@@ -36,7 +36,7 @@ a list object.

 }

 \description{

 \code{geom_taxalink} supports data.frame as input,

-the \code{colour}, \code{size}, \code{linetype} and \code{alpha} can be mapped. When the \code{data} was provided,

+the \code{colour}, \code{linewidth}, \code{linetype} and \code{alpha} can be mapped. When the \code{data} was provided,

 the \code{mapping} should be also provided, which \code{taxa1} and \code{taxa2} should be mapped created

 by \code{aes}, \code{aes_} or \code{aes_string}. In addition, the \code{hratio}, control the height of curve line,

 when tree layout is \code{cirular}, default is 1. \code{ncp}, the number of control points used to draw the

@@ -52,7 +52,7 @@ a column of data.

 \item \code{group} group category of link.

 \item \code{colour} control the color of line, default is black.

 \item \code{linetype} control the type of line, default is 1 (solid).

-\item \code{size} control the width of line, default is 0.5.

+\item \code{linewidth} control the width of line, default is 0.5.

 \item \code{curvature} control the curvature of line, default is 0.5,

 it will be created automatically in polar coordinate .

 \item \code{hratio} control the height of curve line, default is 1.

@@ -47,15 +47,16 @@ a column of data.

 \code{geom_taxalink()} understands the following aesthethics (required aesthetics are in bold):

 \itemize{

-\item \strong{\code{taxa1}}

-\item \strong{\code{taxa2}}

-\item \code{group}

-\item \code{colour}

-\item \code{linetype}

-\item \code{size}

-\item \code{curvature}

-\item \code{hratio}

-\item \code{ncp}

+\item \strong{\code{taxa1}} label or node number of tree.

+\item \strong{\code{taxa2}} label or node number of tree.

+\item \code{group} group category of link.

+\item \code{colour} control the color of line, default is black.

+\item \code{linetype} control the type of line, default is 1 (solid).

+\item \code{size} control the width of line, default is 0.5.

+\item \code{curvature} control the curvature of line, default is 0.5,

+it will be created automatically in polar coordinate .

+\item \code{hratio} control the height of curve line, default is 1.

+\item \code{ncp} control the smooth of curve line, default is 1.

 }

 }

@@ -2,49 +2,60 @@

 % Please edit documentation in R/geom_taxalink.R

 \name{geom_taxalink}

 \alias{geom_taxalink}

-\title{geom_taxalink}

+\title{link between taxa}

 \usage{

 geom_taxalink(

-  taxa1,

-  taxa2,

-  curvature = 0.5,

-  arrow = NULL,

-  arrow.fill = NULL,

+  data = NULL,

+  mapping = NULL,

+  taxa1 = NULL,

+  taxa2 = NULL,

   offset = NULL,

-  hratio = 1,

-  outward = TRUE,

+  outward = "auto",

   ...

 )

 }

 \arguments{

-\item{taxa1}{taxa1, can be label or node number}

+\item{data}{data.frame, The data to be displayed in this layer, default is NULL.}

-\item{taxa2}{taxa2, can be label or node number}

+\item{mapping}{Set of aesthetic mappings, default is NULL.}

-\item{curvature}{A numeric value giving the amount of curvature.

-Negative values produce left-hand curves,

-positive values produce right-hand curves, and zero produces a straight line.}

+\item{taxa1}{can be label or node number.}

-\item{arrow}{specification for arrow heads, as created by arrow().}

-

-\item{arrow.fill}{fill color to usse for the arrow head (if closed). \code{NULL} means use \code{colour} aesthetic.}

+\item{taxa2}{can be label or node number.}

 \item{offset}{numeric, control the shift of curve line (the ratio of axis value,

 range is "(0-1)"), default is NULL.}

-\item{hratio}{numeric, the height of curve line, default is 1.}

-

 \item{outward}{logical, control the orientation of curve when the layout of tree is circular,

-fan or other layout in polar coordinate, default is TRUE.}

+fan or other layout in polar coordinate, default is "auto", meaning It will automatically.}

-\item{...}{additional parameter.}

+\item{..., }{additional parameter.}

 }

 \value{

-ggplot layer

+a list object.

 }

 \description{

-link between taxa

+\code{geom_taxalink} supports data.frame as input,

+the \code{colour}, \code{size}, \code{linetype} and \code{alpha} can be mapped. When the \code{data} was provided,

+the \code{mapping} should be also provided, which \code{taxa1} and \code{taxa2} should be mapped created

+by \code{aes}, \code{aes_} or \code{aes_string}. In addition, the \code{hratio}, control the height of curve line,

+when tree layout is \code{cirular}, default is 1. \code{ncp}, the number of control points used to draw the

+curve, more control points creates a smoother curve, default is 1. They also can be mapped to

+a column of data.

 }

-\author{

-Guangchuang Yu

+\section{Aesthetics}{

+

+\code{geom_taxalink()} understands the following aesthethics (required aesthetics are in bold):

+\itemize{

+\item \strong{\code{taxa1}}

+\item \strong{\code{taxa2}}

+\item \code{group}

+\item \code{colour}

+\item \code{linetype}

+\item \code{size}

+\item \code{curvature}

+\item \code{hratio}

+\item \code{ncp}

 }

+}

+

@@ -10,8 +10,9 @@ geom_taxalink(

   curvature = 0.5,

   arrow = NULL,

   arrow.fill = NULL,

-  xexpand = NULL,

-  hratio = 0.5,

+  offset = NULL,

+  hratio = 1,

+  outward = TRUE,

   ...

 )

 }

@@ -28,12 +29,15 @@ positive values produce right-hand curves, and zero produces a straight line.}

 \item{arrow.fill}{fill color to usse for the arrow head (if closed). \code{NULL} means use \code{colour} aesthetic.}

-\item{xexpand}{numeric, control the shift of curve line (the ratio of axis value,

-rang is "(0-1)"), default is NULL.}

+\item{offset}{numeric, control the shift of curve line (the ratio of axis value,

+range is "(0-1)"), default is NULL.}

-\item{hratio}{numeric, the height of curve line, default is 0.5.}

+\item{hratio}{numeric, the height of curve line, default is 1.}

-\item{...}{additional parameter}

+\item{outward}{logical, control the orientation of curve when the layout of tree is circular,

+fan or other layout in polar coordinate, default is TRUE.}

+

+\item{...}{additional parameter.}

 }

 \value{

 ggplot layer

@@ -10,6 +10,8 @@ geom_taxalink(

   curvature = 0.5,

   arrow = NULL,

   arrow.fill = NULL,

+  xexpand = NULL,

+  hratio = 0.5,

   ...

 )

 }

@@ -26,6 +28,11 @@ positive values produce right-hand curves, and zero produces a straight line.}

 \item{arrow.fill}{fill color to usse for the arrow head (if closed). \code{NULL} means use \code{colour} aesthetic.}

+\item{xexpand}{numeric, control the shift of curve line (the ratio of axis value,

+rang is "(0-1)"), default is NULL.}

+

+\item{hratio}{numeric, the height of curve line, default is 0.5.}

+

 \item{...}{additional parameter}

 }

 \value{

@@ -4,8 +4,14 @@

 \alias{geom_taxalink}

 \title{geom_taxalink}

 \usage{

-geom_taxalink(taxa1, taxa2, curvature = 0.5, arrow = NULL,

-  arrow.fill = NULL, ...)

+geom_taxalink(

+  taxa1,

+  taxa2,

+  curvature = 0.5,

+  arrow = NULL,

+  arrow.fill = NULL,

+  ...

+)

 }

 \arguments{

 \item{taxa1}{taxa1, can be label or node number}

@@ -18,7 +18,7 @@ positive values produce right-hand curves, and zero produces a straight line.}

 \item{arrow}{specification for arrow heads, as created by arrow().}

-\item{arrow.fill}{fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.}

+\item{arrow.fill}{fill color to usse for the arrow head (if closed). \code{NULL} means use \code{colour} aesthetic.}

 \item{...}{additional parameter}

 }

@@ -4,7 +4,8 @@

 \alias{geom_taxalink}

 \title{geom_taxalink}

 \usage{

-geom_taxalink(taxa1, taxa2, curvature = 0.5, ...)

+geom_taxalink(taxa1, taxa2, curvature = 0.5, arrow = NULL,

+  arrow.fill = NULL, ...)

 }

 \arguments{

 \item{taxa1}{taxa1, can be label or node number}

@@ -15,6 +16,10 @@ geom_taxalink(taxa1, taxa2, curvature = 0.5, ...)

 Negative values produce left-hand curves,

 positive values produce right-hand curves, and zero produces a straight line.}

+\item{arrow}{specification for arrow heads, as created by arrow().}

+

+\item{arrow.fill}{fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.}

+

 \item{...}{additional parameter}

 }

 \value{

@@ -26,4 +26,3 @@ link between taxa

 \author{

 Guangchuang Yu

 }

-

@@ -26,3 +26,4 @@ link between taxa

 \author{

 Guangchuang Yu

 }

+

@@ -26,4 +26,3 @@ link between taxa

 \author{

 Guangchuang Yu

 }

-

@@ -4,7 +4,7 @@

 \alias{geom_taxalink}

 \title{geom_taxalink}

 \usage{

-geom_taxalink(taxa1, taxa2, curvature = -0.5, ...)

+geom_taxalink(taxa1, taxa2, curvature = 0.5, ...)

 }

 \arguments{

 \item{taxa1}{taxa1, can be label or node number}

new file mode 100644

@@ -0,0 +1,29 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_taxalink.R

+\name{geom_taxalink}

+\alias{geom_taxalink}

+\title{geom_taxalink}

+\usage{

+geom_taxalink(taxa1, taxa2, curvature = -0.5, ...)

+}

+\arguments{

+\item{taxa1}{taxa1, can be label or node number}

+

+\item{taxa2}{taxa2, can be label or node number}

+

+\item{curvature}{A numeric value giving the amount of curvature.

+Negative values produce left-hand curves,

+positive values produce right-hand curves, and zero produces a straight line.}

+

+\item{...}{additional parameter}

+}

+\value{

+ggplot layer

+}

+\description{

+link between taxa

+}

+\author{

+Guangchuang Yu

+}

+