[Phylobase-commits] r283 - branches/pdcgsoc/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Aug 18 22:39:59 CEST 2008
Author: pdc
Date: 2008-08-18 22:39:58 +0200 (Mon, 18 Aug 2008)
New Revision: 283
Added:
branches/pdcgsoc/man/phyloXXYY.Rd
branches/pdcgsoc/man/phylobubbles.Rd
branches/pdcgsoc/man/segs.Rd
branches/pdcgsoc/man/tree.plot.Rd
branches/pdcgsoc/man/treePlot.Rd
Log:
docs for functions
Added: branches/pdcgsoc/man/phyloXXYY.Rd
===================================================================
--- branches/pdcgsoc/man/phyloXXYY.Rd (rev 0)
+++ branches/pdcgsoc/man/phyloXXYY.Rd 2008-08-18 20:39:58 UTC (rev 283)
@@ -0,0 +1,33 @@
+\name{phyloXXYY}
+\alias{phyloXXYY}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Calculate node x and y coordinates }
+\description{
+Calculates the node x and y locations for plotting a phylogenetic tree.}
+\usage{
+phyloXXYY(phy, tip.order = NULL)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{phy}{ A \code{phylo4} or \code{phylo4d} object. }
+ \item{tip.order}{ Unused. A character vector indicating the ordering of tip nodes}
+}
+\details{
+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{phy}{A \code{phylo4} or \code{phylo4d} object}
+ \item{phy.orig}{The original \code{phylo4} or \code{phylo4d} object}
+}
+
+% \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}}}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==> Define data, use random,
+##-- or do help(data=index) for the standard data sets.
+}
+\keyword{methods}
Added: branches/pdcgsoc/man/phylobubbles.Rd
===================================================================
--- branches/pdcgsoc/man/phylobubbles.Rd (rev 0)
+++ branches/pdcgsoc/man/phylobubbles.Rd 2008-08-18 20:39:58 UTC (rev 283)
@@ -0,0 +1,31 @@
+\name{phylobubbles}
+\alias{phylobubbles}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Bubble plots for phylo4d objects }
+\description{
+Plots either circles or squares corresponding to the magnitude of each cell of a \code{phylo4d} object.}
+\usage{
+phylobubbles(XXYY, square = FALSE, grid = TRUE)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{XXYY}{ A list generated by the \code{phyloXXYY} function }
+ \item{square}{ A logical indicating whether squares should be plotted instead of circles }
+ \item{grid}{ A logical indicating whether a grey grid should be plotted behind the bubbles }
+}
+\value{A list consisting of:
+\item{max}{ The maximum data value }
+\item{min}{ The minimum data value }
+\item{has.na}{ logical indicating whether the data contains \code{NA}s }
+\item{bubscale}{ a numeric giving the radius of the largest bubble in inches}
+}
+
+\author{Peter Cowan \email{pdc at berkeley.edu}}
+
+\seealso{ \code{\link{phyloXXYY}}, \code{\link{treePlot}} }
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==> Define data, use random,
+##-- or do help(data=index) for the standard data sets.
+}
+\keyword{methods}
\ No newline at end of file
Added: branches/pdcgsoc/man/segs.Rd
===================================================================
--- branches/pdcgsoc/man/segs.Rd (rev 0)
+++ branches/pdcgsoc/man/segs.Rd 2008-08-18 20:39:58 UTC (rev 283)
@@ -0,0 +1,36 @@
+\name{segs}
+\alias{segs}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Calculate the line segment vectors }
+\description{
+Calculates the line segments necessary to draw a phylogenetic tree.
+}
+\usage
+segs(XXYY)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{XXYY}{ A list generated by the \code{\line{phyloXXYY}} function }
+}
+\value{
+A list containing:
+ \item{ v0x }{ A vector with the beginning vertical line x values}
+ \item{ v1x }{ A vector with the end vertical line x values}
+ \item{ v0y }{ A vector with the beginning vertical line y values}
+ \item{ v1y }{ A vector with the end vertical line y values}
+ \item{ h0x }{ A vector with the beginning horizontal line x values}
+ \item{ h1x }{ A vector with the end horizontal line x values}
+ \item{ h0Y }{ A vector with the beginning horizontal line y values}
+ \item{ h1Y }{ A vector with the end horizontal line y values}
+}
+\author{Peter Cowan \email{pdc at berkeley.edu}}
+
+\seealso{ \code{\line{phyloXXYY}}, \code{\line{treePlot}}, \code{\line{tree.plot}} }
+
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==> Define data, use random,
+##-- or do help(data=index) for the standard data sets.
+}
+
+\keyword{methods}
Added: branches/pdcgsoc/man/tree.plot.Rd
===================================================================
--- branches/pdcgsoc/man/tree.plot.Rd (rev 0)
+++ branches/pdcgsoc/man/tree.plot.Rd 2008-08-18 20:39:58 UTC (rev 283)
@@ -0,0 +1,39 @@
+\name{tree.plot}
+\alias{tree.plot}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Plot a phylo4 object }
+\description{
+ Plots the phylogenetic tree contained in a \code{phylo4} or \code{phylo4d} object.
+}
+\usage{
+tree.plot(xxyy, type, show.tip.label, show.node.label,
+ edge.color, node.color, tip.color, edge.width, rot)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{xxyy}{ A list created by the \code{\link{phyloXXYY}} function }
+ \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{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{rot}{ Numeric indicating the rotation of the plot in degrees }
+}
+% \details{
+% ~~ If necessary, more details than the description above ~~
+% }
+\value{
+Returns no values, function invoked for the plotting side effect.}
+
+\author{Peter Cowan \email{pdc at berkeley.edu}}
+
+\seealso{ \code{\link{treePlot}}, \code{\link{phyloXXYY}} }
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==> Define data, use random,
+##-- or do help(data=index) for the standard data sets.
+}
+
+\keyword{methods}
Added: branches/pdcgsoc/man/treePlot.Rd
===================================================================
--- branches/pdcgsoc/man/treePlot.Rd (rev 0)
+++ branches/pdcgsoc/man/treePlot.Rd 2008-08-18 20:39:58 UTC (rev 283)
@@ -0,0 +1,34 @@
+\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}
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