R/geom_edge_elbow.R

In YTLogos/ggraph: An Implementation of Grammar of Graphics for Graphs and Networks

#' Draw edges as elbows
#'
#' This geom draws edges as an angle in the same manner as known from classic
#' dendrogram plots of hierarchical clustering results. In case a circular
#' transformation has been applied the first line segment will be drawn as an
#' arc as expected. This geom is only applicable to layouts that return a
#' direction for the edges (currently \code{\link{layout_dendrogram_dendrogram}}
#' and \code{\link{layout_dendrogram_dendrogram}}).
#'
#' @details
#' Many geom_edge_* layers comes in 3 flavors depending on the level of control
#' needed over the drawing. The default (no numeric postfix) generate a number
#' of points (\code{n}) along the edge and draws it as a path. Each point along
#' the line has a numeric value associated with it giving the position along the
#' path, and it is therefore possible to show the direction of the edge by
#' mapping to this e.g. \code{colour = ..index..}. The version postfixed with a
#' "2" uses the "long" edge format (see \code{\link{get_edges}}) and makes it
#' possible to interpolate node parameter between the start and end node along
#' the edge. It is considerable less performant so should only be used if this
#' is needed. The version postfixed with a "0" draws the edge in the most
#' performant way, often directly using an appropriate grob from the grid
#' package, but does not allow for gradients along the edge.
#'
#' Often it is beneficial to stop the drawing of the edge before it reaches the
#' node, for instance in cases where an arrow should be drawn and the arrowhead
#' shouldn't lay ontop or below the node point. geom_edge_* and geom_edge_*2
#' supports this through the start_cap and end_cap aesthetics that takes a
#' \code{\link{geometry}} specification and dynamically caps the termini of the
#' edges based on the given specifications. This means that if
#' \code{end_cap = circle(1, 'cm')} the edges will end at a distance of 1cm even
#' during resizing of the plot window.
#'
#' All \code{geom_edge_*} and \code{geom_edge_*2} have the ability to draw a
#' label along the edge. The reason this is not a separate geom is that in order
#' for the label to know the location of the edge it needs to know the edge type
#' etc. Labels are drawn by providing a label aesthetic. The label_pos can be
#' used to specify where along the edge it should be drawn by supplying a number
#' between 0 and 1. The label_size aesthetic can be used to control the size of
#' the label. Often it is needed to have the label written along the direction
#' of the edge, but since the actual angle is dependent on the plot dimensions
#' this cannot be calculated beforehand. Using the angle_calc argument allows
#' you to specify whether to use the supplied angle aesthetic or whether to draw
#' the label along or across the edge.
#'
#' @note In order to avoid excessive typing edge aesthetic names are
#' automatically expanded. Because of this it is not necessary to write
#' \code{edge_colour} within the \code{aes()} call as \code{colour} will
#' automatically be renamed appropriately.
#'
#' @section Aesthetics:
#' geom_edge_elbow and geom_edge_elbow0 understand the following
#' aesthetics. Bold aesthetics are automatically set, but can be overridden.
#' \itemize{
#'  \item{\strong{x}}
#'  \item{\strong{y}}
#'  \item{\strong{xend}}
#'  \item{\strong{yend}}
#'  \item{\strong{circular}}
#'  \item{\strong{direction}}
#'  \item{edge_colour}
#'  \item{edge_width}
#'  \item{edge_linetype}
#'  \item{edge_alpha}
#'  \item{filter}
#' }
#' geom_edge_elbow2 understand the following aesthetics. Bold aesthetics are
#' automatically set, but can be overridden.
#' \itemize{
#'  \item{\strong{x}}
#'  \item{\strong{y}}
#'  \item{\strong{group}}
#'  \item{\strong{circular}}
#'  \item{\strong{direction}}
#'  \item{edge_colour}
#'  \item{edge_width}
#'  \item{edge_linetype}
#'  \item{edge_alpha}
#'  \item{filter}
#' }
#' geom_edge_elbow and geom_edge_elbow2 furthermore takes the following
#' aesthetics.
#' \itemize{
#'   \item{start_cap}
#'   \item{end_cap}
#'   \item{label}
#'   \item{label_pos}
#'   \item{label_size}
#'   \item{angle}
#'   \item{hjust}
#'   \item{vjust}
#'   \item{family}
#'   \item{fontface}
#'   \item{lineheight}
#' }
#'
#' @section Computed variables:
#'
#' \describe{
#'  \item{index}{The position along the path (not computed for the *0 version)}
#' }
#'
#' @inheritParams geom_edge_link
#' @inheritParams ggplot2::geom_path
#' @inheritParams geom_edge_diagonal
#'
#' @author Thomas Lin Pedersen
#'
#' @family geom_edge_*
#'
#' @examples
#' irisDen <- as.dendrogram(
#'   hclust(dist(iris[1:4],
#'               method='euclidean', ),
#'          method='ward.D2')
#' )
#' irisDen <- dendrapply(irisDen, function(x) {
#'   attr(x, 'nodePar') <- list(class = sample(letters[1:3], 1))
#'   attr(x, 'edgePar') <- list(class = sample(letters[1:3], 1))
#'   x
#' })
#'
#' ggraph(irisDen, 'even', circular = TRUE) +
#'   geom_edge_elbow(aes(alpha = ..index..))
#'
#' ggraph(irisDen, 'even') +
#'   geom_edge_elbow2(aes(colour = node.class))
#'
#' ggraph(irisDen, 'dendrogram') +
#'   geom_edge_elbow0(aes(colour = class))
#'
#' @rdname geom_edge_elbow
#' @name geom_edge_elbow
#'
NULL

#' @rdname ggraph-extensions
#' @format NULL
#' @usage NULL
#' @importFrom ggforce radial_trans
#' @export
StatEdgeElbow <- ggproto('StatEdgeElbow', Stat,
    compute_panel = function(data, scales, flipped = FALSE, n = 100) {
        if (data$circular[1] && n %% 2 == 1) {
            n <- n + 1
        }
        if (!data$circular[1] && n %% 2 == 0) {
            n <- n + 1
        }
        index <- seq(0, 1, length.out = n)
        if (any(data$circular)) {
            circId <- which(data$circular)
            dataCirc <- data[circId, ]
            radial <- radial_trans(c(0, 1), c(2*pi, 0), pad = 0, offset = 0)
            start <- atan2(dataCirc$y, dataCirc$x)
            radiiStart <- sqrt(dataCirc$x^2 + dataCirc$y^2)
            radiiEnd <- sqrt(dataCirc$xend^2 + dataCirc$yend^2)
            angelDiff <- (dataCirc$x*dataCirc$xend + dataCirc$y*dataCirc$yend) /
             (radiiStart*radiiEnd)
            angelDiff[is.nan(angelDiff)] <- 0
            angelDiff <- suppressWarnings(acos(angelDiff))
            angelDiff[is.nan(angelDiff)] <- 0
            end <- start + ifelse(dataCirc$direction == 'left',
                                  -angelDiff, angelDiff)
            angles <- unlist(Map(seq, from = start, to = end, length.out = n/2))
            radii <- rep(sqrt(data$y[circId]^2 + data$x[circId]^2), each = n/2)
            pathCirc <- radial$transform(r = radii, a = angles)
            pathCirc$group <- rep(circId, each = n/2)
            pathCirc$index <- rep(index[seq_len(n/2)], length(circId))
            radiiRel <- radiiStart / radiiEnd
            elbowX <- dataCirc$xend * radiiRel
            elbowY <- dataCirc$yend * radiiRel
            elbowX <- unlist(Map(seq, from = elbowX, to = dataCirc$xend,
                                 length.out = n/2))
            elbowY <- unlist(Map(seq, from = elbowY, to = dataCirc$yend,
                                 length.out = n/2))
            pathCirc <- rbind(pathCirc,
                              data.frame(x = elbowX,
                                         y = elbowY,
                                         group = pathCirc$group,
                                         index = rep(index[seq_len(n/2) + n/2],
                                                     length(circId))))
            pathCirc <- cbind(pathCirc, data[pathCirc$group, !names(data) %in%
                                                 c('x', 'y', 'xend', 'yend')])
        }
        if (any(!data$circular)) {
            pathLin <- lapply(which(!data$circular), function(i) {
                if (flipped) {
                    path <- data.frame(
                        x = approx(c(data$x[i], data$x[i], data$xend[i]),
                                   n = n)$y,
                        y = approx(c(data$y[i], data$yend[i], data$yend[i]),
                                   n = n)$y,
                        group = i,
                        index = index
                    )
                } else {
                    path <- data.frame(
                        x = approx(c(data$x[i], data$xend[i], data$xend[i]),
                                   n = n)$y,
                        y = approx(c(data$y[i], data$y[i], data$yend[i]),
                                   n = n)$y,
                        group = i,
                        index = index
                    )
                }
                cbind(path, data[rep(i, nrow(path)), !names(data) %in%
                                     c('x', 'y', 'xend', 'yend')])
            })
            pathLin <- do.call(rbind, pathLin)

            if (any(data$circular)) {
                paths <- rbind(pathLin, pathCirc)
            } else {
                paths <- pathLin
            }
        } else {
            paths <- pathCirc
        }
        paths[order(paths$group), ]
    },
    setup_data = function(data, params) {
        if (any(names(data) == 'filter')) {
            if (!is.logical(data$filter)) {
                stop('filter must be logical')
            }
            data <- data[data$filter, names(data) != 'filter']
        }
        data
    },
    default_aes = aes(filter = TRUE),
    required_aes = c('x', 'y', 'xend', 'yend', 'circular', 'direction')
)
#' @rdname geom_edge_elbow
#'
#' @export
geom_edge_elbow <- function(mapping = NULL, data = get_edges(),
                            position = "identity", arrow = NULL,
                            flipped = FALSE, n = 100, lineend = "butt",
                            linejoin = "round", linemitre = 1,
                            label_colour = 'black',  label_alpha = 1,
                            label_parse = FALSE, check_overlap = FALSE,
                            angle_calc = 'rot', force_flip = TRUE,
                            label_dodge = NULL, label_push = NULL,
                            show.legend = NA, ...) {
    mapping <- completeEdgeAes(mapping)
    mapping <- aesIntersect(mapping, aes_(x=~x, y=~y, xend=~xend, yend=~yend,
                                          circular=~circular,
                                          direction=~direction))
    layer(data = data, mapping = mapping, stat = StatEdgeElbow,
          geom = GeomEdgePath, position = position, show.legend = show.legend,
          inherit.aes = FALSE,
          params = expand_edge_aes(
              list(arrow = arrow, lineend = lineend, linejoin = linejoin,
                   linemitre = linemitre, na.rm = FALSE, n = n,
                   interpolate = FALSE, flipped = flipped,
                   label_colour = label_colour, label_alpha = label_alpha,
                   label_parse = label_parse, check_overlap = check_overlap,
                   angle_calc = angle_calc, force_flip = force_flip,
                   label_dodge = label_dodge, label_push = label_push, ...)
          )
    )
}
#' @rdname ggraph-extensions
#' @format NULL
#' @usage NULL
#' @export
StatEdgeElbow2 <- ggproto('StatEdgeElbow2', Stat,
    compute_panel = function(data, scales, flipped = FALSE, n = 100) {
        posCols <- c('x', 'y', 'group', 'circular', 'direction', 'PANEL')
        data <- data[order(data$group), ]
        posData <- cbind(data[c(TRUE, FALSE), posCols], data[c(FALSE, TRUE),
                                                             c('x', 'y')])
        names(posData) <- c(posCols, 'xend', 'yend')
        newData <- StatEdgeElbow$compute_panel(posData, scales, flipped, n)
        extraCols <- !names(data) %in% posCols
        index <- match(seq_len(nrow(posData)), newData$group)
        index <- as.vector(rbind(index, index + 1))
        newData$.interp <- TRUE
        newData$.interp[index] <- FALSE
        if (sum(extraCols) != 0) {
            for (i in names(data)[extraCols]) {
                newData[[i]] <- NA
                newData[[i]][index] <- data[[i]]
            }
        }
        newData
    },
    setup_data = function(data, params) {
        if (any(names(data) == 'filter')) {
            if (!is.logical(data$filter)) {
                stop('filter must be logical')
            }
            data <- data[data$filter, names(data) != 'filter']
        }
        data
    },
    default_aes = aes(filter = TRUE),
    required_aes = c('x', 'y', 'group', 'circular', 'direction')
)
#' @rdname geom_edge_elbow
#'
#' @export
geom_edge_elbow2 <- function(mapping = NULL, data = get_edges('long'),
                             position = "identity", arrow = NULL,
                             flipped = FALSE, n = 100, lineend = "butt",
                             linejoin = "round", linemitre = 1,
                             label_colour = 'black',  label_alpha = 1,
                             label_parse = FALSE, check_overlap = FALSE,
                             angle_calc = 'rot', force_flip = TRUE,
                             label_dodge = NULL, label_push = NULL,
                             show.legend = NA, ...) {
    mapping <- completeEdgeAes(mapping)
    mapping <- aesIntersect(mapping, aes_(x=~x, y=~y, group=~edge.id,
                                          circular=~circular,
                                          direction=~direction))
    layer(data = data, mapping = mapping, stat = StatEdgeElbow2,
          geom = GeomEdgePath, position = position, show.legend = show.legend,
          inherit.aes = FALSE,
          params = expand_edge_aes(
              list(arrow = arrow, lineend = lineend, linejoin = linejoin,
                   linemitre = linemitre, na.rm = FALSE, n = n,
                   interpolate = TRUE, flipped = flipped,
                   label_colour = label_colour, label_alpha = label_alpha,
                   label_parse = label_parse, check_overlap = check_overlap,
                   angle_calc = angle_calc, force_flip = force_flip,
                   label_dodge = label_dodge, label_push = label_push, ...)
          )
    )
}
#' @rdname ggraph-extensions
#' @format NULL
#' @usage NULL
#' @export
StatEdgeElbow0 <- ggproto('StatEdgeElbow0', Stat,
    compute_panel = function(data, scales, flipped = FALSE) {
        if (any(data$circular)) {
            circId <- which(data$circular)
            dataCirc <- data[circId, ]
            radial <- radial_trans(c(0, 1), c(2*pi, 0), pad = 0, offset = 0)
            start <- atan2(dataCirc$y, dataCirc$x)
            angelDiff <- (dataCirc$x*dataCirc$xend + dataCirc$y*dataCirc$yend) /
                (sqrt(dataCirc$x^2 + dataCirc$y^2) *
                     sqrt(dataCirc$xend^2 + dataCirc$yend^2))
            angelDiff[is.nan(angelDiff)] <- 0
            angelDiff <- suppressWarnings(acos(angelDiff))
            angelDiff[is.nan(angelDiff)] <- 0
            end <- start + ifelse(dataCirc$direction == 'left',
                                  -angelDiff, angelDiff)
            angles <- unlist(Map(seq, from = start, to = end, length.out = 50))
            radii <- rep(sqrt(data$y[circId]^2 + data$x[circId]^2), each = 50)
            pathCirc <- radial$transform(r = radii, a = angles)
            pathCirc$group <- rep(circId, each = 50)
            pathCirc <- rbind(pathCirc,
                              data.frame(x = data$xend[circId],
                                         y = data$yend[circId],
                                         group = circId))
            pathCirc <- cbind(pathCirc, data[pathCirc$group, !names(data) %in%
                                                 c('x', 'y', 'xend', 'yend')])
        }
        if (any(!data$circular)) {
            pathLin <- lapply(which(!data$circular), function(i) {
                if (flipped) {
                    path <- data.frame(
                        x = c(data$x[i], data$x[i], data$xend[i]),
                        y = c(data$y[i], data$yend[i], data$yend[i]),
                        group = i
                    )
                } else {
                    path <- data.frame(
                        x = c(data$x[i], data$xend[i], data$xend[i]),
                        y = c(data$y[i], data$y[i], data$yend[i]),
                        group = i
                    )
                }
                cbind(path, data[rep(i, nrow(path)), !names(data) %in%
                                     c('x', 'y', 'xend', 'yend')])
            })
            pathLin <- do.call(rbind, pathLin)

            if (any(data$circular)) {
                paths <- rbind(pathLin, pathCirc)
            } else {
                paths <- pathLin
            }
        } else {
            paths <- pathCirc
        }
        paths[order(paths$group), ]
    },
    setup_data = function(data, params) {
        if (any(names(data) == 'filter')) {
            if (!is.logical(data$filter)) {
                stop('filter must be logical')
            }
            data <- data[data$filter, names(data) != 'filter']
        }
        data
    },
    default_aes = aes(filter = TRUE),
    required_aes = c('x', 'y', 'xend', 'yend', 'circular', 'direction')
)
#' @rdname geom_edge_elbow
#'
#' @export
geom_edge_elbow0 <- function(mapping = NULL, data = get_edges(),
                            position = "identity", arrow = NULL, flipped = FALSE,
                            lineend = "butt", show.legend = NA, ...) {
    mapping <- completeEdgeAes(mapping)
    mapping <- aesIntersect(mapping, aes_(x=~x, y=~y, xend=~xend, yend=~yend,
                                          circular=~circular,
                                          direction=~direction))
    layer(data = data, mapping = mapping, stat = StatEdgeElbow0,
          geom = GeomEdgePath, position = position, show.legend = show.legend,
          inherit.aes = FALSE,
          params = expand_edge_aes(
              list(arrow = arrow, lineend = lineend, na.rm = FALSE,
                        interpolate = FALSE, flipped = flipped, ...)
          )
    )
}