inst/doc/Grid-based_flowcharts.R

In Gmisc: Descriptive Statistics, Transition Plots, and More

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)

## ---- fig.height = 7, fig.width = 6-------------------------------------------
library(Gmisc, quietly = TRUE)
library(glue)
library(htmlTable)
library(grid)
library(magrittr)

org_cohort <- boxGrob(glue("Stockholm population",
                           "n = {pop}",
                           pop = txtInt(1632798),
                           .sep = "\n"))
eligible <- boxGrob(glue("Eligible",
                          "n = {pop}",
                           pop = txtInt(10032),
                           .sep = "\n"))
included <- boxGrob(glue("Randomized",
                         "n = {incl}",
                         incl = txtInt(122),
                         .sep = "\n"))
grp_a <- boxGrob(glue("Treatment A",
                      "n = {recr}",
                      recr = txtInt(43),
                      .sep = "\n"))

grp_b <- boxGrob(glue("Treatment B",
                      "n = {recr}",
                      recr = txtInt(122 - 43 - 30),
                      .sep = "\n"))

excluded <- boxGrob(glue("Excluded (n = {tot}):",
                         " - not interested: {uninterested}",
                         " - contra-indicated: {contra}",
                         tot = 30,
                         uninterested = 12,
                         contra = 30 - 12,
                         .sep = "\n"),
                    just = "left")

grid.newpage()
vert <- spreadVertical(org_cohort,
                       eligible = eligible,
                       included = included,
                       grps = grp_a)
grps <- alignVertical(reference = vert$grps,
                      grp_a, grp_b) %>%
  spreadHorizontal()
vert$grps <- NULL

excluded <- moveBox(excluded,
                    x = .8,
                    y = coords(vert$included)$top + distance(vert$eligible, vert$included, half = TRUE, center = FALSE))

for (i in 1:(length(vert) - 1)) {
  connectGrob(vert[[i]], vert[[i + 1]], type = "vert") %>%
    print
}
connectGrob(vert$included, grps[[1]], type = "N")
connectGrob(vert$included, grps[[2]], type = "N")

connectGrob(vert$eligible, excluded, type = "L")

# Print boxes
vert
grps
excluded

## ----basic_box, fig.height = 1.5, fig.width = 3, message = FALSE--------------
grid.newpage()
txt <-
"Just a plain box
with some text
- Note that newline is OK"
boxGrob(txt)

## ----styled_box, fig.height = 3, fig.width = 3--------------------------------
grid.newpage()
boxGrob("A large\noffset\nyellow\nbox",
        width = .8, height = .8,
        x = 0, y = 0,
        bjust = c("left", "bottom"),
        txt_gp = gpar(col = "darkblue", cex = 2),
        box_gp = gpar(fill = "lightyellow", col = "darkblue"))

## ----prop_box, fig.height = 2, fig.width = 4----------------------------------
grid.newpage()
boxPropGrob("A box with proportions",
            "Left side", "Right side",
            prop = .7)

## ---- fig.height = 3, fig.width = 4-------------------------------------------
grid.newpage()
smpl_bx <- boxGrob(
  label = "A simple box",
  x = .5,
  y = .9,
  just = "center")

prop_bx <- boxPropGrob(
  label = "A split box",
  label_left = "Left side",
  label_right = "Right side",
  x = .5,
  y = .3,
  prop = .3,
  just = "center")

plot(smpl_bx)
plot(prop_bx)

smpl_bx_coords <- coords(smpl_bx)
grid.circle(y = smpl_bx_coords$y,
            x = smpl_bx_coords$x,
            r = unit(2, "mm"),
            gp = gpar(fill = "#FFFFFF99", col = "black"))
grid.circle(y = smpl_bx_coords$bottom,
            x = smpl_bx_coords$right,
            r = unit(1, "mm"),
            gp = gpar(fill = "red"))
grid.circle(y = smpl_bx_coords$top,
            x = smpl_bx_coords$right,
            r = unit(1, "mm"),
            gp = gpar(fill = "purple"))
grid.circle(y = smpl_bx_coords$bottom,
            x = smpl_bx_coords$left,
            r = unit(1, "mm"),
            gp = gpar(fill = "blue"))
grid.circle(y = smpl_bx_coords$top,
            x = smpl_bx_coords$left,
            r = unit(1, "mm"),
            gp = gpar(fill = "orange"))

prop_bx_coords <- coords(prop_bx)
grid.circle(y = prop_bx_coords$y,
            x = prop_bx_coords$x,
            r = unit(2, "mm"),
            gp = gpar(fill = "#FFFFFF99", col = "black"))
grid.circle(y = prop_bx_coords$bottom,
            x = prop_bx_coords$right_x,
            r = unit(1, "mm"),
            gp = gpar(fill = "red"))
grid.circle(y = prop_bx_coords$top,
            x = prop_bx_coords$right_x,
            r = unit(1, "mm"),
            gp = gpar(fill = "purple"))
grid.circle(y = prop_bx_coords$bottom,
            x = prop_bx_coords$left_x,
            r = unit(1, "mm"),
            gp = gpar(fill = "blue"))
grid.circle(y = prop_bx_coords$top,
            x = prop_bx_coords$left_x,
            r = unit(1, "mm"),
            gp = gpar(fill = "orange"))

grid.circle(y = prop_bx_coords$bottom,
            x = prop_bx_coords$right,
            r = unit(2, "mm"),
            gp = gpar(fill = "red"))
grid.circle(y = prop_bx_coords$top,
            x = prop_bx_coords$right,
            r = unit(2, "mm"),
            gp = gpar(fill = "purple"))
grid.circle(y = prop_bx_coords$bottom,
            x = prop_bx_coords$left,
            r = unit(2, "mm"),
            gp = gpar(fill = "blue"))
grid.circle(y = prop_bx_coords$top,
            x = prop_bx_coords$left,
            r = unit(2, "mm"),
            gp = gpar(fill = "orange"))

## ----"Connected boxes", fig.width = 7, fig.height = 5-------------------------
grid.newpage()
# Initiate the boxes that we want to connect
side <- boxPropGrob("Side", "Left", "Right",
                    prop = .3,
                    x = 0, y = .9,
                    bjust = c(0,1))
start <- boxGrob("Top",
                 x = .6, y = coords(side)$y,
                 box_gp = gpar(fill = "yellow"))
bottom <- boxGrob("Bottom",
                  x = .6, y = 0,
                  bjust = "bottom")


sub_side_left <- boxGrob("Left",
                         x = coords(side)$left_x,
                         y = 0,
                         bjust = "bottom")
sub_side_right <- boxGrob("Right",
                          x = coords(side)$right_x,
                          y = 0,
                          bjust = "bottom")

odd <- boxGrob("Odd\nbox",
               x = coords(side)$right,
               y = .5)

odd2 <- boxGrob("Also odd",
               x = coords(odd)$right +
                 distance(bottom, odd, type = "h", half = TRUE) -
                 unit(2, "mm"),
               y = 0,
               bjust = c(1,0))

exclude <- boxGrob("Exclude:\n - Too sick\n - Prev. surgery",
                   x = 1,
                   y = coords(bottom)$top +
                     distance(start, bottom, type = "v", half = TRUE),
                   just = "left", bjust = "right")

# Connect the boxes and print/plot them
connectGrob(start, bottom, "vertical")
connectGrob(start, side, "horizontal")
connectGrob(bottom, odd, "Z", "l")
connectGrob(odd, odd2, "N", "l")
connectGrob(side, sub_side_left, "v", "l")
connectGrob(side, sub_side_right, "v", "r")
connectGrob(start, exclude, "-",
            lty_gp = gpar(lwd = 2, col = "darkred", fill = "darkred"))

# Print the grobs
start
bottom
side
exclude
sub_side_left
sub_side_right
odd
odd2

## ----horizontal_alignment, fig.width=10, fig.height=6-------------------------
align_1 <- boxGrob("Align 1",
                   y = .9,
                   x = 0,
                   bjust = c(0),
                   box_gp = gpar(fill = "#E6E8EF"))

align_2 <- boxPropGrob("Align 2",
                       "Placebo",
                       "Treatment",
                       prop = .7,
                       y = .8,
                       x = .5)

align_3 <- boxGrob("Align 3\nvertical\ntext",
                   y = 1,
                   x = 1,
                   bjust = c(1, 1),
                   box_gp = gpar(fill = "#E6E8EF"))

b1 <- boxGrob("B1",
              y = .3,
              x = .1,
              bjust = c(0))
b2 <- boxGrob("B2 with long\ndescription",
              y = .6,
              x = .5)
b3 <- boxGrob("B3",
              y = .2,
              x = .8,
              bjust = c(0, 1))

grid.newpage()
align_1
alignHorizontal(reference = align_1,
                b1, b2, b3,
                .position = "left")

align_2
alignHorizontal(reference = align_2,
                b1, b2, b3,
                .position = "center",
                .sub_position = "left")
alignHorizontal(reference = align_2,
                b1, b2, b3,
                .position = "left",
                .sub_position = "right")

align_3
alignHorizontal(reference = align_3,
                b1, b2, b3,
                .position = "right")

## ----vertical_alignment, fig.width=10, fig.height=6---------------------------
align_1 <- boxGrob("Align 1\nvertical\ntext",
                   y = 1,
                   x = 1,
                   bjust = c(1, 1),
                   box_gp = gpar(fill = "#E6E8EF"))

align_2 <- boxPropGrob("Align 2",
                       "Placebo",
                       "Treatment",
                       prop = .7,
                       y = .5,
                       x = .6)

align_3 <- boxGrob("Align 3",
                   y = 0,
                   x = 0,
                   bjust = c(0, 0),
                   box_gp = gpar(fill = "#E6E8EF"))


b1 <- boxGrob("B1",
              y = .3,
              x = 0.1,
              bjust = c(0, 0))
b2 <- boxGrob("B2 with long\ndescription",
              y = .6,
              x = .3)
b3 <- boxGrob("B3",
              y = .2,
              x = .85,
              bjust = c(0, 1))

grid.newpage()
align_1
alignVertical(reference = align_1,
              b1, b2, b3,
              .position = "top")

align_2
alignVertical(reference = align_2,
              b1, b2, b3,
              .position = "center")

align_3
alignVertical(reference = align_3,
              b1, b2, b3,
              .position = "bottom")

## ----horizontal_spread, fig.width=11, fig.height=6----------------------------
b1 <- boxGrob("B1",
              y = .85,
              x = 0.1,
              bjust = c(0, 0))
b2 <- boxGrob("B2",
              y = .65,
              x = .6)
b3 <- boxGrob("B3",
              y = .45,
              x = .6)
b4 <- boxGrob("B4 with long\ndescription",
              y = .7,
              x = .8)

from <- boxGrob("from",
                y = .25,
                x = .05,
                box_gp = gpar(fill = "darkgreen"),
                txt_gp = gpar(col = "white"))
to <- boxGrob("to this wide box",
              y = coords(from)$y,
              x = .95,
              bjust = "right",
              box_gp = gpar(fill = "darkred"),
              txt_gp = gpar(col = "white"))


txtOut <- function(txt, refBx) {
  grid.text(txt, 
            x = unit(2, "mm"), 
            y = coords(refBx)$top + unit(2, "mm"), 
            just = c("left", "bottom"))
  grid.lines(y = coords(refBx)$top + unit(1, "mm"),
             gp = gpar(col = "grey"))
}
grid.newpage()
txtOut("Basic", b1)
alignVertical(reference = b1, 
              b1, b2, b3, b4,
              .position = "top") %>% 
  spreadHorizontal()

txtOut("From-to", b2)
alignVertical(reference = b2, 
              b1, b2, b3, b4,
              .position = "top") %>% 
  spreadHorizontal(.from = .2,
                   .to = .7)

txtOut("From-to with center and reverse the box order", b3)
alignVertical(reference = b3, 
              b1, b2, b3, b4,
              .position = "top") %>% 
  spreadHorizontal(.from = .7,
                   .to = .2,
                   .type = "center")

txtOut("Between boxes", from)
from
to
alignVertical(reference = from, 
              b1, b2, b3, b4,
              .position = "top") %>% 
  spreadHorizontal(.from = from,
                   .to = to)

# Now we switch the order and set the type to center the distance between the boxes
bottom_from <- moveBox(from, x = coords(to)$right, y = 0, just = c(1, 0))
bottom_to <- moveBox(to, x = coords(from)$left, y = 0, just = c(0, 0))
bottom_from
bottom_to
alignVertical(reference = bottom_from, 
              b1, b2, b3, b4,
              .position = "bottom") %>% 
  spreadHorizontal(.from = bottom_from,
                   .to = bottom_to,
                   .type = "center")

## ----vertical_spread, fig.width=6, fig.height=6-------------------------------
b1 <- boxGrob("B1",
              y = .8,
              x = 0.1,
              bjust = c(0, 0))
b2 <- boxGrob("B2 with long\ndescription",
              y = .5,
              x = .5)
b3 <- boxGrob("B3",
              y = .2,
              x = .8)
b4 <- boxGrob("B4",
              y = .7,
              x = .8)


txtOut <- function(txt, refBx) {
  grid.text(txt, 
            x = coords(refBx)$left - unit(2, "mm"), 
            y = .5, 
            just = c("center", "bottom"),
            rot = 90)
  grid.lines(x = coords(refBx)$left - unit(1, "mm"),
             gp = gpar(col = "grey"))
}

grid.newpage()
txtOut("Basic", b1)
alignHorizontal(reference = b1, 
                b1, b2, b3, b4,
                .position = "left") %>% 
  spreadVertical()

txtOut("From-to", b2)
alignHorizontal(reference = b2, 
                b1, b2, b3, b4,
                .position = "left") %>% 
  spreadVertical(.from = .2,
                 .to = .7)

txtOut("From-to with center and reverse the box order", b3)
alignHorizontal(reference = b3, 
                b1, b2, b3, b4,
                .position = "left") %>% 
  spreadVertical(.from = .7,
                 .to = .2,
                 .type = "center")

## ----math_expressions, fig.width=6, fig.height=3------------------------------
grid.newpage()
###############
# Expressions #
###############
# Font style
alignVertical(
  reference = 1,
  .position = "top",
  boxGrob(expression(bold("Bold text"))),
  boxGrob(expression(italic("Italics text"))),
  boxGrob(expression(paste("Mixed: ", italic("Italics"), " and ", bold("bold"))))) %>% 
  spreadHorizontal

# Math
alignVertical(
  reference = .5,
  boxGrob(expression(paste("y = ", beta[0], " + ", beta[1], X[1], " + ", beta[2], X[2]^2))),
  boxGrob(expression(sum(n, i == 1, x) %subset% " \u211D")),
  boxGrob(expression(beta ~~ gamma ~~ Gamma))) %>% 
  spreadHorizontal

##########
# Quotes #
##########
a = 5
alignVertical(
  reference = 0,
  .position = "bottom",
  bquote(alpha == theta[1] * .(a) + ldots) %>% boxGrob,
  paste("argument", sQuote("x"), "\nmust be non-zero") %>% boxGrob) %>% 
  spreadHorizontal(.from = .2, .to = .8)

## ----basic_plot, fig.height = 2, fig.width = 2--------------------------------
# Load the grid library
# part of standard R libraries so no need installing
library(grid)

# Create a new graph
grid.newpage()

pushViewport(viewport(width = .5, height = .8))

grid.rect(gp = gpar(fill = "#D8F0D1"))

popViewport()

## ----relative_lines, fig.height = 3, fig.width = 3----------------------------
grid.newpage()
pushViewport(viewport(width = .5, height = .8, clip = "on"))
grid.rect(gp = gpar(lty = 2, fill = "lightyellow"))
lg <- linesGrob(x = unit(c(.2, 1), "npc"),
                y = unit(c(.2, 1), "npc"),
                gp = gpar(lwd = 2))
grid.draw(lg)
pushViewport(viewport(x = 0, y = .6, just = "left", width = .4, height = .4, angle = 20))
grid.rect(gp = gpar(fill = "lightblue")) # A translucent box to indicate the new viewport
grid.draw(lg)
popViewport()

## ----absolute_lines, fig.height = 3, fig.width = 3----------------------------
grid.newpage()
pushViewport(viewport(width = .5, height = .8, clip = "on"))
grid.rect(gp = gpar(lty = 2, fill = "lightyellow"))
lg <- linesGrob(x = unit(c(2, 10), "mm"),
                y = unit(c(2, 10), "mm"),
                gp = gpar(lwd = 2))
grid.draw(lg)
pushViewport(viewport(x = 0, y = .6, just = "left", width = .4, height = .4, angle = 20))
grid.rect(gp = gpar(fill = "lightblue")) # A translucent box to indicate the new viewport
grid.draw(lg)
popViewport()