ggalign (version 1.0.1)

ggmark: Add a plot to annotate selected observations

Description

Add a plot to annotate selected observations

Usage

ggmark(
  mark,
  data = waiver(),
  mapping = aes(),
  ...,
  group1 = NULL,
  group2 = NULL,
  obs_size = 1,
  size = NULL,
  active = NULL
)

Arguments

mark

A mark_draw() object to define how to draw the links. Like mark_line(), mark_tetragon(). Note the names of the pair links will be used to define the panel names so must be unique.

data

The following options can be used:

• NULL: No data is set.

• waiver(): Inherits the data from the layout matrix.

• A function (including purrr-like lambda syntax): Applied to the layout matrix to transform the data before use. To transform the final plot data, please use scheme_data().

• A matrix, data.frame, or atomic vector.

mapping

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

...

<dyn-dots> Additional arguments passed to fortify_data_frame().

group1, group2

A single boolean value indicating whether to use the panel group information from the layout as the paired groups. By default, if no specific observations are selected in mark, ggmark() will automatically connect all observations and group them according to the layout's defined groups.

obs_size

A single numeric value that indicates the size of a single observation, ranging from (0, 1].

size

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

active

A active() object that defines the context settings when added to a layout.

ggplot2 specification

ggmark initializes a ggplot object. The underlying data is created using fortify_data_frame(). Please refer to it for more details.

In addition, the following columns will be added to the data frame:

• .panel: the panel for the aligned axis. It means x-axis for vertical stack layout (including top and bottom annotation), y-axis for horizontal stack layout (including left and right annotation).

• .names (vec_names()) and .index (vec_size()/NROW()): a character names (only applicable when names exists) and an integer of index of the original data.

• .hand: A factor with levels c("left", "right") for horizontal stack layouts, or c("top", "bottom") for vertical stack layouts, indicating the position of the linked observations.

Examples

set.seed(123)
small_mat <- matrix(rnorm(56), nrow = 7)
rownames(small_mat) <- paste0("row", seq_len(nrow(small_mat)))
colnames(small_mat) <- paste0("column", seq_len(ncol(small_mat)))

# mark_line
ggheatmap(small_mat) +
    theme(axis.text.x = element_text(hjust = 0, angle = -60)) +
    anno_right() +
    align_kmeans(3L) +
    ggmark(mark_line(I(1:3) ~ NULL)) +
    geom_boxplot(aes(.names, value)) +
    theme(plot.margin = margin(l = 0.1, t = 0.1, unit = "npc"))

# mark_tetragon
ggheatmap(small_mat) +
    theme(axis.text.x = element_text(hjust = 0, angle = -60)) +
    anno_right() +
    align_kmeans(3L) +
    ggmark(mark_tetragon(I(1:3) ~ NULL)) +
    geom_boxplot(aes(.names, value)) +
    theme(plot.margin = margin(l = 0.1, t = 0.1, unit = "npc"))