##' link between taxa ##' ##' ##' @title geom_taxalink ##' @param taxa1 taxa1, can be label or node number ##' @param taxa2 taxa2, can be label or node number ##' @param 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. ##' @param ... additional parameter ##' @return ggplot layer ##' @export ##' @importFrom ggplot2 GeomCurve ##' @author Guangchuang Yu geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) { position = "identity" show.legend = NA na.rm = TRUE inherit.aes = FALSE mapping <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y) layer(stat=StatTaxalink, mapping=mapping, geom=GeomCurve, position='identity', show.legend=show.legend, inherit.aes = inherit.aes, params = list(taxa1 = taxa1, taxa2 = taxa2, curvature = curvature, na.rm = na.rm, ...), if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE ) } StatTaxalink <- ggproto("StatTaxalink", Stat, compute_group = function(self, data, scales, params, taxa1, taxa2) { node1 <- taxa2node(data, taxa1) node2 <- taxa2node(data, taxa2) x <- data\$x y <- data\$y data.frame(x = x[node1], xend = x[node2], y = y[node1], yend = y[node2]) }, required_aes = c("x", "y", "xend", "yend") )