---
title: "Building a flowchart"
author: "Max Gordon"
date: "11 January 2026"
output:
  rmarkdown::html_vignette:
    toc: true
vignette: >
  %\VignetteIndexEntry{Building a flowchart}
  %\VignetteEncoding{UTF-8}
  %\usepackage[utf8]{inputenc}
  %\VignetteEngine{knitr::rmarkdown}
editor_options:
  chunk_output_type: console
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)

library(Gmisc, quietly = TRUE)
library(glue)
library(htmlTable)
library(grid)
```

# Flowchart

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.

```{r flowchart-example, fig.height = 7, fig.width = 8}
grid.newpage()
flowchart(source = glue("Stockholm population",
                        "n = {pop}",
                        pop = txtInt(1632798),
                        .sep = "\n"),
          eligible = glue("Eligible",
                          "n = {pop}",
                          pop = txtInt(10032),
                          .sep = "\n"),
          included = glue("Randomized",
                         "n = {incl}",
                         incl = txtInt(122),
                         .sep = "\n"),
          groups = list(
            glue("Treatment A",
                 "n = {recr}",
                 recr = txtInt(43),
                 .sep = "\n"),
            glue("Treatment B",
                 "n = {recr}",
                 recr = txtInt(122 - 43 - 30),
                 .sep = "\n")
          )) |>
  spread(axis = "y") |>
  spread(subelement = "groups", axis = "x") |>
  insert(list(excluded = boxHeaderGrob(header = glue("Excluded (n = {tot}):", tot = 30),
                          body = glue(" - not interested: {uninterested}",
                                      " - contra-indicated: {contra}",
                                      uninterested = 12,
                                      contra = 30 - 12,
                                      .sep = "\n"),
                          bjust = "left",
                          header_gp = getOption("boxGrobTxt", default = gpar(
                            color = "black",
                            cex = 1
                          )))),
         after = "eligible",
         name = "excluded") |>
  move(name = "excluded", x = .8) |>
  connect("source", "eligible", type = "vert") |>
  connect("eligible", "included", type = "vert") |>
  connect("included", "groups", type = "N") |>
  connect("eligible", "excluded", type = "L", label = "Excluded")
```

# Basic components explained

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.

# A basic box

We can start with outputting a single box:

```{r 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)
```

We can position and style this box as any element:

```{r 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"))
```

# A box with proportiions

The `boxPropGrob` is for displaying proportions as the name indicates.

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

# The box coordinates

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:

```{r, 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"))
```

# Additional box shapes

You can create alternate box shapes by passing a custom `box_fn` to `boxGrob`,
or use the convenience helpers `boxDiamondGrob()`, `boxEllipseGrob()` and
`boxRackGrob()` that ship with the package.

```{r extra_shapes, fig.height = 3, fig.width = 6}
# --- Branch labels + sharp diamond variant ---
grid.newpage()

# rounded and sharp diamond examples
d_rounded <- boxDiamondGrob("Decision", box_gp = gpar(fill = "#FFF4E6"))
d_sharp   <- boxDiamondGrob("Decision\n(sharp)", rounded = FALSE, box_gp = gpar(fill = "#FFF4E6"))

# outcomes
e <- boxEllipseGrob("Local", box_gp = gpar(fill = "#E6FFF4"))
r <- boxServerGrob("Server", box_gp = gpar(fill = "#E8F0FF"))

# arrange and draw
boxes <- list(decision = d_rounded, outcomes = list(e, r)) |>
  spreadHorizontal(from = unit(.1, "npc"), to = unit(.9, "npc"), subelement = "outcomes") |>
  spreadVertical() |>
  print()

# 1) quick many-to-many style connector (no labels)
con <- connectGrob(boxes$decision, boxes$outcomes, type = "N")
print(con)

# 2) explicit per-branch connectors with labels (preferred when you want text)
connectGrob(boxes$decision, boxes$outcomes[[1]], type = "N", label = "Local") |> print()
connectGrob(boxes$decision, boxes$outcomes[[2]], type = "N", label = "Server") |> print()

# 3) If you prefer the single connector and want labels on each branch:
#    place text at the midpoint of each returned grob (example)
con_list <- connectGrob(boxes$decision, boxes$outcomes, type = "N")
# Preferred: attach labels and let `print()` handle rendering
con_list <- setConnectorLabels(con_list, c("Local", "Server"))
print(con_list)
```

# Standard flowchart shapes

Below are a few commonly-used flowchart shapes demonstrating their typical
appearance and usage.

```{r standard_shapes, fig.height = 3.5, fig.width = 8}
# Arrange shapes in three rows for better readability
# 1) Grid-based objects (basic boxGrob / boxPropGrob / rect)
row1 <- list(
  boxGrob("Box (default)", box_gp = gpar(fill = "#EFEFEF"), y = unit(.85, "npc")),
  boxPropGrob("Prop", "Left", "Right", prop = .4, box_left_gp = gpar(fill = "#EFEFAF"), box_right_gp = gpar(fill = "#EFAFEF"), y = unit(.85, "npc")),
  boxGrob("Rectangle", box_fn = rectGrob, box_gp = gpar(fill = "#EFEFEF"), y = unit(.85, "npc"))
)

# 2) Gmisc row 1 (rounded/sharp diamond + ellipse + rack + server)
row2 <- list(
  boxDiamondGrob("Diamond\n(rounded)", box_gp = gpar(fill = "#FFF4E6"), y = unit(.55, "npc")),
  boxDiamondGrob("Diamond\n(sharp)", rounded = FALSE, box_gp = gpar(fill = "#FFF4E6"), y = unit(.55, "npc")),
  boxEllipseGrob("Ellipse", box_gp = gpar(fill = "#E6FFF4"), y = unit(.55, "npc")),
  boxRackGrob("Rack", box_gp = gpar(fill = "#E8F0FF"), y = unit(.55, "npc")),
  boxServerGrob("Server", box_gp = gpar(fill = "#E8F0FF"), y = unit(.55, "npc"))
)

# 3) Gmisc row 2 (database, document, documents, tape)
row3 <- list(
  boxDatabaseGrob("Database", box_gp = gpar(fill = "#DFF4E6"), y = unit(.25, "npc")),
  boxDocumentGrob("Document", box_gp = gpar(fill = "#FFF6E6"), y = unit(.25, "npc")),
  boxDocumentsGrob("Documents", box_gp = gpar(fill = "#FFF6E6"), y = unit(.25, "npc")),
  boxTapeGrob("Tape", box_gp = gpar(fill = "#E6F0FF"), y = unit(.25, "npc"))
)

# Spread each row across the horizontal span
spreadHorizontal(row1, from = unit(.05, "npc"), to = unit(.95, "npc"))
spreadHorizontal(row2, from = unit(.05, "npc"), to = unit(.95, "npc"))
spreadHorizontal(row3, from = unit(.05, "npc"), to = unit(.95, "npc"))
```

# Connecting the boxes

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:

```{r "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
```

`connectGrob()` also supports connecting one box to many boxes, or many boxes to one box.
For merging many boxes into one, `type = "fan_in_top"` distributes the attachment points evenly along the top edge of the destination box, with an optional margin.

```{r connect_multi, fig.width = 4, fig.height = 4}
grid.newpage()

# Three upstream boxes + one side box
a_boxes <- paste("A", 1:3) |>
  lapply(\(x) boxGrob(x, box_gp = gpar(fill = "#E6F2FF"))) |>
  spreadHorizontal(from = unit(.1, "npc"), to = unit(1, "npc") - unit(1, "cm")) |>
  alignVertical(position="top",
                reference = unit(1, "npc")) |>
  print()

b_side <- boxGrob("B",  y = .70, box_gp = gpar(fill = "#FFF3BF")) |>
  moveBox(x = unit(1, "npc"),
          just = 1) |>
  print()

# Target box
c <- boxGrob("C", x = .50, box_gp = gpar(fill = "#D3F9D8"), width = unit(4, "cm")) |>
  moveBox(y = unit(0, "npc"),
          just = "bottom") |>
  print()


# Many -> one: merge on top with evenly distributed attachment points + margin
connectGrob(c(a_boxes, list(b_side)), c,
            type = "fan_in_top",
            margin = 4)
```

# Alignment

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

```{r 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")
```

Here are similar examples of vertical alignment:

```{r 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")
```

# Spreading

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.

Numeric `.from`, `.to`, and `.margin` values are interpreted as proportions of the current viewport (`npc`).
If only one of `.from` or `.to` is specified, the other defaults to the full span (`0 npc` or `1 npc`).
The `.margin` argument adds padding at both ends of the span (also when using `.from`/`.to`).

```{r horizontal_spread, fig.width = 11, fig.height = 8}
b1 <- boxGrob("B1", y = .85, x = .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, y_top) {
  grid.text(txt,
            x = unit(2, "mm"),
            y = y_top + unit(2, "mm"),
            just = c("left", "bottom"))
  grid.lines(y = y_top + unit(1, "mm"),
             gp = gpar(col = "grey"))
}

drawRow <- function(label, row_y, spread_args = list()) {
  row <- alignVertical(reference = row_y, b1, b2, b3, b4, position = "top")
  txtOut(label, coords(row[[1]])$top)
  do.call(spreadHorizontal, c(list(row), spread_args))
}

rowYs <- unit(c(.93, .76, .59, .42, .25, .12), "npc")

grid.newpage()

drawRow("Basic (viewport)", rowYs[1])
drawRow("From–to + margin (numeric = npc)", rowYs[2],
        spread_args = list(from = .2, to = .7, margin = .05))
drawRow("Only to (defaults from = 0)", rowYs[3],
        spread_args = list(to = .7))
drawRow("Only from (defaults to = 1)", rowYs[4],
        spread_args = list(from = .2))

# Row 5: Between boxes (box-to-box span)
row5_y <- rowYs[5]
row5 <- alignVertical(reference = row5_y, b1, b2, b3, b4, position = "top")
txtOut("Between boxes", coords(row5[[1]])$top)

span <- alignVertical(reference = row5_y, from  = from, to = to, position = "top")
span
spreadHorizontal(row5, .from = span$from, .to = span$to)

# Row 6: Reverse box order + center distribution
row6_y <- unit(.10, "npc")

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

row6 <- alignVertical(reference = bottom_from, b1, b2, b3, b4, position = "bottom")
txtOut("Reverse box order + center", coords(row6[[4]])$top)

spreadHorizontal(row6,
                 from = bottom_from,
                 to = bottom_to,
                 type = "center")


```

Vertical spreading follows the same pattern:

```{r 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")
```

# Complex nested flowcharts with boxHeaderGrob

The `boxHeaderGrob()` function creates boxes with centered headers and left-justified body text, perfect for flowcharts with structured information like timelines or protocols. Here's an example of a randomized trial flowchart with shared criteria and two treatment arms:

```{r complex_nested, fig.width = 7, fig.height = 8}
# Helper function to convert nested structure to grobs
make_boxes <- function(x) {
  if (is.list(x) && !inherits(x, "box_header")) {
    return(lapply(x, make_boxes))
  }

  if (inherits(x, "box_header")) {
    return(do.call(boxHeaderGrob, x))
  }

  # Simple text box fallback
  args <- attr(x, "args")
  if (is.null(args)) return(boxGrob(label = x))

  args$label <- x
  do.call(boxGrob, args)
}

# Define styling for different elements
arm_a_style <- list(
  header = gpar(fill = "#E8F5E9", col = "#2E7D32", lwd = 1.4),
  box = gpar(fill = "#F1F8E9", col = "#43A047")
)

arm_b_style <- list(
  header = gpar(fill = "#FFF8E1", col = "#EF6C00", lwd = 1.4),
  box = gpar(fill = "#FFFDE7", col = "#F9A825")
)

# Build flowchart structure
flowchart <- list(
  # Shared inclusion criteria
  criteria = structure(
    list(
      header = "Inclusion Criteria",
      body = paste(
        "• Adults aged 18-65",
        "• Confirmed diagnosis",
        "• Written informed consent",
        "• No contraindications",
        "• Available for 6-month follow-up",
        sep = "\n"
      ),
      box_gp = gpar(fill = "#E3F2FD", col = "#1E88E5", lwd = 1.4),
      body_gp = gpar(fontsize = 10)
    ),
    class = "box_header"
  ),

  # Two treatment arms
  arms = list(
    arm_a = list(
      # Arm header
      structure("Intensive Protocol", args = list(
        box_gp = arm_a_style$header,
        txt_gp = gpar(fontsize = 11, fontface = "bold")
      )),

      # Timeline boxes
      structure(list(
        header = "Week 0-1",
        body = "• Daily sessions\n• Supervised therapy\n",
        box_gp = arm_a_style$box,
        body_gp = gpar(fontsize = 9.5)
      ), class = "box_header"),

      structure(list(
        header = "Week 2-4",
        body = "• 3× weekly sessions\n• Progressive loading",
        box_gp = arm_a_style$box,
        body_gp = gpar(fontsize = 9.5)
      ), class = "box_header"),

      structure(list(
        header = "Week 5-8",
        body = "• Home program\n• Monthly check-ins\n• Return to activity",
        box_gp = arm_a_style$box,
        body_gp = gpar(fontsize = 9.5)
      ), class = "box_header")
    ),

    arm_b = list(
      # Arm header
      structure("Standard Care", args = list(
        box_gp = arm_b_style$header,
        txt_gp = gpar(fontsize = 11, fontface = "bold")
      )),

      # Timeline boxes - different schedule
      structure(list(
        header = "Month 0",
        body = "• Initial consultation\n• Exercise booklet",
        box_gp = arm_b_style$box,
        body_gp = gpar(fontsize = 9.5)
      ), class = "box_header"),

      structure(list(
        header = "Month 3",
        body = "• Follow-up visit\n• Progress review",
        box_gp = arm_b_style$box,
        body_gp = gpar(fontsize = 9.5)
      ), class = "box_header"),

      structure(list(
        header = "Month 6",
        body = "• Final assessment\n• Discharge planning",
        box_gp = arm_b_style$box,
        body_gp = gpar(fontsize = 9.5)
      ), class = "box_header")
    )
  )
)

# Convert to grobs and layout
grid.newpage()
boxes <- flowchart |>
  make_boxes() |>
  spreadVertical() |>
  spreadHorizontal(subelement = "arms", from = 0.15, to = 0.85) |>
  spreadVertical(subelement = c("arms", "arm_a"), from = 0.65) |>
  spreadVertical(subelement = c("arms", "arm_b"), from = 0.65) |>
  print()

# Connect criteria to both arms
connectGrob(boxes$criteria, boxes$arms, type = "N")

# Connect timeline within each arm
for (arm_name in names(boxes$arms)) {
  arm_boxes <- boxes$arms[[arm_name]]
  for (i in 2:length(arm_boxes)) {
    connectGrob(arm_boxes[[i-1]], arm_boxes[[i]], type = "v") |> print()
  }
}
```

# The S3 Layout API

The package provides a pipelined API where you can construct your flowchart as a single object (a list of boxes with connection attributes) and then print/plot it. This reduces the need for manual loops and `print()` calls for connectors.

```{r s3_api_example, fig.height=8, fig.width=6, eval=FALSE}
grid.newpage()

# Define the nodes
b1 <- boxGrob("Start", y = 0.8)
b2 <- boxGrob("Process", y = 0.5)
b3 <- boxGrob("End", y = 0.2)

# Pipeline: list -> align -> connect -> print
list(start = b1, process = b2, end = b3) |>
  align(axis = "y") |>
  spread(axis = "x") |>
  connect("start", "process", type = "horizontal") |>
  connect("process", "end", type = "horizontal") |>
  print()
```

# Math expressions in boxes

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])`

```{r math_expressions, fig.width=6, fig.height=3}
grid.newpage()
###############
# Expressions #
###############
# Font style
list(expression(bold("Bold text")),
     expression(italic("Italics text")),
     expression(paste("Mixed: ", italic("Italics"), " and ", bold("bold")))) |>
  lapply(boxGrob) |>
  alignVertical(reference = unit(1, "npc"),
                position = "top") |>
  spreadHorizontal()

# Math
list(expression(paste("y = ", beta[0], " + ", beta[1], X[1], " + ", beta[2], X[2]^2)),
     expression(paste(hat(mu) == sum(frac(x[i], n), i == 1, n))),
     expression(paste(int(a, b, f(x) * dx) == F(b) - F(a)))) |>
  lapply(boxGrob) |>
  alignVertical(reference = unit(0.5, "npc"),
                position = "center") |>
  spreadHorizontal()

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

See the `plotmath` help file for more details.

# Grid & some background info

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.

## Basics

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:

```{r 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()
```

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

## 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:

```{r 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 units

- `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:

```{r 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()
```

# A complex example

Here is a more complex example demonstrating the power of the grid-based flowcharts. This example uses `flowchart`, `spread`, `align` and `connect` functions to create a detailed clinical study flowchart.

```{r complex_example, fig.height = 9, fig.width = 9}
# Define the boxes
org_cohort <- glue("Proximal humerus fracture",
                   "  - \u2265 18 years",
                   "  - \u2264 4 weeks of trauma",
                   "  - Not pathological",
                   .sep = "\n") |>
  boxGrob(just = "left",
          box_gp = gpar(fill = "#E3F2FD"))

surgery <- glue("Surgery",
                "  - Direct (\u2248 4%)",
                "  - Delayed (\u2248 4%)",
                .sep = "\n") |>
  boxGrob(just = "left",
          box_gp = gpar(fill = "#F8BBD0"))

randomize <- boxGrob("Non-surgical\nRandomise",
                     box_gp = gpar(fill = "#FFF3E0"))

treatments <- list(early = boxGrob("Early rehab",
                                   box_gp = gpar(fill = "#DCEDC8")),
                   late = boxGrob("Late rehab",
                                  box_gp = gpar(fill = "#DCEDC8")),
                   obs = boxGrob("Observation",
                                 box_gp = gpar(fill = "#E0E0E0")))

early_followup <- glue("Early follow-up",
                       "  - 2 weeks [PNRS]",
                       "  - 4 weeks [PNRS]",
                       .sep = "\n") |>
  boxGrob(just = "left",
          box_gp = gpar(fill = "#E0F7FA"))

late_followup <- glue("Late follow-up",
                      "  - 2-10 months (random) [OSS, PNRS]",
                      "  - 1 year [OSS, PNRS, accelerometer]",
                      "  - 2 years [OSS, PNRS]",
                      "  - 5 years [OSS, PNRS]",
                      .sep = "\n") |>
  boxGrob(just = "left",
                       box_gp = gpar(fill = "#E0F7FA"))

# Create the flowchart
grid.newpage()
flowchart(start = org_cohort,
          step_1 = list(surgery = surgery,
                        `non-surgical` = randomize),
          treatment = treatments,
          early_followup = early_followup,
          followup = late_followup) |>
  spread(axis = "y") |>
  spread(axis = "x", subelement = "step_1") |>
  spread(axis = "x", subelement = "treatment", from = 0.35) |>
  align(axis = "x",
        reference = c("treatment", "late"),
        subelement = c("step_1", "non-surgical")) |>
  connect(from = "start", to = "step_1", type = "N") |>
  connect(from = "step_1$non-surgical", to = "treatment", type = "N") |>
  connect(from = "treatment", to = "early_followup", type = "fan_in_center") |>
  connect(from = "early_followup", to = "followup", type = "v") |>
  connect(from = "early_followup", to = "step_1$surgery", type = "Z",
          label = "Crossover\nto surgery") |>
  connect(from = "step_1$surgery", to = "followup", type = "L") |>
  print()
```

# Tips for debugging

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.
