ggalign (version 0.0.5)

align_reorder: Reorders layout observations based on specific statistics.

Description

Reorders layout observations based on specific statistics.

Usage

align_reorder(
  stat,
  ...,
  reverse = FALSE,
  strict = TRUE,
  data = NULL,
  active = NULL,
  set_context = deprecated(),
  name = deprecated()
)

Value

A "AlignReorder" object.

Arguments

stat

A summary function which accepts a data and returns the statistic, which we'll call order2() to extract the ordering information.

...

<dyn-dots> Additional arguments passed to function provided in stat argument.

reverse

A boolean value. Should the sort order be in reverse?

strict

A boolean value indicates whether the order should be strict. If previous groups has been established, and strict is FALSE, this will reorder the observations in each group.

data

A matrix, data frame, or atomic vector used as the input for the stat function. Alternatively, you can specify a function (including purrr-like lambda syntax) that will be applied to the layout matrix, transforming it as necessary for statistic calculations. By default, it will inherit from the layout matrix.

active

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

set_context

Please use active argument instead.

name

Please use active argument instead.

Axis Alignment for Observations

It is important to note that we consider rows as observations, meaning vec_size(data)/NROW(data) must match the number of observations along the axis used for alignment (x-axis for a vertical stack layout, y-axis for a horizontal stack layout).

• quad_layout()/ggheatmap(): For column annotation, the layout matrix will be transposed before use (if data is a function, it is applied to the transposed matrix), as column annotation uses columns as observations but alignment requires rows.

• stack_layout(): The layout matrix is used as is, aligning all plots along a single axis.

Details

The align_reorder() function differs from align_order() in that the wts argument in align_order() must return atomic weights for each observation. In contrast, the stat argument in align_reorder() can return more complex structures, such as hclust or dendrogram, among others.

Typically, you can achieve the functionality of align_reorder() using align_order() by manually extracting the ordering information from the statistic.

See Also

order2()

Examples

ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_left() +
    align_reorder(hclust2)