A flowchart is a type of diagram that represents a workflow or
process. In research we often want to explain how we recruited our
patients, how many that were available from the start, how many that
were excluded and how many were left at the final analysis. The
**Gmisc** package provides a convenient set of functions
for doing this using the R’s built-in `grid`

package with
some bells and whistles. Below is a simple example that illustrates what
we’re aiming for.

```
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
```

There is a basic set of components that are used for generating flowcharts:

- Boxes, these are generated through the
`boxGrob`

and`boxPropGrob`

functions. - Arrows between boxes, these are generated through the
`connectGrob`

function.

These can be positioned directly or preferably manipulated according to the following principles:

- Spread - we want to use the full plot and either we position each
element or we automatically spread them in a vertical or horizontal
direction,
`spreadHorizontal`

and`spreadVertical`

functions. - Alignment of boxes - before or after spreading we may want to align
boxes:
`alignHorizontal`

and`alignVertical`

functions.

We can start with outputting a single box:

We can position and style this box as any element:

The `boxPropGrob`

is for displaying proportions as the
name indicates.

The boxes have coordinates that allow you to easily draw lines to and
from it. The coordinates are stored in the `coords`

attribute. Below is an illustration of the coordinates for the two
boxes:

```
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"))
```

In order to make connecting boxes with an arrow there is the
`connectGrob`

function. Here’s an example of how you can use
it for connecting a set of boxes:

```
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
```

We frequently want to align boxes in either a horizontal or a
vertical row. For this there are two functions,
`alignHorizontal()`

and `alignVertical()`

.

```
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")
```

Here are similar examples of vertical alignment:

```
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")
```

Similarly to alignment we often want to spread our boxes within a
space so that we use all the available space in the
`viewport`

. This can be done through the
`spreadHorizontal()`

and `spreadVertical()`

. You
can both spread the entire span or only between a subspan that is
defined using the `.to`

and `.from`

arguments.

```
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 spreading follows the same pattern:

```
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")
```

It is possible to use the R `expression`

or the
`bquote`

functions to produce bold or italics text, or even
formulas.

A few pointers on `expression`

…

- expressions with multiple elements should be combined using
`paste`

. E.g.`expression(paste(beta, "1"))`

would produce \(\beta1\) - the behavior of
`paste`

when used in expression is more like the normal behavior or`paste0`

(i.e. no separating space) - Greek letters can be entered outside of quotes by typing the name
e.g.
`expression(beta)`

will become \(\beta\) and`expression(Gamma)`

will become \(\Gamma\) (note the case, not all Greek letters are available in upper case) - superscripts are done via
`expression(x^2)`

and subscripts via`expression(x[2])`

```
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)
```

See the `plotmath`

help file for more details.

The `grid`

package is what makes R graphics great. All the
popular tools with awesome graphics use the `grid`

as the
back-end, e.g. `ggplot2`

and `lattice`

. When I
started working on the `forestplot`

package I first
encountered the `grid`

and it was instant love. In this
vignette I’ll show how you can use the flowchart-functions in this
package together with `grid`

in order to generate a
flowchart.

The grid package splits the plot into views. You can define a
`viewport`

and it will work as an isolated part of the plot,
ignorant of the world around it. You do this via
`viewport()`

, below I create a plot and add a rectangle to
it:

```
# 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()
```

Important to note is that the grid allows you to define precise units or relative units.

`npc`

- ranges from 0-1 where 1 is 100% of the`viewport`

width.`snpc`

- similar to`npc`

but is the same length in height/width.`lines`

- the height of a line. The go-to method if you want to know the height of a few lines of text. It’s relative to the`viewport`

’s`fontsize`

and`lineheight`

.`char`

- the`lines`

without the`lineheight`

part.

Below we draw a line with relative units in two nested viewports.
Note that the to lines are generated from the exact same
`grob`

object but appear different depending on the
`viewport`

they are in:

```
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()
```

`mm`

- probably my go-to unit when I want something absolute.`inch`

- if you prefer inches I guess this is the go-to choice.

Below we draw a line with absolute units in two nested
`viewports`

. Note that the lines have the exact same
length:

```
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()
```

If you find that your elements don’t look as expected make sure that
your not changing `viewport`

/device. While most coordinates
are relative some of them need to be fixed and therefore changing the
`viewport`

may impact where elements are rendered.