating the colors of the tip labels }
+ \item{edge.width}{ A vector in the order of \code{edges(phy)} indicating the widths of edge lines}
+ \item{newpage}{ Logical indicating whether the page should be cleared before plotting }
+ \item{\dots}{ Currently unused, parameters to be passed on to \code{gpar} }
+}
+
+\value{ No return value, function invoked for plotting side effect
+}
+\author{Peter Cowan \email{pdc at berkeley.edu}}
+
+\seealso{ \code{\link{phylobubbles}} }
+
+
+\keyword{methods}
Deleted: branches/pdcgsoc/man/treePlot.Rd
===================================================================
--- branches/pdcgsoc/man/treePlot.Rd 2008-08-18 20:39:58 UTC (rev 283)
+++ branches/pdcgsoc/man/treePlot.Rd 2008-08-20 05:02:58 UTC (rev 284)
@@ -1,34 +0,0 @@
-\name{treePlot}
-\alias{treePlot}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ ~~function to do ... ~~ }
-\description{
- ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-treePlot(phy, type = c("phylogram", "cladogram", "fan"), show.tip.label = TRUE, show.node.label = FALSE, tip.order = NULL, plot.data = is(phy, "phylo4d"), rot = 0, tip.plot.fun = "bubbles", edge.color = "black", node.color = "black", tip.color = "black", edge.width = 1, newpage = TRUE, ...)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
- \item{phy}{ A \code{phylo4} or \code{phylo4d} object }
- \item{type}{ A character string indicating the shape of plotted tree }
- \item{show.tip.label}{ Logical, indicating whether tip labels should be shown }
- \item{show.node.label}{ Logical, indicating whether node labels should be shown }
- \item{tip.order}{ Unused, a character vector of tip labels, indicating they're order along the y axis }
- \item{plot.data}{ Logical indicating whether \code{phylo4d} data should be plotted }
- \item{rot}{ Numeric indicating the rotation of the plot in degrees }
- \item{tip.plot.fun}{ A function used to generate plot at the each tip of the phylogenetic trees }
- \item{edge.color}{ A vector of colors in the order of \code{edges(phy)} }
- \item{node.color}{ A vector of colors indicating the colors of the node labels }
- \item{tip.color}{ A vector of colors indicating the colors of the tip labels }
- \item{edge.width}{ A vector in the order of \code{edges(phy)} indicating the widths of edge lines}
- \item{newpage}{ Logical indicating whether the page should be cleared before plotting }
- \item{\dots}{ Currently unused, parameters to be passed on to \code{gpar} }
-}
-
-\value{ No return value, function invoked for plotting side effect
-}
-\author{Peter Cowan \email{pdc at berkeley.edu}}
-
-\seealso{ \code{\link{phylobubbles}} }
-\keyword{methods}
More information about the Phylobase-commits
mailing list