README.md

ggdiagram

ggdiagram is a package to facilitate the creation of schematic diagrams commonly used to describe biological and engineering processes. By specifying the dimensions and attirubtes (color, line-type, size, etc) of shapes and which shapes to connect with arrows, highly customized diagrams can be created for inclusion in markdown reports, shiny apps, and to create compelling animations.

Installation

library(devtools)
install_github("mhismail/ggdiagram")

Features

The package is comprised of several functions to create shapes for rectangles, squares, circles, and ellipses. Arrows can be created to be straight or curved and their positions on the shapes can be specified. Some examples are given below.

Example 1

library(ggdiagram)

PD_comp <- gg_ellipse(label = "Response",radiusx = 20, radiusy = 15)
point1 <- gg_point(center = c(-40, 0))
point2 <- gg_point(center = c(40, 0))
stim_input <- gg_rect(center = c(-36, 12), 
                      height = 15, 
                      width = 5, 
                      label = "I", 
                      fill = "black",
                      label_color = "white")
inhib_input <-  gg_rect(center = c(-28, 12), 
                        height = 15, 
                        width = 5, 
                        label = "III", 
                        fill = "white",
                        label_color = "black")
stim_output <- gg_rect(center = c(26, 12), 
                      height = 15, 
                      width = 5, 
                      label = "II", 
                      fill = "black",
                      label_color = "white")
inhib_output <-  gg_rect(center = c(34, 12), 
                        height = 15, 
                        width = 5, 
                        label = "IV", 
                        fill = "white",
                        label_color = "black")
kin_label <- gg_point(center = c(-32, -4), label = expression(paste("k"["in"])))
kout_label <- gg_point(center = c(30, -4), label =  expression(paste("k"["out"])))

ggdiagram() + 
  PD_comp +
  gg_arrow(c(point1, PD_comp), 
           connection1 =  "near", 
           connection2 =  "l",
           shiftxend = -1) +
  gg_arrow(c(PD_comp, point2), 
           connection1 =  "r",
           shiftx= 1) +
  stim_input +
  inhib_input +
  stim_output +
  inhib_output +
  kin_label +
  kout_label

Example 2

The package can be paired with animation to make animated gifs.

library(ggdiagram)
library(animation)

 


clockani<- function () {
  a <- gg_circle(radius = 40, size = 2)
  b <- gg_point(center = c(0, 33), label = "12", label_size = 8)
  c <- gg_point(center = c(0, 33), label = "1", rotate = -30, 
                rotateabout = c(0, 0), label_size = 8)
  d <- gg_point(center=c(0, 33), label = "2", rotate = -60, 
                rotateabout = c(0, 0), label_size = 8)
  e <- gg_point(center = c(0, 33), label = "3", rotate = -90, 
                rotateabout = c(0, 0), label_size = 8)
  f <- gg_point(center = c(0, 33), label = "4", rotate = -120, 
                rotateabout = c(0, 0), label_size = 8)
  g <- gg_point(center = c(0, 33), label = "5", rotate = -150, 
                rotateabout = c(0, 0),label_size = 8)
  h <- gg_point(center = c(0, 33), label = "6", rotate = -180, 
                rotateabout = c(0, 0), label_size = 8)
  j <- gg_point(center = c(0, 33), label = "7", rotate = -210, 
                rotateabout = c(0, 0), label_size = 8)
  k <- gg_point(center = c(0, 33), label = "8", rotate = -240, 
                rotateabout = c(0, 0), label_size = 8)
  l <- gg_point(center = c(0, 33), label = "9", rotate = -270, 
                rotateabout = c(0, 0), label_size = 8)
  m <- gg_point(center = c(0, 33), label = "10", rotate = -300, 
                rotateabout = c(0, 0), label_size = 8)
  n <- gg_point(center = c(0, 33), label = "11", rotate = -330, 
                rotateabout = c(0, 0), label_size = 8)
  point1 <- gg_square(c(0, -5), sidelength = 10, color = "blue", fill = NA)
  
  for (i in 1:(2*60)){ 
    point2 <- gg_point(c(0, 27), rotate = -i * 6/12, rotateabout = c(0, 0))
    point3 <- gg_point(c(0, 20), rotate = -i * 6, rotateabout = c(0, 0))
    hours <- gg_arrow(c(point1, point2), "up")
    minutes <- gg_arrow(c(point1, point3), "up", color = "red")
    
    print(ggdiagram() + list(c(a, b, c, d, e, f, g, h, j, k, l, m, n)) + 
            hours + 
            minutes)
  } 
}

saveGIF(clockani(), 
        replace=T,
        movie.name = 'circle.gif', 
        ani.width = 600, 
        ani.height = 600, 
        interval=.1)

Example 3

The motivating factor behind creating this package was to illustrate the transfer of drug between body organs by way of animation. The graphics below are two such examples. The heights of the colored rectangles were scaled based on a physiologically-based pharmacokinetic model to create the effect of drug being transferred from compartment to compartment.

In the visual below, red is the parent drug and blue is metabolite.

Example 4

sun <- gg_circle(c(0, -10), radius = 30, fill = "gold", color = NA)
grass <- gg_rect(c(0, -30), height = 40, width = 100, color = "green2", fill = "green2")
grass1 <- gg_rect(c(0, -17.5), height = 5, width = 100, color = "green3", fill = "green3")
grass2 <- gg_rect(c(0, -27.5), height = 5, width = 100, color = "green3", fill = "green3")
grass3 <- gg_rect(c(0, -37.5), height = 5, width = 100, color = "green3", fill = "green3")
grass4 <- gg_rect(c(0, -47.5), height = 5, width = 100, color = "green3", fill = "green3")

sky <- gg_rect(c(0, 15), height = 70, width = 100, color = "blue", fill = "blue", alpha = .4)
cloud1 <- gg_ellipse(c(-30, 35), radiusx = 10, radiusy = 7, color = "white", fill = "white")
cloud2 <- gg_ellipse(c(30, 39), radiusx = 10, radiusy = 5, color = "white", fill = "white")
cloud3 <- gg_ellipse(c(-40, 15), radiusx = 10, radiusy = 5, color = "white", fill = "white")

ggdiagram() + 
  list(c(sky, sun, grass, cloud1, cloud2, cloud3, grass1, grass2, grass3, grass4))