brickchart: Brick Chart

In stopsack/khsmisc: Miscellaneous functions for epidemiology research

Brick Chart

Description

Plot bars of proportions that consist of "bricks" showing individual observations.

Usage

brickchart(
  data,
  outcome,
  by,
  group,
  colors = NULL,
  guide = FALSE,
  flip = TRUE,
  clip = "on",
  ...
)

Arguments

data	Data set.
outcome	Outcome expression, e.g., event == TRUE.
by	Exposure variable.
group	Optional: Grouping variable, e.g., an effect modifier.
colors	Optional: Color list. Must be a list consisting of two-element color code vectors with the dark and bright colors for each level of the exposure variable (by). Example: list(c("darkred", "red"), c("darkblue", "lightblue")). If not provided, colors will be generated from the viridis_pal palette.
guide	Optional: Show legend? Defaults to FALSE. May not work with ggplot version 3.3.4 or newer.
flip	Optional: Flip x and y axes? Defaults to TRUE.
clip	Optional: Clip graph? Defaults to "on".
...	Optional: further arguments passed to the call of facet_grid, used for group.

Value

ggplot. Modify further with standard ggplot functions. The additional variables label_outcomes (outcome count), label_total (per-group total), and label_prop (proportion) can also be accessed. See example.

Examples

data(cancer, package = "survival")
cancer <- cancer %>%
  tibble::as_tibble() %>%
  dplyr::mutate(sex = factor(sex, levels = 1:2,
                             labels = c("Men", "Women")))

cancer %>%
  dplyr::filter(ph.ecog < 3) %>%  # drop missing/near-empty categories
  brickchart(outcome = status == 2,
             by = ph.ecog)

# Stratified version
# Note- Color fill may be off with ggplot v3.3.4+ if guide = TRUE
cancer %>%
  dplyr::filter(ph.ecog < 3) %>%
  brickchart(outcome = status == 2,
             by = ph.ecog,
             group = sex) +
  # Modify graph with standard ggplot functions
  # Refer to axes before flipping x <-> y. Here, y is horizontal:
  ggplot2::labs(y = "Risk (cumulative incidence)",
                fill = "ECOG status",  # Color label
                title = "Mortality by ECOG performance status") +
  # Themes refer to axes as shown--'y' is now vertical
  ggplot2::theme(axis.title.y = ggplot2::element_blank()) +
  # add label
  ggplot2::geom_text(
    mapping = ggplot2::aes(
      label = paste0(round(label_prop * 100), "%"),
      y = label_prop + 0.05))

stopsack/khsmisc documentation built on Sept. 22, 2023, 12:26 p.m.