ggalign (version 0.0.4)

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,
  set_context = FALSE,
  name = NULL
)

Value

A new Align 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 a simple vector. If an atomic vector is provided, it will be converted into a one-column matrix. When data = NULL, the internal layout data will be used by default. Additionally, data can be a function (including purrr-like lambdas), which will be applied to the layout data.

It is important to note that we consider the rows as the observations. It means the NROW(data) must return the same number with the specific layout axis (meaning the x-axis for vertical stack layout, or y-axis for horizontal stack layout).

• heatmap_layout(): for column annotation, the layout data will be transposed before using (If data is a function, it will be applied with the transposed matrix). This is necessary because column annotation uses heatmap columns as observations, but we need rows.

• stack_layout(): the layout data will be used as it is since we place all plots along a single axis.

set_context

A single boolean value indicates whether to set the active context to current plot. If TRUE, all subsequent ggplot elements will be added into this plot.

name

A string of the plot name. Used to switch the active context in hmanno() or stack_active().

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)) +
    hmanno("l") +
    align_reorder(hclust2)