xiangpin authored on 06/07/2022 13:33:17
| ... | ... |
@@ -52,6 +52,6 @@ below to see their documentation. |
| 52 | 52 |
|
| 53 | 53 |
\item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}}
|
| 54 | 54 |
|
| 55 |
- \item{tidytree}{\code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 55 |
+ \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 56 | 56 |
}} |
| 57 | 57 |
|
Guangchuang Yu authored on 01/04/2022 08:21:52
| ... | ... |
@@ -30,6 +30,7 @@ |
| 30 | 30 |
\alias{arrow}
|
| 31 | 31 |
\alias{unit}
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| 32 | 32 |
\alias{plot_list}
|
| 33 |
+\alias{identify}
|
|
| 33 | 34 |
\title{Objects exported from other packages}
|
| 34 | 35 |
\keyword{internal}
|
| 35 | 36 |
\description{
|
| ... | ... |
@@ -43,6 +44,8 @@ below to see their documentation. |
| 43 | 44 |
|
| 44 | 45 |
\item{dplyr}{\code{\link[dplyr:compute]{collapse}}}
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| 45 | 46 |
|
| 47 |
+ \item{ggfun}{\code{\link[ggfun:reexports]{identify}}}
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|
| 48 |
+ |
|
| 46 | 49 |
\item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2:scale_continuous]{scale_x_continuous}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}
|
| 47 | 50 |
|
| 48 | 51 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
|
Guangchuang Yu authored on 23/03/2022 04:13:34
| ... | ... |
@@ -25,9 +25,11 @@ |
| 25 | 25 |
\alias{scale_colour_manual}
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| 26 | 26 |
\alias{scale_color_manual}
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| 27 | 27 |
\alias{scale_fill_manual}
|
| 28 |
+\alias{scale_x_continuous}
|
|
| 28 | 29 |
\alias{margin}
|
| 29 | 30 |
\alias{arrow}
|
| 30 | 31 |
\alias{unit}
|
| 32 |
+\alias{plot_list}
|
|
| 31 | 33 |
\title{Objects exported from other packages}
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| 32 | 34 |
\keyword{internal}
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| 33 | 35 |
\description{
|
| ... | ... |
@@ -37,9 +39,11 @@ below to see their documentation. |
| 37 | 39 |
\describe{
|
| 38 | 40 |
\item{ape}{\code{\link[ape]{read.tree}}, \code{\link[ape]{rtree}}}
|
| 39 | 41 |
|
| 42 |
+ \item{aplot}{\code{\link[aplot]{plot_list}}}
|
|
| 43 |
+ |
|
| 40 | 44 |
\item{dplyr}{\code{\link[dplyr:compute]{collapse}}}
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| 41 | 45 |
|
| 42 |
- \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}
|
|
| 46 |
+ \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2:scale_continuous]{scale_x_continuous}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}
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|
| 43 | 47 |
|
| 44 | 48 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
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| 45 | 49 |
|
Guangchuang Yu authored on 03/09/2020 02:53:24
| ... | ... |
@@ -37,14 +37,14 @@ below to see their documentation. |
| 37 | 37 |
\describe{
|
| 38 | 38 |
\item{ape}{\code{\link[ape]{read.tree}}, \code{\link[ape]{rtree}}}
|
| 39 | 39 |
|
| 40 |
- \item{dplyr}{\code{\link[dplyr]{collapse}}}
|
|
| 40 |
+ \item{dplyr}{\code{\link[dplyr:compute]{collapse}}}
|
|
| 41 | 41 |
|
| 42 |
- \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2]{margin}}, \code{\link[ggplot2]{scale_color_manual}}, \code{\link[ggplot2]{scale_colour_manual}}, \code{\link[ggplot2]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{xlim}}}
|
|
| 42 |
+ \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}
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|
| 43 | 43 |
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| 44 | 44 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
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| 45 | 45 |
|
| 46 |
- \item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
|
| 46 |
+ \item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}}
|
|
| 47 | 47 |
|
| 48 |
- \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 48 |
+ \item{tidytree}{\code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 49 | 49 |
}} |
| 50 | 50 |
|
Guangchuang Yu authored on 02/09/2020 14:41:30
| ... | ... |
@@ -37,14 +37,14 @@ below to see their documentation. |
| 37 | 37 |
\describe{
|
| 38 | 38 |
\item{ape}{\code{\link[ape]{read.tree}}, \code{\link[ape]{rtree}}}
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| 39 | 39 |
|
| 40 |
- \item{dplyr}{\code{\link[dplyr:compute]{collapse}}}
|
|
| 40 |
+ \item{dplyr}{\code{\link[dplyr]{collapse}}}
|
|
| 41 | 41 |
|
| 42 |
- \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}
|
|
| 42 |
+ \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2]{margin}}, \code{\link[ggplot2]{scale_color_manual}}, \code{\link[ggplot2]{scale_colour_manual}}, \code{\link[ggplot2]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{xlim}}}
|
|
| 43 | 43 |
|
| 44 | 44 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
|
| 45 | 45 |
|
| 46 |
- \item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}}
|
|
| 46 |
+ \item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
|
| 47 | 47 |
|
| 48 |
- \item{tidytree}{\code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 48 |
+ \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 49 | 49 |
}} |
| 50 | 50 |
|
Guangchuang Yu authored on 16/07/2020 10:06:20
| ... | ... |
@@ -37,14 +37,14 @@ below to see their documentation. |
| 37 | 37 |
\describe{
|
| 38 | 38 |
\item{ape}{\code{\link[ape]{read.tree}}, \code{\link[ape]{rtree}}}
|
| 39 | 39 |
|
| 40 |
- \item{dplyr}{\code{\link[dplyr]{collapse}}}
|
|
| 40 |
+ \item{dplyr}{\code{\link[dplyr:compute]{collapse}}}
|
|
| 41 | 41 |
|
| 42 |
- \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2]{margin}}, \code{\link[ggplot2]{scale_color_manual}}, \code{\link[ggplot2]{scale_colour_manual}}, \code{\link[ggplot2]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{xlim}}}
|
|
| 42 |
+ \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}
|
|
| 43 | 43 |
|
| 44 | 44 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
|
| 45 | 45 |
|
| 46 |
- \item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
|
| 46 |
+ \item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}}
|
|
| 47 | 47 |
|
| 48 |
- \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 48 |
+ \item{tidytree}{\code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 49 | 49 |
}} |
| 50 | 50 |
|
Guangchuang Yu authored on 16/07/2020 01:51:43
| ... | ... |
@@ -37,14 +37,14 @@ below to see their documentation. |
| 37 | 37 |
\describe{
|
| 38 | 38 |
\item{ape}{\code{\link[ape]{read.tree}}, \code{\link[ape]{rtree}}}
|
| 39 | 39 |
|
| 40 |
- \item{dplyr}{\code{\link[dplyr:compute]{collapse}}}
|
|
| 40 |
+ \item{dplyr}{\code{\link[dplyr]{collapse}}}
|
|
| 41 | 41 |
|
| 42 |
- \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}
|
|
| 42 |
+ \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2]{margin}}, \code{\link[ggplot2]{scale_color_manual}}, \code{\link[ggplot2]{scale_colour_manual}}, \code{\link[ggplot2]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{xlim}}}
|
|
| 43 | 43 |
|
| 44 | 44 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
|
| 45 | 45 |
|
| 46 |
- \item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}}
|
|
| 46 |
+ \item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
|
| 47 | 47 |
|
| 48 |
- \item{tidytree}{\code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 48 |
+ \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 49 | 49 |
}} |
| 50 | 50 |
|
xiangpin authored on 13/07/2020 03:00:16
| ... | ... |
@@ -37,14 +37,14 @@ below to see their documentation. |
| 37 | 37 |
\describe{
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| 38 | 38 |
\item{ape}{\code{\link[ape]{read.tree}}, \code{\link[ape]{rtree}}}
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| 39 | 39 |
|
| 40 |
- \item{dplyr}{\code{\link[dplyr]{collapse}}}
|
|
| 40 |
+ \item{dplyr}{\code{\link[dplyr:compute]{collapse}}}
|
|
| 41 | 41 |
|
| 42 |
- \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2]{margin}}, \code{\link[ggplot2]{scale_color_manual}}, \code{\link[ggplot2]{scale_colour_manual}}, \code{\link[ggplot2]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{xlim}}}
|
|
| 42 |
+ \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2:geom_text]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2:element]{margin}}, \code{\link[ggplot2:scale_manual]{scale_color_manual}}, \code{\link[ggplot2:scale_manual]{scale_colour_manual}}, \code{\link[ggplot2:scale_manual]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2:lims]{xlim}}}
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|
| 43 | 43 |
|
| 44 | 44 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
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| 45 | 45 |
|
| 46 |
- \item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
|
| 46 |
+ \item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}}
|
|
| 47 | 47 |
|
| 48 |
- \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 48 |
+ \item{tidytree}{\code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
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|
| 49 | 49 |
}} |
| 50 | 50 |
|
Guangchuang Yu authored on 06/12/2019 03:01:17
| ... | ... |
@@ -35,16 +35,16 @@ These objects are imported from other packages. Follow the links |
| 35 | 35 |
below to see their documentation. |
| 36 | 36 |
|
| 37 | 37 |
\describe{
|
| 38 |
- \item{ape}{\code{\link[ape]{rtree}}, \code{\link[ape]{read.tree}}}
|
|
| 38 |
+ \item{ape}{\code{\link[ape]{read.tree}}, \code{\link[ape]{rtree}}}
|
|
| 39 | 39 |
|
| 40 | 40 |
\item{dplyr}{\code{\link[dplyr]{collapse}}}
|
| 41 | 41 |
|
| 42 |
- \item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2]{scale_colour_manual}}, \code{\link[ggplot2]{scale_color_manual}}, \code{\link[ggplot2]{scale_fill_manual}}, \code{\link[ggplot2]{margin}}}
|
|
| 42 |
+ \item{ggplot2}{\code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2]{margin}}, \code{\link[ggplot2]{scale_color_manual}}, \code{\link[ggplot2]{scale_colour_manual}}, \code{\link[ggplot2]{scale_fill_manual}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{xlim}}}
|
|
| 43 | 43 |
|
| 44 | 44 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
|
| 45 | 45 |
|
| 46 | 46 |
\item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
| 47 | 47 |
|
| 48 |
- \item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}, \code{\link[tidytree]{MRCA}}}
|
|
| 48 |
+ \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 49 | 49 |
}} |
| 50 | 50 |
|
Guangchuang Yu authored on 29/11/2019 07:47:41
| ... | ... |
@@ -21,6 +21,11 @@ |
| 21 | 21 |
\alias{geom_text}
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| 22 | 22 |
\alias{geom_label}
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| 23 | 23 |
\alias{geom_point}
|
| 24 |
+\alias{guide_legend}
|
|
| 25 |
+\alias{scale_colour_manual}
|
|
| 26 |
+\alias{scale_color_manual}
|
|
| 27 |
+\alias{scale_fill_manual}
|
|
| 28 |
+\alias{margin}
|
|
| 24 | 29 |
\alias{arrow}
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| 25 | 30 |
\alias{unit}
|
| 26 | 31 |
\title{Objects exported from other packages}
|
| ... | ... |
@@ -34,7 +39,7 @@ below to see their documentation. |
| 34 | 39 |
|
| 35 | 40 |
\item{dplyr}{\code{\link[dplyr]{collapse}}}
|
| 36 | 41 |
|
| 37 |
- \item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
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| 42 |
+ \item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{guide_legend}}, \code{\link[ggplot2]{scale_colour_manual}}, \code{\link[ggplot2]{scale_color_manual}}, \code{\link[ggplot2]{scale_fill_manual}}, \code{\link[ggplot2]{margin}}}
|
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| 38 | 43 |
|
| 39 | 44 |
\item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
|
| 40 | 45 |
|
Guangchuang Yu authored on 28/09/2019 10:22:18
| ... | ... |
@@ -21,6 +21,8 @@ |
| 21 | 21 |
\alias{geom_text}
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| 22 | 22 |
\alias{geom_label}
|
| 23 | 23 |
\alias{geom_point}
|
| 24 |
+\alias{arrow}
|
|
| 25 |
+\alias{unit}
|
|
| 24 | 26 |
\title{Objects exported from other packages}
|
| 25 | 27 |
\keyword{internal}
|
| 26 | 28 |
\description{
|
| ... | ... |
@@ -34,6 +36,8 @@ below to see their documentation. |
| 34 | 36 |
|
| 35 | 37 |
\item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
| 36 | 38 |
|
| 39 |
+ \item{grid}{\code{\link[grid]{arrow}}, \code{\link[grid]{unit}}}
|
|
| 40 |
+ |
|
| 37 | 41 |
\item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
| 38 | 42 |
|
| 39 | 43 |
\item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}, \code{\link[tidytree]{MRCA}}}
|
Guangchuang Yu authored on 21/08/2019 05:59:44
| ... | ... |
@@ -10,6 +10,7 @@ |
| 10 | 10 |
\alias{groupClade}
|
| 11 | 11 |
\alias{nodeid}
|
| 12 | 12 |
\alias{nodelab}
|
| 13 |
+\alias{MRCA}
|
|
| 13 | 14 |
\alias{collapse}
|
| 14 | 15 |
\alias{fortify}
|
| 15 | 16 |
\alias{ggplot}
|
| ... | ... |
@@ -35,6 +36,6 @@ below to see their documentation. |
| 35 | 36 |
|
| 36 | 37 |
\item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
| 37 | 38 |
|
| 38 |
- \item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 39 |
+ \item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}, \code{\link[tidytree]{MRCA}}}
|
|
| 39 | 40 |
}} |
| 40 | 41 |
|
Guangchuang Yu authored on 09/08/2019 03:15:25
| ... | ... |
@@ -8,6 +8,8 @@ |
| 8 | 8 |
\alias{read.tree}
|
| 9 | 9 |
\alias{groupOTU}
|
| 10 | 10 |
\alias{groupClade}
|
| 11 |
+\alias{nodeid}
|
|
| 12 |
+\alias{nodelab}
|
|
| 11 | 13 |
\alias{collapse}
|
| 12 | 14 |
\alias{fortify}
|
| 13 | 15 |
\alias{ggplot}
|
| ... | ... |
@@ -33,6 +35,6 @@ below to see their documentation. |
| 33 | 35 |
|
| 34 | 36 |
\item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
| 35 | 37 |
|
| 36 |
- \item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}}
|
|
| 38 |
+ \item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 37 | 39 |
}} |
| 38 | 40 |
|
Guangchuang Yu authored on 24/07/2019 07:38:11
| ... | ... |
@@ -6,7 +6,6 @@ |
| 6 | 6 |
\alias{\%>\%}
|
| 7 | 7 |
\alias{rtree}
|
| 8 | 8 |
\alias{read.tree}
|
| 9 |
-\alias{read.nexus}
|
|
| 10 | 9 |
\alias{groupOTU}
|
| 11 | 10 |
\alias{groupClade}
|
| 12 | 11 |
\alias{collapse}
|
| ... | ... |
@@ -19,22 +18,6 @@ |
| 19 | 18 |
\alias{geom_text}
|
| 20 | 19 |
\alias{geom_label}
|
| 21 | 20 |
\alias{geom_point}
|
| 22 |
-\alias{read.astral}
|
|
| 23 |
-\alias{read.beast}
|
|
| 24 |
-\alias{read.codeml}
|
|
| 25 |
-\alias{read.codeml_mlc}
|
|
| 26 |
-\alias{read.hyphy}
|
|
| 27 |
-\alias{read.iqtree}
|
|
| 28 |
-\alias{read.jplace}
|
|
| 29 |
-\alias{read.jtree}
|
|
| 30 |
-\alias{read.mrbayes}
|
|
| 31 |
-\alias{read.newick}
|
|
| 32 |
-\alias{read.nhx}
|
|
| 33 |
-\alias{read.paml_rst}
|
|
| 34 |
-\alias{read.phylip}
|
|
| 35 |
-\alias{read.phyloT}
|
|
| 36 |
-\alias{read.r8s}
|
|
| 37 |
-\alias{read.raxml}
|
|
| 38 | 21 |
\title{Objects exported from other packages}
|
| 39 | 22 |
\keyword{internal}
|
| 40 | 23 |
\description{
|
| ... | ... |
@@ -42,16 +25,14 @@ These objects are imported from other packages. Follow the links |
| 42 | 25 |
below to see their documentation. |
| 43 | 26 |
|
| 44 | 27 |
\describe{
|
| 45 |
- \item{ape}{\code{\link[ape]{rtree}}, \code{\link[ape]{read.tree}}, \code{\link[ape]{read.nexus}}}
|
|
| 28 |
+ \item{ape}{\code{\link[ape]{rtree}}, \code{\link[ape]{read.tree}}}
|
|
| 46 | 29 |
|
| 47 | 30 |
\item{dplyr}{\code{\link[dplyr]{collapse}}}
|
| 48 | 31 |
|
| 49 |
- \item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
|
| 32 |
+ \item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
|
| 50 | 33 |
|
| 51 | 34 |
\item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
| 52 | 35 |
|
| 53 | 36 |
\item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}}
|
| 54 |
- |
|
| 55 |
- \item{treeio}{\code{\link[treeio]{read.astral}}, \code{\link[treeio]{read.beast}}, \code{\link[treeio]{read.codeml}}, \code{\link[treeio]{read.codeml_mlc}}, \code{\link[treeio]{read.hyphy}}, \code{\link[treeio]{read.iqtree}}, \code{\link[treeio]{read.jplace}}, \code{\link[treeio]{read.jtree}}, \code{\link[treeio]{read.mrbayes}}, \code{\link[treeio]{read.newick}}, \code{\link[treeio]{read.nhx}}, \code{\link[treeio]{read.paml_rst}}, \code{\link[treeio]{read.phylip}}, \code{\link[treeio]{read.phyloT}}, \code{\link[treeio]{read.r8s}}, \code{\link[treeio]{read.raxml}}}
|
|
| 56 | 37 |
}} |
| 57 | 38 |
|
Guangchuang Yu authored on 25/01/2019 21:12:11
| ... | ... |
@@ -3,6 +3,7 @@ |
| 3 | 3 |
\docType{import}
|
| 4 | 4 |
\name{reexports}
|
| 5 | 5 |
\alias{reexports}
|
| 6 |
+\alias{\%>\%}
|
|
| 6 | 7 |
\alias{rtree}
|
| 7 | 8 |
\alias{read.tree}
|
| 8 | 9 |
\alias{read.nexus}
|
| ... | ... |
@@ -47,6 +48,8 @@ below to see their documentation. |
| 47 | 48 |
|
| 48 | 49 |
\item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
| 49 | 50 |
|
| 51 |
+ \item{magrittr}{\code{\link[magrittr]{\%>\%}}}
|
|
| 52 |
+ |
|
| 50 | 53 |
\item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}}
|
| 51 | 54 |
|
| 52 | 55 |
\item{treeio}{\code{\link[treeio]{read.astral}}, \code{\link[treeio]{read.beast}}, \code{\link[treeio]{read.codeml}}, \code{\link[treeio]{read.codeml_mlc}}, \code{\link[treeio]{read.hyphy}}, \code{\link[treeio]{read.iqtree}}, \code{\link[treeio]{read.jplace}}, \code{\link[treeio]{read.jtree}}, \code{\link[treeio]{read.mrbayes}}, \code{\link[treeio]{read.newick}}, \code{\link[treeio]{read.nhx}}, \code{\link[treeio]{read.paml_rst}}, \code{\link[treeio]{read.phylip}}, \code{\link[treeio]{read.phyloT}}, \code{\link[treeio]{read.r8s}}, \code{\link[treeio]{read.raxml}}}
|
Guangchuang Yu authored on 07/08/2018 12:07:15
| ... | ... |
@@ -4,67 +4,35 @@ |
| 4 | 4 |
\name{reexports}
|
| 5 | 5 |
\alias{reexports}
|
| 6 | 6 |
\alias{rtree}
|
| 7 |
-\alias{reexports}
|
|
| 8 | 7 |
\alias{read.tree}
|
| 9 |
-\alias{reexports}
|
|
| 10 | 8 |
\alias{read.nexus}
|
| 11 |
-\alias{reexports}
|
|
| 12 | 9 |
\alias{groupOTU}
|
| 13 |
-\alias{reexports}
|
|
| 14 | 10 |
\alias{groupClade}
|
| 15 |
-\alias{reexports}
|
|
| 16 | 11 |
\alias{collapse}
|
| 17 |
-\alias{reexports}
|
|
| 18 | 12 |
\alias{fortify}
|
| 19 |
-\alias{reexports}
|
|
| 20 | 13 |
\alias{ggplot}
|
| 21 |
-\alias{reexports}
|
|
| 22 | 14 |
\alias{xlim}
|
| 23 |
-\alias{reexports}
|
|
| 24 | 15 |
\alias{theme}
|
| 25 |
-\alias{reexports}
|
|
| 26 | 16 |
\alias{ggsave}
|
| 27 |
-\alias{reexports}
|
|
| 28 | 17 |
\alias{aes}
|
| 29 |
-\alias{reexports}
|
|
| 30 |
-\alias{fortify}
|
|
| 31 |
-\alias{reexports}
|
|
| 32 | 18 |
\alias{geom_text}
|
| 33 |
-\alias{reexports}
|
|
| 34 | 19 |
\alias{geom_label}
|
| 35 |
-\alias{reexports}
|
|
| 36 | 20 |
\alias{geom_point}
|
| 37 |
-\alias{reexports}
|
|
| 38 | 21 |
\alias{read.astral}
|
| 39 |
-\alias{reexports}
|
|
| 40 | 22 |
\alias{read.beast}
|
| 41 |
-\alias{reexports}
|
|
| 42 | 23 |
\alias{read.codeml}
|
| 43 |
-\alias{reexports}
|
|
| 44 | 24 |
\alias{read.codeml_mlc}
|
| 45 |
-\alias{reexports}
|
|
| 46 | 25 |
\alias{read.hyphy}
|
| 47 |
-\alias{reexports}
|
|
| 48 | 26 |
\alias{read.iqtree}
|
| 49 |
-\alias{reexports}
|
|
| 50 | 27 |
\alias{read.jplace}
|
| 51 |
-\alias{reexports}
|
|
| 52 | 28 |
\alias{read.jtree}
|
| 53 |
-\alias{reexports}
|
|
| 54 | 29 |
\alias{read.mrbayes}
|
| 55 |
-\alias{reexports}
|
|
| 56 | 30 |
\alias{read.newick}
|
| 57 |
-\alias{reexports}
|
|
| 58 | 31 |
\alias{read.nhx}
|
| 59 |
-\alias{reexports}
|
|
| 60 | 32 |
\alias{read.paml_rst}
|
| 61 |
-\alias{reexports}
|
|
| 62 | 33 |
\alias{read.phylip}
|
| 63 |
-\alias{reexports}
|
|
| 64 | 34 |
\alias{read.phyloT}
|
| 65 |
-\alias{reexports}
|
|
| 66 | 35 |
\alias{read.r8s}
|
| 67 |
-\alias{reexports}
|
|
| 68 | 36 |
\alias{read.raxml}
|
| 69 | 37 |
\title{Objects exported from other packages}
|
| 70 | 38 |
\keyword{internal}
|
guangchuang yu authored on 03/07/2018 02:44:33
| ... | ... |
@@ -27,6 +27,8 @@ |
| 27 | 27 |
\alias{reexports}
|
| 28 | 28 |
\alias{aes}
|
| 29 | 29 |
\alias{reexports}
|
| 30 |
+\alias{fortify}
|
|
| 31 |
+\alias{reexports}
|
|
| 30 | 32 |
\alias{geom_text}
|
| 31 | 33 |
\alias{reexports}
|
| 32 | 34 |
\alias{geom_label}
|
| ... | ... |
@@ -75,7 +77,7 @@ below to see their documentation. |
| 75 | 77 |
|
| 76 | 78 |
\item{dplyr}{\code{\link[dplyr]{collapse}}}
|
| 77 | 79 |
|
| 78 |
- \item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
|
| 80 |
+ \item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
|
| 79 | 81 |
|
| 80 | 82 |
\item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}}
|
| 81 | 83 |
|
guangchuang yu authored on 17/04/2018 11:05:21
| ... | ... |
@@ -33,6 +33,8 @@ |
| 33 | 33 |
\alias{reexports}
|
| 34 | 34 |
\alias{geom_point}
|
| 35 | 35 |
\alias{reexports}
|
| 36 |
+\alias{read.astral}
|
|
| 37 |
+\alias{reexports}
|
|
| 36 | 38 |
\alias{read.beast}
|
| 37 | 39 |
\alias{reexports}
|
| 38 | 40 |
\alias{read.codeml}
|
| ... | ... |
@@ -77,6 +79,6 @@ below to see their documentation. |
| 77 | 79 |
|
| 78 | 80 |
\item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}}
|
| 79 | 81 |
|
| 80 |
- \item{treeio}{\code{\link[treeio]{read.beast}}, \code{\link[treeio]{read.codeml}}, \code{\link[treeio]{read.codeml_mlc}}, \code{\link[treeio]{read.hyphy}}, \code{\link[treeio]{read.iqtree}}, \code{\link[treeio]{read.jplace}}, \code{\link[treeio]{read.jtree}}, \code{\link[treeio]{read.mrbayes}}, \code{\link[treeio]{read.newick}}, \code{\link[treeio]{read.nhx}}, \code{\link[treeio]{read.paml_rst}}, \code{\link[treeio]{read.phylip}}, \code{\link[treeio]{read.phyloT}}, \code{\link[treeio]{read.r8s}}, \code{\link[treeio]{read.raxml}}}
|
|
| 82 |
+ \item{treeio}{\code{\link[treeio]{read.astral}}, \code{\link[treeio]{read.beast}}, \code{\link[treeio]{read.codeml}}, \code{\link[treeio]{read.codeml_mlc}}, \code{\link[treeio]{read.hyphy}}, \code{\link[treeio]{read.iqtree}}, \code{\link[treeio]{read.jplace}}, \code{\link[treeio]{read.jtree}}, \code{\link[treeio]{read.mrbayes}}, \code{\link[treeio]{read.newick}}, \code{\link[treeio]{read.nhx}}, \code{\link[treeio]{read.paml_rst}}, \code{\link[treeio]{read.phylip}}, \code{\link[treeio]{read.phyloT}}, \code{\link[treeio]{read.r8s}}, \code{\link[treeio]{read.raxml}}}
|
|
| 81 | 83 |
}} |
| 82 | 84 |
|
guangchuang yu authored on 17/04/2018 05:57:33
| ... | ... |
@@ -41,6 +41,8 @@ |
| 41 | 41 |
\alias{reexports}
|
| 42 | 42 |
\alias{read.hyphy}
|
| 43 | 43 |
\alias{reexports}
|
| 44 |
+\alias{read.iqtree}
|
|
| 45 |
+\alias{reexports}
|
|
| 44 | 46 |
\alias{read.jplace}
|
| 45 | 47 |
\alias{reexports}
|
| 46 | 48 |
\alias{read.jtree}
|
| ... | ... |
@@ -75,6 +77,6 @@ below to see their documentation. |
| 75 | 77 |
|
| 76 | 78 |
\item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}}
|
| 77 | 79 |
|
| 78 |
- \item{treeio}{\code{\link[treeio]{read.beast}}, \code{\link[treeio]{read.codeml}}, \code{\link[treeio]{read.codeml_mlc}}, \code{\link[treeio]{read.hyphy}}, \code{\link[treeio]{read.jplace}}, \code{\link[treeio]{read.jtree}}, \code{\link[treeio]{read.mrbayes}}, \code{\link[treeio]{read.newick}}, \code{\link[treeio]{read.nhx}}, \code{\link[treeio]{read.paml_rst}}, \code{\link[treeio]{read.phylip}}, \code{\link[treeio]{read.phyloT}}, \code{\link[treeio]{read.r8s}}, \code{\link[treeio]{read.raxml}}}
|
|
| 80 |
+ \item{treeio}{\code{\link[treeio]{read.beast}}, \code{\link[treeio]{read.codeml}}, \code{\link[treeio]{read.codeml_mlc}}, \code{\link[treeio]{read.hyphy}}, \code{\link[treeio]{read.iqtree}}, \code{\link[treeio]{read.jplace}}, \code{\link[treeio]{read.jtree}}, \code{\link[treeio]{read.mrbayes}}, \code{\link[treeio]{read.newick}}, \code{\link[treeio]{read.nhx}}, \code{\link[treeio]{read.paml_rst}}, \code{\link[treeio]{read.phylip}}, \code{\link[treeio]{read.phyloT}}, \code{\link[treeio]{read.r8s}}, \code{\link[treeio]{read.raxml}}}
|
|
| 79 | 81 |
}} |
| 80 | 82 |
|
guangchuang yu authored on 03/01/2018 09:55:53
| ... | ... |
@@ -7,10 +7,18 @@ |
| 7 | 7 |
\alias{reexports}
|
| 8 | 8 |
\alias{read.tree}
|
| 9 | 9 |
\alias{reexports}
|
| 10 |
+\alias{read.nexus}
|
|
| 11 |
+\alias{reexports}
|
|
| 10 | 12 |
\alias{groupOTU}
|
| 11 | 13 |
\alias{reexports}
|
| 12 | 14 |
\alias{groupClade}
|
| 13 | 15 |
\alias{reexports}
|
| 16 |
+\alias{collapse}
|
|
| 17 |
+\alias{reexports}
|
|
| 18 |
+\alias{fortify}
|
|
| 19 |
+\alias{reexports}
|
|
| 20 |
+\alias{ggplot}
|
|
| 21 |
+\alias{reexports}
|
|
| 14 | 22 |
\alias{xlim}
|
| 15 | 23 |
\alias{reexports}
|
| 16 | 24 |
\alias{theme}
|
| ... | ... |
@@ -24,6 +32,34 @@ |
| 24 | 32 |
\alias{geom_label}
|
| 25 | 33 |
\alias{reexports}
|
| 26 | 34 |
\alias{geom_point}
|
| 35 |
+\alias{reexports}
|
|
| 36 |
+\alias{read.beast}
|
|
| 37 |
+\alias{reexports}
|
|
| 38 |
+\alias{read.codeml}
|
|
| 39 |
+\alias{reexports}
|
|
| 40 |
+\alias{read.codeml_mlc}
|
|
| 41 |
+\alias{reexports}
|
|
| 42 |
+\alias{read.hyphy}
|
|
| 43 |
+\alias{reexports}
|
|
| 44 |
+\alias{read.jplace}
|
|
| 45 |
+\alias{reexports}
|
|
| 46 |
+\alias{read.jtree}
|
|
| 47 |
+\alias{reexports}
|
|
| 48 |
+\alias{read.mrbayes}
|
|
| 49 |
+\alias{reexports}
|
|
| 50 |
+\alias{read.newick}
|
|
| 51 |
+\alias{reexports}
|
|
| 52 |
+\alias{read.nhx}
|
|
| 53 |
+\alias{reexports}
|
|
| 54 |
+\alias{read.paml_rst}
|
|
| 55 |
+\alias{reexports}
|
|
| 56 |
+\alias{read.phylip}
|
|
| 57 |
+\alias{reexports}
|
|
| 58 |
+\alias{read.phyloT}
|
|
| 59 |
+\alias{reexports}
|
|
| 60 |
+\alias{read.r8s}
|
|
| 61 |
+\alias{reexports}
|
|
| 62 |
+\alias{read.raxml}
|
|
| 27 | 63 |
\title{Objects exported from other packages}
|
| 28 | 64 |
\keyword{internal}
|
| 29 | 65 |
\description{
|
| ... | ... |
@@ -31,10 +67,14 @@ These objects are imported from other packages. Follow the links |
| 31 | 67 |
below to see their documentation. |
| 32 | 68 |
|
| 33 | 69 |
\describe{
|
| 34 |
- \item{ape}{\code{\link[ape]{rtree}}, \code{\link[ape]{read.tree}}}
|
|
| 70 |
+ \item{ape}{\code{\link[ape]{rtree}}, \code{\link[ape]{read.tree}}, \code{\link[ape]{read.nexus}}}
|
|
| 35 | 71 |
|
| 36 |
- \item{ggplot2}{\code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
|
| 72 |
+ \item{dplyr}{\code{\link[dplyr]{collapse}}}
|
|
| 73 |
+ |
|
| 74 |
+ \item{ggplot2}{\code{\link[ggplot2]{fortify}}, \code{\link[ggplot2]{ggplot}}, \code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
|
| 37 | 75 |
|
| 38 | 76 |
\item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}}
|
| 77 |
+ |
|
| 78 |
+ \item{treeio}{\code{\link[treeio]{read.beast}}, \code{\link[treeio]{read.codeml}}, \code{\link[treeio]{read.codeml_mlc}}, \code{\link[treeio]{read.hyphy}}, \code{\link[treeio]{read.jplace}}, \code{\link[treeio]{read.jtree}}, \code{\link[treeio]{read.mrbayes}}, \code{\link[treeio]{read.newick}}, \code{\link[treeio]{read.nhx}}, \code{\link[treeio]{read.paml_rst}}, \code{\link[treeio]{read.phylip}}, \code{\link[treeio]{read.phyloT}}, \code{\link[treeio]{read.r8s}}, \code{\link[treeio]{read.raxml}}}
|
|
| 39 | 79 |
}} |
| 40 | 80 |
|
guangchuang yu authored on 14/12/2017 08:47:21
| 1 | 1 |
new file mode 100644 |
| ... | ... |
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| 1 |
+% Generated by roxygen2: do not edit by hand |
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| 2 |
+% Please edit documentation in R/reexports.R |
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| 3 |
+\docType{import}
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| 4 |
+\name{reexports}
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|
| 5 |
+\alias{reexports}
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|
| 6 |
+\alias{rtree}
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| 7 |
+\alias{reexports}
|
|
| 8 |
+\alias{read.tree}
|
|
| 9 |
+\alias{reexports}
|
|
| 10 |
+\alias{groupOTU}
|
|
| 11 |
+\alias{reexports}
|
|
| 12 |
+\alias{groupClade}
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|
| 13 |
+\alias{reexports}
|
|
| 14 |
+\alias{xlim}
|
|
| 15 |
+\alias{reexports}
|
|
| 16 |
+\alias{theme}
|
|
| 17 |
+\alias{reexports}
|
|
| 18 |
+\alias{ggsave}
|
|
| 19 |
+\alias{reexports}
|
|
| 20 |
+\alias{aes}
|
|
| 21 |
+\alias{reexports}
|
|
| 22 |
+\alias{geom_text}
|
|
| 23 |
+\alias{reexports}
|
|
| 24 |
+\alias{geom_label}
|
|
| 25 |
+\alias{reexports}
|
|
| 26 |
+\alias{geom_point}
|
|
| 27 |
+\title{Objects exported from other packages}
|
|
| 28 |
+\keyword{internal}
|
|
| 29 |
+\description{
|
|
| 30 |
+These objects are imported from other packages. Follow the links |
|
| 31 |
+below to see their documentation. |
|
| 32 |
+ |
|
| 33 |
+\describe{
|
|
| 34 |
+ \item{ape}{\code{\link[ape]{rtree}}, \code{\link[ape]{read.tree}}}
|
|
| 35 |
+ |
|
| 36 |
+ \item{ggplot2}{\code{\link[ggplot2]{xlim}}, \code{\link[ggplot2]{theme}}, \code{\link[ggplot2]{ggsave}}, \code{\link[ggplot2]{aes}}, \code{\link[ggplot2]{geom_text}}, \code{\link[ggplot2]{geom_label}}, \code{\link[ggplot2]{geom_point}}}
|
|
| 37 |
+ |
|
| 38 |
+ \item{tidytree}{\code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{groupClade}}}
|
|
| 39 |
+}} |
|
| 40 |
+ |
GuangchuangYu authored on 20/12/2016 16:39:07
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deleted file mode 100644 |
| ... | ... |
@@ -1,16 +0,0 @@ |
| 1 |
-% Generated by roxygen2: do not edit by hand |
|
| 2 |
-% Please edit documentation in R/ape.R |
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| 3 |
-\docType{import}
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|
| 4 |
-\name{reexports}
|
|
| 5 |
-\alias{read.tree}
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|
| 6 |
-\alias{reexports}
|
|
| 7 |
-\title{Objects exported from other packages}
|
|
| 8 |
-\description{
|
|
| 9 |
-These objects are imported from other packages. Follow the links |
|
| 10 |
-below to see their documentation. |
|
| 11 |
- |
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| 12 |
-\describe{
|
|
| 13 |
- \item{ape}{\code{\link[ape]{read.tree}}}
|
|
| 14 |
-}} |
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| 15 |
-\keyword{internal}
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| 16 |
- |
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118925 bc3139a8-67e5-0310-9ffc-ced21a209358
g.yu authored on 24/06/2016 06:22:28
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,16 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/ape.R |
|
| 3 |
+\docType{import}
|
|
| 4 |
+\name{reexports}
|
|
| 5 |
+\alias{read.tree}
|
|
| 6 |
+\alias{reexports}
|
|
| 7 |
+\title{Objects exported from other packages}
|
|
| 8 |
+\description{
|
|
| 9 |
+These objects are imported from other packages. Follow the links |
|
| 10 |
+below to see their documentation. |
|
| 11 |
+ |
|
| 12 |
+\describe{
|
|
| 13 |
+ \item{ape}{\code{\link[ape]{read.tree}}}
|
|
| 14 |
+}} |
|
| 15 |
+\keyword{internal}
|
|
| 16 |
+ |