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<p>OK, so I couldn't resist it, I did a plot based upon the grid package as @agstudy suggested. A few things still bother me:</p> <ul> <li>The bezier arrows don't follow the line but point straight in to the box instead of coming in at an angle.</li> <li>I'm not aware of a nice grading option of bezier curves, there seems to be in general little support for gradients in R (most solutions that I've read are about mutliple lines)</li> </ul> <h1>Fixed it</h1> <p>Ok, after a lot of work I finally got it exactly right. The new 0.5.3.0 version of my package has the code for the plot.</p> <p><img src="https://i.stack.imgur.com/HAoKU.png" alt="enter image description here"></p> <h1>Old code</h1> <p>Here's the plot:</p> <p><img src="https://i.stack.imgur.com/QHdau.png" alt="Example"></p> <p>And the code:</p> <pre><code>#' A transition plot #' #' This plot purpose is to illustrate how states change before and #' after. In my research I use it before surgery and after surgery #' but it can be used in any situation where you have a change from #' one state to another #' #' @param transition_flow This should be a matrix with the size of the transitions. #' The unit for each cell should be number of observations, row/column-proportions #' will show incorrect sizes. The matrix needs to be square. The best way to generate #' this matrix is probably just do a \code{table(starting_state, end_state)}. The rows #' represent the starting positions, while the columns the end positions. I.e. the first #' rows third column is the number of observations that go from the first class to the #' third class. #' @param box_txt The text to appear inside of the boxes. If you need line breaks #' then you need to manually add a \\n inside the string. #' @param tot_spacing The proportion of the vertical space that is to be left #' empty. It is then split evenly between the boxes. #' @param box_width The width of the box. By default the box is one fourth of #' the plot width. #' @param fill_start_box The fill color of the start boxes. This can either #' be a single value ore a vector if you desire different colors for each #' box. #' @param txt_start_clr The text color of the start boxes. This can either #' be a single value ore a vector if you desire different colors for each #' box. #' @param fill_end_box The fill color of the end boxes. This can either #' be a single value ore a vector if you desire different colors for each #' box. #' @param txt_end_clr The text color of the end boxes. This can either #' be a single value ore a vector if you desire different colors for each #' box. #' @param pt The point size of the text #' @param min_lwd The minimum width of the line that we want to illustrate the #' tranisition with. #' @param max_lwd The maximum width of the line that we want to illustrate the #' tranisition with. #' @param lwd_prop_total The width of the lines may be proportional to either the #' other flows from that box, or they may be related to all flows. This is a boolean #' parameter that is set to true by default, i.e. relating to all flows. #' @return void #' @example examples/transitionPlot_example.R #' #' @author max #' @import grid #' @export transitionPlot <- function (transition_flow, box_txt = rownames(transition_flow), tot_spacing = 0.2, box_width = 1/4, fill_start_box = "darkgreen", txt_start_clr = "white", fill_end_box = "steelblue", txt_end_clr = "white", pt=20, min_lwd = 1, max_lwd = 6, lwd_prop_total = TRUE) { # Just for convenience no_boxes <- nrow(transition_flow) # Do some sanity checking of the variables if (tot_spacing < 0 || tot_spacing > 1) stop("Total spacing, the tot_spacing param,", " must be a fraction between 0-1,", " you provided ", tot_spacing) if (box_width < 0 || box_width > 1) stop("Box width, the box_width param,", " must be a fraction between 0-1,", " you provided ", box_width) # If the text element is a vector then that means that # the names are the same prior and after if (is.null(box_txt)) box_txt = matrix("", ncol=2, nrow=no_boxes) if (is.null(dim(box_txt)) && is.vector(box_txt)) if (length(box_txt) != no_boxes) stop("You have an invalid length of text description, the box_txt param,", " it should have the same length as the boxes, ", no_boxes, ",", " but you provided a length of ", length(box_txt)) else box_txt <- cbind(box_txt, box_txt) else if (nrow(box_txt) != no_boxes || ncol(box_txt) != 2) stop("Your box text matrix doesn't have the right dimension, ", no_boxes, " x 2, it has: ", paste(dim(box_txt), collapse=" x ")) # Make sure that the clrs correspond to the number of boxes fill_start_box <- rep(fill_start_box, length.out=no_boxes) txt_start_clr <- rep(txt_start_clr, length.out=no_boxes) fill_end_box <- rep(fill_end_box, length.out=no_boxes) txt_end_clr <- rep(txt_end_clr, length.out=no_boxes) if(nrow(transition_flow) != ncol(transition_flow)) stop("Invalid input array, the matrix is not square but ", nrow(transition_flow), " x ", ncol(transition_flow)) # Set the proportion of the start/end sizes of the boxes prop_start_sizes <- rowSums(transition_flow)/sum(transition_flow) prop_end_sizes <- colSums(transition_flow)/sum(transition_flow) if (sum(prop_end_sizes) == 0) stop("You can't have all empty boxes after the transition") getBoxPositions <- function (no, side){ empty_boxes <- ifelse(side == "left", sum(prop_start_sizes==0), sum(prop_end_sizes==0)) # Calculate basics space <- tot_spacing/(no_boxes-1-empty_boxes) # Do the y-axis ret <- list(height=(1-tot_spacing)*ifelse(side == "left", prop_start_sizes[no], prop_end_sizes[no])) if (no == 1){ ret$top <- 1 }else{ ret$top <- 1 - ifelse(side == "left", sum(prop_start_sizes[1:(no-1)]), sum(prop_end_sizes[1:(no-1)])) * (1-tot_spacing) - space*(no-1) } ret$bottom <- ret$top - ret$height ret$y <- mean(c(ret$top, ret$bottom)) ret$y_exit <- rep(ret$y, times=no_boxes) ret$y_entry_height <- ret$height/3 ret$y_entry <- seq(to=ret$y-ret$height/6, from=ret$y+ret$height/6, length.out=no_boxes) # Now the x-axis if (side == "right"){ ret$left <- 1-box_width ret$right <- 1 }else{ ret$left <- 0 ret$right <- box_width } txt_margin <- box_width/10 ret$txt_height <- ret$height - txt_margin*2 ret$txt_width <- box_width - txt_margin*2 ret$x <- mean(c(ret$left, ret$right)) return(ret) } plotBoxes <- function (no_boxes, width, txt, fill_start_clr, fill_end_clr, lwd=2, line_col="#000000") { plotBox <- function(bx, bx_txt, fill){ grid.roundrect(y=bx$y, x=bx$x, height=bx$height, width=width, gp = gpar(lwd=lwd, fill=fill, col=line_col)) if (bx_txt != ""){ grid.text(bx_txt,y=bx$y, x=bx$x, just="centre", gp=gpar(col=txt_start_clr, fontsize=pt)) } } for(i in 1:no_boxes){ if (prop_start_sizes[i] > 0){ bx_left <- getBoxPositions(i, "left") plotBox(bx=bx_left, bx_txt = txt[i, 1], fill=fill_start_clr[i]) } if (prop_end_sizes[i] > 0){ bx_right <- getBoxPositions(i, "right") plotBox(bx=bx_right, bx_txt = txt[i, 2], fill=fill_end_clr[i]) } } } # Do the plot require("grid") plot.new() vp1 <- viewport(x = 0.51, y = 0.49, height=.95, width=.95) pushViewport(vp1) shadow_clr <- rep(grey(.8), length.out=no_boxes) plotBoxes(no_boxes, box_width, txt = matrix("", nrow=no_boxes, ncol=2), # Don't print anything in the shadow boxes fill_start_clr = shadow_clr, fill_end_clr = shadow_clr, line_col=shadow_clr[1]) popViewport() vp1 <- viewport(x = 0.5, y = 0.5, height=.95, width=.95) pushViewport(vp1) plotBoxes(no_boxes, box_width, txt = box_txt, fill_start_clr = fill_start_box, fill_end_clr = fill_end_box) for (i in 1:no_boxes){ bx_left <- getBoxPositions(i, "left") for (flow in 1:no_boxes){ if (transition_flow[i,flow] > 0){ bx_right <- getBoxPositions(flow, "right") a_l <- (box_width/4) a_angle <- atan(bx_right$y_entry_height/(no_boxes+.5)/2/a_l)*180/pi if (lwd_prop_total) lwd <- min_lwd + (max_lwd-min_lwd)*transition_flow[i,flow]/max(transition_flow) else lwd <- min_lwd + (max_lwd-min_lwd)*transition_flow[i,flow]/max(transition_flow[i,]) # Need to adjust the end of the arrow as it otherwise overwrites part of the box # if it is thick right <- bx_right$left-.00075*lwd grid.bezier(x=c(bx_left$right, .5, .5, right), y=c(bx_left$y_exit[flow], bx_left$y_exit[flow], bx_right$y_entry[i], bx_right$y_entry[i]), gp=gpar(lwd=lwd, fill="black"), arrow=arrow(type="closed", angle=a_angle, length=unit(a_l, "npc"))) # TODO: A better option is probably bezierPoints } } } popViewport() } </code></pre> <p>And the example was generated with:</p> <pre><code># Settings no_boxes <- 3 # Generate test setting transition_matrix <- matrix(NA, nrow=no_boxes, ncol=no_boxes) transition_matrix[1,] <- 200*c(.5, .25, .25) transition_matrix[2,] <- 540*c(.75, .10, .15) transition_matrix[3,] <- 340*c(0, .2, .80) transitionPlot(transition_matrix, box_txt = c("First", "Second", "Third")) </code></pre> <p>I've also added this to my <a href="http://gforge.se/gmisc/" rel="noreferrer">Gmisc-package</a>. Enjoy!</p>
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1. CO@agstudy: See the new version of the plot. Now it's exactly the way I want it, almost like a graph pro :-D
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