[Phylobase-commits] r908 - pkg/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 8 18:57:26 CEST 2014
Author: francois
Date: 2014-04-08 18:57:26 +0200 (Tue, 08 Apr 2014)
New Revision: 908
Modified:
pkg/R/treePlot.R
Log:
updated/formatted docs for treePlot functions.
Modified: pkg/R/treePlot.R
===================================================================
--- pkg/R/treePlot.R 2014-04-08 16:53:45 UTC (rev 907)
+++ pkg/R/treePlot.R 2014-04-08 16:57:26 UTC (rev 908)
@@ -1,57 +1,58 @@
-#' Phylogeny plotting
-#'
-#' Plot \code{phylo4} or \code{phylo4d} objects, including associated data.
-#'
-#'
-#' @name treePlot-methods
-#' @aliases treePlot plot,ANY,ANY-method plot,pdata,missing-method
-#' plot,phylo4,missing-method treePlot-method treePlot,phylo4,phylo4d-method
-#' @docType methods
-#' @param phy A \code{phylo4} or \code{phylo4d} object
-#' @param type A character string indicating the shape of plotted tree
-#' @param show.tip.label Logical, indicating whether tip labels should be shown
-#' @param show.node.label Logical, indicating whether node labels should be
-#' shown
-#' @param tip.order If NULL the tree is plotted with tips in preorder, if "rev"
-#' this is reversed. Otherwise, it is a character vector of tip labels,
-#' indicating their order along the y axis (from top to bottom). Or, a numeric
-#' vector of tip node IDs indicating the order.
-#' @param plot.data Logical indicating whether \code{phylo4d} data should be
-#' plotted
-#' @param rot Numeric indicating the rotation of the plot in degrees
-#' @param tip.plot.fun A function used to generate plot at the each tip of the
-#' phylogenetic trees
-#' @param edge.color A vector of colors in the order of \code{edges(phy)}
-#' @param node.color A vector of colors indicating the colors of the node
-#' labels
-#' @param tip.color A vector of colors indicating the colors of the tip labels
-#' @param edge.width A vector in the order of \code{edges(phy)} indicating the
-#' widths of edge lines
-#' @param newpage Logical indicating whether the page should be cleared before
-#' plotting
-#' @param \dots Currently unused, parameters to be passed on to \code{gpar}
-#' @return No return value, function invoked for plotting side effect
-#' @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.} }
-#' @author Peter Cowan \email{pdc@@berkeley.edu}
-#' @seealso \code{\link{phylobubbles}}
-#' @keywords methods
-#' @examples
-#'
-#'
-#' ## example of plotting two grid plots on the same page
-#' data(geospiza)
-#' geotree <- extractTree(geospiza)
-#' grid.newpage()
-#' pushViewport(viewport(layout=grid.layout(nrow=1, ncol=2), name="base"))
-#' pushViewport(viewport(layout.pos.col=1, name="plot1"))
-#' treePlot(geotree, newpage=FALSE)
-#' popViewport()
-#'
-#' pushViewport(viewport(layout.pos.col=2, name="plot2"))
-#' treePlot(geotree, newpage=FALSE, rot=180)
-#' popViewport(2)
+##' Phylogeny plotting
+##'
+##' Plot \code{phylo4} or \code{phylo4d} objects, including associated data.
+##'
+##'
+##' @name treePlot-methods
+##' @aliases treePlot plot,ANY,ANY-method plot,pdata,missing-method
+##' plot,phylo4,missing-method treePlot-method treePlot,phylo4,phylo4d-method
+##' @docType methods
+##' @param phy A \code{phylo4} or \code{phylo4d} object
+##' @param type A character string indicating the shape of plotted tree
+##' @param show.tip.label Logical, indicating whether tip labels should be shown
+##' @param show.node.label Logical, indicating whether node labels should be
+##' shown
+##' @param tip.order If NULL the tree is plotted with tips in preorder, if "rev"
+##' this is reversed. Otherwise, it is a character vector of tip labels,
+##' indicating their order along the y axis (from top to bottom). Or, a numeric
+##' vector of tip node IDs indicating the order.
+##' @param plot.data Logical indicating whether \code{phylo4d} data should be
+##' plotted
+##' @param rot Numeric indicating the rotation of the plot in degrees
+##' @param tip.plot.fun A function used to generate plot at the each tip of the
+##' phylogenetic trees
+##' @param edge.color A vector of colors in the order of \code{edges(phy)}
+##' @param node.color A vector of colors indicating the colors of the node
+##' labels
+##' @param tip.color A vector of colors indicating the colors of the tip labels
+##' @param edge.width A vector in the order of \code{edges(phy)} indicating the
+##' widths of edge lines
+##' @param newpage Logical indicating whether the page should be cleared before
+##' plotting
+##' @param \dots Currently unused, parameters to be passed on to \code{gpar}
+##' @return No return value, function invoked for plotting side effect
+##' @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.} }
+##' @author Peter Cowan \email{pdc@@berkeley.edu}
+##' @seealso \code{\link{phylobubbles}}
+##' @keywords methods
+##' @export
+##' @examples
+##'
+##'
+##' ## example of plotting two grid plots on the same page
+##' data(geospiza)
+##' geotree <- extractTree(geospiza)
+##' grid.newpage()
+##' pushViewport(viewport(layout=grid.layout(nrow=1, ncol=2), name="base"))
+##' pushViewport(viewport(layout.pos.col=1, name="plot1"))
+##' treePlot(geotree, newpage=FALSE)
+##' popViewport()
+##'
+##' pushViewport(viewport(layout.pos.col=2, name="plot2"))
+##' treePlot(geotree, newpage=FALSE, rot=180)
+##' popViewport(2)
`treePlot` <- function(phy,
type = c('phylogram', 'cladogram', 'fan'),
show.tip.label = TRUE,
@@ -161,50 +162,51 @@
-#' Plot a phylo4 object
-#'
-#' Plots the phylogenetic tree contained in a \code{phylo4} or \code{phylo4d}
-#' object.
-#'
-#'
-#' @param xxyy A list created by the \code{\link{phyloXXYY}} function
-#' @param type A character string indicating the shape of plotted tree
-#' @param show.tip.label Logical, indicating whether tip labels should be shown
-#' @param show.node.label Logical, indicating whether node labels should be
-#' shown
-#' @param edge.color A vector of colors in the order of \code{edges(phy)}
-#' @param node.color A vector of colors indicating the colors of the node
-#' labels
-#' @param tip.color A vector of colors indicating the colors of the tip labels
-#' @param edge.width A vector in the order of \code{edges(phy)} indicating the
-#' widths of edge lines
-#' @param rot Numeric indicating the rotation of the plot in degrees
-#' @return Returns no values, function invoked for the plotting side effect.
-#' @author Peter Cowan \email{pdc@@berkeley.edu}
-#' @seealso \code{treePlot}, \code{\link{phyloXXYY}}
-#' @keywords methods
-#' @examples
-#'
-#'
-#' data(geospiza)
-#' grid.newpage()
-#' xxyy <- phyloXXYY(geospiza)
-#' plotOneTree(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))
-#' plotOneTree(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()
-#'
-#'
+##' Plot a phylo4 object
+##'
+##' Plots the phylogenetic tree contained in a \code{phylo4} or \code{phylo4d}
+##' object.
+##'
+##'
+##' @param xxyy A list created by the \code{\link{phyloXXYY}} function
+##' @param type A character string indicating the shape of plotted tree
+##' @param show.tip.label Logical, indicating whether tip labels should be shown
+##' @param show.node.label Logical, indicating whether node labels should be
+##' shown
+##' @param edge.color A vector of colors in the order of \code{edges(phy)}
+##' @param node.color A vector of colors indicating the colors of the node
+##' labels
+##' @param tip.color A vector of colors indicating the colors of the tip labels
+##' @param edge.width A vector in the order of \code{edges(phy)} indicating the
+##' widths of edge lines
+##' @param rot Numeric indicating the rotation of the plot in degrees
+##' @return Returns no values, function invoked for the plotting side effect.
+##' @author Peter Cowan \email{pdc@@berkeley.edu}
+##' @seealso \code{treePlot}, \code{\link{phyloXXYY}}
+##' @export
+##' @keywords methods
+##' @examples
+##'
+##'
+##' data(geospiza)
+##' grid.newpage()
+##' xxyy <- phyloXXYY(geospiza)
+##' plotOneTree(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))
+##' plotOneTree(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()
+##'
+##'
plotOneTree <- function(xxyy, type, show.tip.label, show.node.label, edge.color,
node.color, tip.color, edge.width, rot)
{
@@ -313,38 +315,39 @@
-#' Calculate node x and y coordinates
-#'
-#' Calculates the node x and y locations for plotting a phylogenetic tree.
-#'
-#' 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.
-#'
-#' @param phy A \code{phylo4} or \code{phylo4d} object.
-#' @param tip.order A character vector of tip labels, indicating their order
-#' along the y axis (from top to bottom). Or, a numeric vector of tip node IDs
-#' indicating the order.
-#' @return \item{yy}{Internal node and tip y coordinates} \item{xx}{Internal
-#' node and tip x coordinates} \item{phy}{A \code{phylo4} or \code{phylo4d}
-#' object} \item{segs}{A list of \code{h0x, h1x, v0x, v1x} and \code{h0y, h1y,
-#' v0y, v1y} describing the start and end points for the plot line segments}
-#' \item{torder}{The tip order provided as \code{tip.order} or if NULL the
-#' preoder tip order} \item{eorder}{The an index of the reordered edges
-#' compared to the result of \code{edges(phy)}}
-#' @author Peter Cowan \email{pdc@@berkeley.edu}
-#' @seealso \code{treePlot}, \code{\link{plotOneTree}}
-#' @keywords methods
-#' @examples
-#'
-#'
-#' data(geospiza)
-#' coor <- phyloXXYY(geospiza)
-#' plot(coor$xx, coor$yy, pch = 20)
-#'
-#'
+##' Calculate node x and y coordinates
+##'
+##' Calculates the node x and y locations for plotting a phylogenetic tree.
+##'
+##' 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.
+##'
+##' @param phy A \code{phylo4} or \code{phylo4d} object.
+##' @param tip.order A character vector of tip labels, indicating their order
+##' along the y axis (from top to bottom). Or, a numeric vector of tip node IDs
+##' indicating the order.
+##' @return \item{yy}{Internal node and tip y coordinates} \item{xx}{Internal
+##' node and tip x coordinates} \item{phy}{A \code{phylo4} or \code{phylo4d}
+##' object} \item{segs}{A list of \code{h0x, h1x, v0x, v1x} and \code{h0y, h1y,
+##' v0y, v1y} describing the start and end points for the plot line segments}
+##' \item{torder}{The tip order provided as \code{tip.order} or if NULL the
+##' preoder tip order} \item{eorder}{The an index of the reordered edges
+##' compared to the result of \code{edges(phy)}}
+##' @author Peter Cowan \email{pdc@@berkeley.edu}
+##' @seealso \code{treePlot}, \code{\link{plotOneTree}}
+##' @export
+##' @keywords methods
+##' @examples
+##'
+##'
+##' data(geospiza)
+##' coor <- phyloXXYY(geospiza)
+##' plot(coor$xx, coor$yy, pch = 20)
+##'
+##'
phyloXXYY <- function(phy, tip.order=NULL)
{
phy.orig <- phy
@@ -469,39 +472,40 @@
-#' Bubble plots for phylo4d objects
-#'
-#' Plots either circles or squares corresponding to the magnitude of each cell
-#' of a \code{phylo4d} object.
-#'
-#'
-#' @param type the type of plot
-#' @param place.tip.label A string indicating whether labels should be plotted
-#' to the right or to the left of the bubble plot
-#' @param show.node.label A logical indicating whether internal node labels
-#' should be plotted
-#' @param rot The number of degrees that the plot should be rotated
-#' @param edge.color A vector of colors for the tree edge segments
-#' @param node.color A vector of colors for the coloring the nodes
-#' @param tip.color A vector of colors for the coloring the tip labels
-#' @param edge.width A vector of line widths for the tree edges
-#' @param newpage Logical to control whether the device is cleared before
-#' plotting, useful for adding plot inside other plots
-#' @param \dots Additional parameters passed to the bubble plotting functions
-#' @param XXYY The out put from the phyloXXYY function
-#' @param square Logical indicating whether the plot 'bubbles' should be
-#' squares
-#' @param grid A logical indicating whether a grey grid should be plotted
-#' behind the bubbles
-#' @author Peter Cowan \email{pdc@@berkeley.edu}
-#' @seealso \code{\link{phyloXXYY}}, \code{treePlot}
-#' @keywords methods
-#' @examples
-#'
-#' ##---- Should be DIRECTLY executable !! ----
-#' ##-- ==> Define data, use random,
-#' ##-- or do help(data=index) for the standard data sets.
-#'
+##' Bubble plots for phylo4d objects
+##'
+##' Plots either circles or squares corresponding to the magnitude of each cell
+##' of a \code{phylo4d} object.
+##'
+##'
+##' @param type the type of plot
+##' @param place.tip.label A string indicating whether labels should be plotted
+##' to the right or to the left of the bubble plot
+##' @param show.node.label A logical indicating whether internal node labels
+##' should be plotted
+##' @param rot The number of degrees that the plot should be rotated
+##' @param edge.color A vector of colors for the tree edge segments
+##' @param node.color A vector of colors for the coloring the nodes
+##' @param tip.color A vector of colors for the coloring the tip labels
+##' @param edge.width A vector of line widths for the tree edges
+##' @param newpage Logical to control whether the device is cleared before
+##' plotting, useful for adding plot inside other plots
+##' @param \dots Additional parameters passed to the bubble plotting functions
+##' @param XXYY The out put from the phyloXXYY function
+##' @param square Logical indicating whether the plot 'bubbles' should be
+##' squares
+##' @param grid A logical indicating whether a grey grid should be plotted
+##' behind the bubbles
+##' @author Peter Cowan \email{pdc@@berkeley.edu}
+##' @export
+##' @seealso \code{\link{phyloXXYY}}, \code{treePlot}
+##' @keywords methods
+##' @examples
+##'
+##' ##---- Should be DIRECTLY executable !! ----
+##' ##-- ==> Define data, use random,
+##' ##-- or do help(data=index) for the standard data sets.
+##'
phylobubbles <- function(type = type,
place.tip.label = "right",
show.node.label = show.node.label,
@@ -669,29 +673,30 @@
-#' Plotting trees and associated data
-#'
-#' Plotting phylogenetic trees and associated data
-#'
-#'
-#' @param xxyy A list created by the \code{\link{phyloXXYY}} function
-#' @param type A character string indicating the shape of plotted tree
-#' @param show.tip.label Logical, indicating whether tip labels should be shown
-#' @param show.node.label Logical, indicating whether node labels should be
-#' shown
-#' @param rot Numeric indicating the rotation of the plot in degrees
-#' @param tip.plot.fun A function used to plot the data elements of a
-#' \code{phylo4d} object
-#' @param edge.color A vector of colors in the order of \code{edges(phy)}
-#' @param node.color A vector of colors indicating the colors of the node
-#' labels
-#' @param tip.color A vector of colors indicating the colors of the tip labels
-#' @param edge.width A vector in the order of \code{edges(phy)} indicating the
-#' widths of edge lines
-#' @param \dots Additional parameters passed to \code{tip.plot.fun}
-#' @return creates a plot on the current graphics device.
-#' @author Peter Cowan
-#' @keywords methods
+##' Plotting trees and associated data
+##'
+##' Plotting phylogenetic trees and associated data
+##'
+##'
+##' @param xxyy A list created by the \code{\link{phyloXXYY}} function
+##' @param type A character string indicating the shape of plotted tree
+##' @param show.tip.label Logical, indicating whether tip labels should be shown
+##' @param show.node.label Logical, indicating whether node labels should be
+##' shown
+##' @param rot Numeric indicating the rotation of the plot in degrees
+##' @param tip.plot.fun A function used to plot the data elements of a
+##' \code{phylo4d} object
+##' @param edge.color A vector of colors in the order of \code{edges(phy)}
+##' @param node.color A vector of colors indicating the colors of the node
+##' labels
+##' @param tip.color A vector of colors indicating the colors of the tip labels
+##' @param edge.width A vector in the order of \code{edges(phy)} indicating the
+##' widths of edge lines
+##' @param \dots Additional parameters passed to \code{tip.plot.fun}
+##' @return creates a plot on the current graphics device.
+##' @author Peter Cowan
+##' @export
+##' @keywords methods
tip.data.plot <- function(
xxyy,
type = c('phylogram', 'cladogram', 'fan'),
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