---
title: "Building a flowchart"
author: "Max Gordon"
date: "`r Sys.Date()`"
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}
# Shared styling
main_box_gp <- gpar(fill = "#ddeeff", col = "#336699", lwd = 1.5)
group_box_gp <- gpar(fill = "#e8f4e8", col = "#2e7d32", lwd = 1.5)
excl_box_gp  <- gpar(fill = "#fff8e1", col = "#cc8800", lwd = 1.2)
main_con_gp  <- gpar(col = "#336699", lwd = 1.5, fill = "#336699")
excl_con_gp  <- gpar(col = "#cc8800", lwd = 1.2, fill = "#cc8800")

grid.newpage()
flowchart(
  source = boxGrob(glue("Stockholm population\nn = {pop}", pop = txtInt(1632798)),
                   box_gp = main_box_gp),
  eligible = boxGrob(glue("Eligible\nn = {pop}", pop = txtInt(10032)),
                     box_gp = main_box_gp),
  included = boxGrob(glue("Randomized\nn = {incl}", incl = txtInt(122)),
                     box_gp = main_box_gp),
  groups = list(
    boxGrob(glue("Treatment A\nn = {n}", n = txtInt(43)),        box_gp = group_box_gp),
    boxGrob(glue("Treatment B\nn = {n}", n = txtInt(122-43-30)), box_gp = group_box_gp)
  )) |>
  spread(axis = "y") |>
  spread(subelement = "groups", axis = "x") |>
  equalizeWidths(subelement = list("source", "eligible", "included")) |>
  equalizeWidths(subelement = "groups") |>
  insert(list(excluded = boxHeaderGrob(
                header = glue("Excluded (n = {tot}):", tot = 30),
                body   = glue(" - not interested: {n1}\n - contra-indicated: {n2}",
                              n1 = 12, n2 = 18),
                bjust      = "left",
                box_gp     = excl_box_gp,
                header_gp  = gpar(col = "#cc8800", cex = 1))),
         after = "eligible",
         name  = "excluded") |>
  move(subelement = "excluded", x = .8) |>
  connect("eligible", "excluded", type = "L",    lty_gp = excl_con_gp, arrow_size = 3,
          label = "Excluded") |>
  connect("source",   "eligible", type = "vert", lty_gp = main_con_gp, arrow_size = 3,
          smooth = TRUE) |>
  connect("eligible", "included", type = "vert", lty_gp = main_con_gp, arrow_size = 3,
          smooth = TRUE) |>
  connect("included", "groups",   type = "N",    lty_gp = main_con_gp, arrow_size = 3,
          smooth = TRUE)
```

# CONSORT phase labels between grouped stages

CONSORT diagrams use phase labels such as allocation, follow-up, and analysis.
These are not part of the patient flow itself — they label a *stage* and sit
just above it, centred between the randomisation arms.

`phaseLabel()` does this in one call per stage:

- It references the **stage it labels** (e.g. `"groups"`), so there is no
  confusing "insert after X" step.
- It places the label slightly above the stage, overlapping the top corners by
  `overlap` (≈ 7% by default), and marks it to be drawn **on top** so it stays
  visible.
- The width adapts to the stage: for two arms the label spans the central gap
  plus a small corner lap; for three or more arms it becomes a banner across the
  full stage width. Pass `width` to override.

Each stage's arms are spread across the viewport with a small outer `margin`,
leaving a clear central gap for the labels to sit in. Equal
arm widths give a symmetric corner overlap — use `equalizeWidths()` if the arms
differ. For custom overlays beyond phase labels, the lower-level
`insert(..., on_top = TRUE)` is still available.

```{r consort-stage-headings, fig.height = 7, fig.width = 8}
old_opts <- options(boxGrobTxtPadding = unit(2, "mm"))

main_box_gp <- gpar(fill = "white", col = "black", lwd = 1)
heading_gp  <- gpar(fill = "#c8daf7", col = "#2f5f9f", lwd = 1)
con_gp      <- gpar(col = "#4f86c6", fill = "#4f86c6", lwd = 1.8)
side_width  <- unit(70, "mm")

flowchart(
  rando = boxGrob("Randomised\nN = 100", box_gp = main_box_gp),
  groups = list(
    boxGrob("Allocated to intervention\nn = 50",
            width = side_width, box_gp = main_box_gp),
    boxGrob("Allocated to control\nn = 50",
            width = side_width, box_gp = main_box_gp)
  ),
  followup = list(
    boxGrob("Lost to follow-up\nn = 1",
            width = side_width, box_gp = main_box_gp),
    boxGrob("Lost to follow-up\nn = 2",
            width = side_width, box_gp = main_box_gp)
  ),
  analysis = list(
    boxGrob("Analysed\nn = 49",
            width = side_width, box_gp = main_box_gp),
    boxGrob("Analysed\nn = 48",
            width = side_width, box_gp = main_box_gp)
  )
) |>
  spread(axis = "y", margin = unit(0.04, "npc")) |>
  # Spread each stage's arms within the viewport, leaving an outer margin —
  # this gives the two arms a clear central gap for the labels to sit in
  spread(subelement = "groups",   axis = "x", margin = unit(0.05, "npc")) |>
  spread(subelement = "followup", axis = "x", margin = unit(0.05, "npc")) |>
  spread(subelement = "analysis", axis = "x", margin = unit(0.05, "npc")) |>
  # One call per stage: centred between the arms, slightly above, drawn on top
  phaseLabel("groups",   "Allocation", box_gp = heading_gp) |>
  phaseLabel("followup", "Follow-up",  box_gp = heading_gp) |>
  phaseLabel("analysis", "Analysis",   box_gp = heading_gp) |>
  connect("rando",    "groups",   type = "N", lty_gp = con_gp, arrow_size = 3,
          smooth = TRUE) |>
  connect("groups",   "followup", type = "v", lty_gp = con_gp, arrow_size = 3) |>
  connect("followup", "analysis", type = "v", lty_gp = con_gp, arrow_size = 3)

options(old_opts)
```

# CONSORT-style flowchart

A CONSORT diagram represents patient flow through a clinical trial. This example
demonstrates the `flowchart()` pipe API at full scale, using named lists for parallel
boxes, `spread()` to position each column, and pairwise `connect()` for the arms.

Key points:

- `arms`, `lost`, and `analysis` are all **named lists** — `connect("arms", "lost", ...)`
  automatically creates one connector per matching pair (same list index).
- `spread(..., exclude = "lost")` keeps side-branch boxes out of the main
  vertical spacing, and `align(..., references = list("arms", "analysis"))`
  then centres them between the rows they describe.
- `type = "L"` exits the **bottom** of the assessed box and turns right, giving the
  classic "down then right" exclusion branch instead of a direct side-exit.
- `insert()` adds the exclusion box; `move(..., just = "right")` places its
  right edge at the outer exclusion margin, and `align(..., references = ...)`
  centres it between the before/after boxes.
- Badge labels extend above the box top and are not counted in the height used by
  `spread()`, so a `margin` of 10 mm is used to leave room at the top.

```{r consort_example, fig.width = 9, fig.height = 6}
old_opts <- options(boxGrobTxtPadding = unit(3, "mm"))

box_fill     <- gpar(fill = "#ddeeff", col = "#336699", lwd = 1.5)
con_gp       <- gpar(col = "#336699", lwd = 1.5, fill = "#336699")
side_gp      <- gpar(col = "#cc8800", lwd = 1.2, fill = "#cc8800")
excl_fill    <- gpar(fill = "#fff8e1", col = "#cc8800", lwd = 1.2)
badge_gp     <- gpar(fill = "#336699", col = NA)
badge_txt_gp <- gpar(col = "white", cex = 0.65)

# Main arms use an inner horizontal span; exclusions use the outer span.
main_arm_margin  <- 0.28
exclusion_margin <- 0.05
main_x           <- 0.5
exclusion_to     <- 1 - exclusion_margin

grid.newpage()
flowchart(
  assessed = boxGrob(
    "Patients assessed for eligibility",
    x = main_x, box_gp = box_fill,
    badge_label = "840", badge_gp = badge_gp, badge_txt_gp = badge_txt_gp
  ),
  randomised = boxGrob(
    "Randomised",
    x = main_x, box_gp = box_fill,
    badge_label = "126", badge_gp = badge_gp, badge_txt_gp = badge_txt_gp
  ),
  arms = list(
    cast     = boxGrob("Randomised to\ncast immobilisation",
                       box_gp = box_fill,
                       badge_label = "62",
                       badge_gp = badge_gp, badge_txt_gp = badge_txt_gp),
    surgical = boxGrob("Randomised to\nsurgery",
                       box_gp = box_fill,
                       badge_label = "64",
                       badge_gp = badge_gp, badge_txt_gp = badge_txt_gp)
  ),
  # Lost-to-follow-up: one per arm, placed on the outer exclusion span
  # and centred vertically between allocation and analysis.
  lost = list(
    lost_cast     = boxGrob("Lost to follow-up (n = 2)\n  1 No response\n  1 Other surgery",
                            just = "left", box_gp = excl_fill),
    lost_surgical = boxGrob("Lost to follow-up (n = 3)\n  2 No response\n  1 Other surgery",
                            just = "left", box_gp = excl_fill)
  ),
  analysis = list(
    analysis_cast     = boxGrob("Included in\nprimary analysis",
                                box_gp = box_fill,
                                badge_label = "60",
                                badge_gp = badge_gp, badge_txt_gp = badge_txt_gp),
    analysis_surgical = boxGrob("Included in\nprimary analysis",
                                box_gp = box_fill,
                                badge_label = "61",
                                badge_gp = badge_gp, badge_txt_gp = badge_txt_gp)
  )
) |>
  # Vertical spacing — lost boxes are side branches, not main pathway rows
  spread(axis = "y", margin = unit(5, "mm"), exclude = "lost") |>
  align(axis = "y", subelement = "lost",
        references = list("arms", "analysis")) |>
  # Make arms and analysis boxes the same width so the same from/to spread
  # places their centres at matching x positions (otherwise the wider arm text
  # shifts centres relative to the narrower analysis text).
  # Alternative: skip equalizeWidths() and explicitly align x-centres,
  # e.g. with `align(axis = "x", reference = "analysis", subelement = "arms")`
  # (equivalent to `alignHorizontal(reference = "analysis", subelement = "arms")`).
  equalizeWidths(subelement = list("arms", "analysis")) |>
  # Arms and analysis in the inner span; lost boxes use the outer span
  # so that lost_cast lands left of cast and lost_surgical right of surgical
  spread(axis = "x", subelement = "arms",     margin = main_arm_margin) |>
  spread(axis = "x", subelement = "analysis", margin = main_arm_margin) |>
  spread(axis = "x", subelement = "lost",     margin = exclusion_margin) |>
  # Exclusion box: right edge on the outer span, vertically centred between rows
  insert(list(excluded = boxGrob(
    "Excluded (n = 714)\n  477 Stable ankle mortise\n   64 Incongruent ankle mortise\n   30 Previous serious trauma\n  143 Other reasons",
    just = "left", box_gp = excl_fill
  )), after = "assessed") |>
  move(subelement = "excluded", x = exclusion_to, just = "right") |>
  align(axis = "y", subelement = "excluded",
        references = list("assessed", "randomised"))  |>
  # type = "L": exits assessed's *bottom* then turns right — the "down then right" branch
  connect("assessed", "excluded", type = "L", lty_gp = side_gp, arrow_size = 3, smooth = TRUE) |>
  # Pairwise arm -> lost: sharp corners (smooth = FALSE) avoid a colour-transition
  # artefact where the orange arc would diverge from the shared blue vertical path
  # a few mm above the junction, making the line appear doubled.
  connect("arms", "lost", type = "L", lty_gp = side_gp, arrow_size = 3, smooth = TRUE) |>
  # Main-flow connectors, put last so that the main lines end up on top of the exclusion/lost lines
  connect("assessed",   "randomised", type = "v", lty_gp = con_gp,  arrow_size = 3, smooth = TRUE) |>
  connect("randomised", "arms",       type = "N", lty_gp = con_gp,  arrow_size = 3, smooth = TRUE) |>
  connect("arms",       "analysis",   type = "v", lty_gp = con_gp,  arrow_size = 3)

options(old_opts)
```

# Dotted return arrows for censored participants

In time-to-event analyses, participants who leave follow-up may still
contribute information until censoring. Dotted side-entry arrows can show that
these participants return to the analysis set instead of being dropped from the
study.

```{r consort_dotted_return_arrows, fig.width = 10, fig.height = 9}
old_opts <- options(boxGrobTxtPadding = unit(1, "mm"))

main_gp <- gpar(fill = "white", col = "black")
main_con_gp <- gpar(col = "black", fill = "black")
dotted_gp <- gpar(col = "black", fill = "black", lty = 2)
arm_from <- .05
arm_to <- .75
box_width <- unit(56, "mm")
ex_width <- unit(36, "mm")
ex_gap <- unit(5, "mm")
ex_offset <- box_width / 2 + ex_width / 2 + ex_gap

grid.newpage()
flowchart(
  rando = boxGrob("Randomised\nN = 197", box_gp = main_gp),
  groups = list(
    boxGrob("96 assigned to\ndecompressive craniectomy\nplus best medical treatment\n95 received allocated\nintervention",
            box_gp = main_gp),
    boxGrob("101 assigned to best medical\ntreatment alone\n93 received allocated\nintervention",
            box_gp = main_gp)
  ),
  ex1 = list(
    boxGrob("8 died\n1 withdrew\nconsent", just = "left", box_gp = main_gp),
    boxGrob("18 died\n1 withdrew\nconsent", just = "left", box_gp = main_gp)
  ),
  groups1 = list(
    boxGrob("87 completed day 30\nfollow-up", box_gp = main_gp),
    boxGrob("79 completed day 30\nfollow-up", box_gp = main_gp)
  ),
  ex2 = list(
    boxGrob("8 died", just = "left", box_gp = main_gp),
    boxGrob("9 died\n1 withdrew\nconsent\n2 lost to follow-up",
            just = "left", box_gp = main_gp)
  ),
  groups2 = list(
    boxGrob("79 completed day 180\nfollow-up", box_gp = main_gp),
    boxGrob("68 completed day 180\nfollow-up", box_gp = main_gp)
  ),
  ex3 = list(
    boxGrob("5 died\n2 lost to\nfollow-up", just = "left", box_gp = main_gp),
    boxGrob("3 died\n2 withdrew\nconsent\n6 lost to follow-up",
            just = "left", box_gp = main_gp)
  ),
  groups3 = list(
    boxGrob("95 included in the primary\noutcome analysis\n1 withdrew consent",
            box_gp = main_gp),
    boxGrob("95 included in the primary\noutcome analysis\n2 withdrew consent\n2 lost to follow-up",
            box_gp = main_gp)
  )
) |>
  spread(axis = "y", margin = unit(0.02, "npc")) |>
  equalizeWidths(subelement = stringr::regex("^groups"), width = box_width) |>
  equalizeHeights(subelement = stringr::regex("^groups")) |>
  equalizeWidths(subelement = stringr::regex("^ex"), width = ex_width) |>
  spread(subelement = stringr::regex("^groups"), axis = "x", from = arm_from, to = arm_to,
         type = "center") |>
  move(subelement = "rando",
       x = position("groups", position = "center", type = "x")) |>
  move(subelement = list(c("ex1", 1), c("ex2", 1), c("ex3", 1)),
       x = position(c("groups", 1), position = "center", type = "x") + ex_offset) |>
  move(subelement = list(c("ex1", 2), c("ex2", 2), c("ex3", 2)),
       x = position(c("groups", 2), position = "center", type = "x") + ex_offset) |>
  connect("rando", "groups", type = "N", lty_gp = main_con_gp, arrow_size = 3) |>
  connect("groups", "groups1", type = "vertical", lty_gp = main_con_gp, arrow_size = 3) |>
  connect("groups1", "groups2", type = "vertical", lty_gp = main_con_gp, arrow_size = 3) |>
  connect("groups2", "groups3", type = "vertical", lty_gp = main_con_gp, arrow_size = 3) |>
  connect("groups", "ex1", type = "L", lty_gp = main_con_gp, arrow_size = 3) |>
  connect("groups1", "ex2", type = "L", lty_gp = main_con_gp, arrow_size = 3) |>
  connect("groups2", "ex3", type = "L", lty_gp = main_con_gp, arrow_size = 3) |>
  connect(stringr::regex("^ex"), "groups3", type = "side",
          lty_gp = dotted_gp, arrow_size = 3,
          side = "right",
          end_side = "right",
          side_route = "outside",
          side_offset = ex_gap)

options(old_opts)
```

# Consistent grouped widths and global text padding

When building grouped flows (for example CONSORT-style diagrams), it is often useful to:

- reduce text padding globally for all `boxGrob()` calls
- make corresponding boxes in different levels share the same width

The snippet below demonstrates both via `options(boxGrobTxtPadding = ...)` and `equalizeWidths()`.

```{r flowchart-group-width-and-padding, fig.height = 5.5, fig.width = 8}
old_opts <- options(boxGrobTxtPadding = unit(2, "mm"))

flowchart(
  rando = glue("Randomised\nN = 100"),
  groups = list(
    glue("Group 1\nn = 50"),
    glue("Group 2\nn = 50")
  ),
  groups2 = list(
    glue("Analysed\nn = 49"),
    glue("Analysed\nn = 48")
  )
) |>
  spread(axis = "y", margin = unit(0.02, "npc")) |>
  spread(subelement = "groups", axis = "x", margin = unit(.05, "npc")) |>
  spread(subelement = "groups2", axis = "x", margin = unit(.05, "npc")) |>
  equalizeWidths(subelement = list("groups", "groups2")) |>
  connect("rando", "groups", type = "N") |>
  connect("groups", "groups2", type = "vertical")

options(old_opts)
```

# Axis-preserving connectors for shared targets

The regular `vertical` and `horizontal` connectors draw a straight line between
the relevant box faces. If the box centres are offset, that straight line can be
diagonal. Use `vertical_axis` or `horizontal_axis` when the connector itself must
stay on the source box's x- or y-axis and land on the target boundary.

This is useful for shared destination boxes: each upstream item can land cleanly
on its own projected position without adding invisible helper boxes.

The layout below is built entirely with `spread()`/`align()`/`move()` — no box is
given an absolute `x`/`y`. The three inputs are spread across the top and drop
onto the shared **validation** tape with `vertical_axis`, while the three issue
diamonds are spread down a left column and project onto the tall **issue log**
with `horizontal_axis`.

```{r axis_preserving_connectors, fig.width = 10, fig.height = 7}
input_gp     <- gpar(fill = "#F3F8FF", col = "#3B73C5", lwd = 1.3)
process_gp   <- gpar(fill = "#FFF4C7", col = "#C69214", lwd = 1.3)
issue_gp     <- gpar(fill = "#FCE4EC", col = "#AD1457", lwd = 1.2)
output_gp    <- gpar(fill = "#E8F5E9", col = "#2E7D32", lwd = 1.3)
con_gp       <- gpar(col = "#555555", fill = "#555555", lwd = 1.3)
issue_con_gp <- gpar(col = "#AD1457", fill = "#AD1457", lwd = 1.1)
main_path    <- list("validation", "clean")

grid.newpage()
flowchart(
  inputs = list(
    web    = boxEllipseGrob("REDCap\nform",   width = unit(42, "mm"), height = unit(24, "mm"), box_gp = input_gp),
    import = boxDatabaseGrob("CSV\nimport",    width = unit(42, "mm"), height = unit(24, "mm"), box_gp = input_gp),
    manual = boxDocumentGrob("Manual\nentry",  width = unit(42, "mm"), height = unit(24, "mm"), box_gp = input_gp)
  ),
  validation = boxTapeGrob(
    "Validation queue\nIDs, dates, ranges, missingness",
    width = unit(.58, "npc"), height = unit(.14, "npc"), box_gp = process_gp
  ),
  issues = list(
    missing   = boxDiamondGrob("Missing\nfields", width = unit(48, "mm"), height = unit(14, "mm"), box_gp = issue_gp),
    duplicate = boxDiamondGrob("Duplicate\nID",   width = unit(48, "mm"), height = unit(14, "mm"), box_gp = issue_gp),
    outlier   = boxDiamondGrob("Outlier\nvalue",  width = unit(48, "mm"), height = unit(14, "mm"), box_gp = issue_gp)
  ),
  log = boxDocumentsGrob(
    "Issue log\nqueries sent\nchanges reviewed",
    width = unit(48, "mm"), height = unit(.44, "npc"), box_gp = issue_gp
  ),
  clean = boxDatabaseGrob(
    "Analysis-ready dataset\nlocked for report",
    width = unit(.44, "npc"), height = unit(.16, "npc"), box_gp = output_gp
  )
) |>
  # Main vertical flow (inputs -> validation -> clean); issues are a side column
  spread(axis = "y", margin = unit(7, "mm"), exclude = "issues") |>
  spread(axis = "x", subelement = "inputs", from = 0, to = 0.7, margin = 0.05, type = "center") |>
  equalizeWidths(subelement = main_path) |>
  align(axis = "x", subelement = "validation", reference = "inputs") |>
  align(axis = "x", subelement = "clean", reference = "validation") |>
  # Place the issue log beside the main flow and stack the diamonds along it
  align(axis = "y", subelement = "log", references = list("validation", "clean")) |>
  spread(axis = "y", subelement = "issues",
         from = position("log", position = "top", type = "y"),
         to   = position("log", position = "bottom", type = "y"),
         margin = unit(2, "mm")) |>
  move(subelement = "issues", x = 0.08, just = "left") |>
  move(subelement = "log",    x = 0.92, just = "right") |>
  connect("inputs", "validation", type = "vertical_axis",   lty_gp = con_gp,       arrow_size = 3) |>
  connect("issues", "log",        type = "horizontal_axis", lty_gp = issue_con_gp, arrow_size = 3) |>
  connect("validation", "clean",  type = "vertical_axis",   lty_gp = con_gp,       arrow_size = 3, smooth = TRUE) |>
  print()
```

# 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 proportions

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 box_coordinates, 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 on alternate shapes ---
grid.newpage()

decision <- boxDiamondGrob("Decision", box_gp = gpar(fill = "#FFF4E6"))
local    <- boxEllipseGrob("Local", box_gp = gpar(fill = "#E6FFF4"))
server   <- boxServerGrob("Server", box_gp = gpar(fill = "#E8F0FF"))

# Position the boxes, then draw them. The ellipse carries extra padding so its
# text fits the curved outline, making it taller than the server box; equalize
# the outcome heights so both branches line up symmetrically.
boxes <- list(decision = decision, outcomes = list(local, server)) |>
  equalizeHeights(subelement = "outcomes") |>
  spreadHorizontal(from = unit(.1, "npc"), to = unit(.9, "npc"), subelement = "outcomes") |>
  spreadVertical() |>
  print()

# Build one N connector for both branches and attach a label to each with
# setConnectorLabels(); print() then draws the lines and labels together.
connectGrob(boxes$decision, boxes$outcomes, type = "N") |>
  setConnectorLabels(c("Local", "Server")) |>
  print()
```

# 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.
