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##' add tip point
##'
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##'
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##' @title geom_tippoint
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##' @inheritParams geom_point2
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##' @return tip point layer
##' @export
##' @author Guangchuang Yu
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geom_tippoint <- function(mapping = NULL, data = NULL,
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position = "identity", na.rm = FALSE,
show.legend = NA, inherit.aes = TRUE, ...) {
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isTip <- NULL
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self_mapping <- aes(subset = isTip)
if (is.null(mapping)) {
mapping <- self_mapping
} else {
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mapping <- modifyList(self_mapping, mapping)
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}
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geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)
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}
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## angle is not supported,
## https://github.com/GuangchuangYu/ggtree/issues/77
##
##
## geom_tippoint2 <- function(mapping=NULL, hjust=0, ...) {
## angle <- NULL
## isTip <- NULL
## m1 <- aes(subset=(isTip & (angle < 90 | angle > 270)), angle=angle)
## m2 <- aes(subset=(isTip & (angle >= 90 & angle <=270)), angle=angle+180)
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## if (!is.null(mapping)) {
## m1 <- modifyList(mapping, m1)
## m2 <- modifyList(mapping, m2)
## }
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## list(geom_tippoint(m1, hjust=hjust, ...),
## geom_tippoint(m2, hjust=1-hjust, ...)
## )
## }
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##' add node point
##'
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##'
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##' @title geom_nodepoint
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##' @inheritParams geom_point2
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##' @return node point layer
##' @export
##' @author Guangchuang Yu
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geom_nodepoint <- function(mapping = NULL, data = NULL,
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position = "identity", na.rm = FALSE,
show.legend = NA, inherit.aes = TRUE, ...) {
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isTip <- NULL
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self_mapping <- aes(subset = !isTip)
if (is.null(mapping)) {
mapping <- self_mapping
} else {
mapping %<>% modifyList(self_mapping)
}
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geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)
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}
##' add root point
##'
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##'
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##' @title geom_rootpoint
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##' @inheritParams geom_point2
|
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##' @return root point layer
##' @export
##' @author Guangchuang Yu
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geom_rootpoint <- function(mapping = NULL, data = NULL,
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position = "identity", na.rm = FALSE,
show.legend = NA, inherit.aes = TRUE, ...) {
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isTip <- node <- parent <- NULL
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self_mapping <- aes(subset = (node == parent))
if (is.null(mapping)) {
mapping <- self_mapping
} else {
mapping %<>% modifyList(self_mapping)
}
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geom_point2(mapping, data, position, na.rm, show.legend, inherit.aes, ...)
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}
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##' geom_point2 support aes(subset) via setup_data
##'
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##'
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##' @title geom_point2
##' @param mapping aes mapping
##' @param data data
##' @param position position
##' @param na.rm logical
##' @param show.legend logical
##' @param inherit.aes logical
##' @param ... addktional parameter
##' @importFrom ggplot2 layer
##' @export
##' @seealso
##' \link[ggplot2]{geom_point}
##' @return point layer
##' @author Guangchuang Yu
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geom_point2 <- function(mapping = NULL, data = NULL,
|
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position = "identity", na.rm = FALSE,
show.legend = NA, inherit.aes = TRUE, ...) {
|
| 90df068e |
|
| 4edbfa25 |
|
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default_aes <- aes_(node=~node)
if (is.null(mapping)) {
mapping <- default_aes
} else {
mapping <- modifyList(mapping, default_aes)
}
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layer(
data = data,
mapping = mapping,
|
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stat = StatTreeData,
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geom = GeomPointGGtree,
position = position,
show.legend = show.legend,
inherit.aes = inherit.aes,
params = list(
na.rm = na.rm,
...
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| a92aaed1 |
),
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if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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)
}
##' @importFrom ggplot2 ggproto
##' @importFrom ggplot2 GeomPoint
##' @importFrom ggplot2 draw_key_point
GeomPointGGtree <- ggproto("GeomPointGGtree", GeomPoint,
setup_data = function(data, params) {
|
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if (is.null(data$subset))
return(data)
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data[data$subset,]
|
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}
## ,
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## draw_panel = function(data, panel_scales, coord, na.rm = FALSE){
## GeomPoint$draw_panel(data, panel_scales, coord, na.rm)
## },
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## draw_key = draw_key_point,
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## required_aes = c("x", "y"),
## default_aes = aes(shape = 19, colour = "black", size = 1.5, fill = NA,
## alpha = NA, stroke = 0.5)
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| f1f0d8d2 |
)
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| 90df068e |
|
