ggalign (version 0.0.4)

align_kmeans: Split layout by k-means clustering groups.

Description

Split layout by k-means clustering groups.

Usage

align_kmeans(centers, ..., data = NULL, set_context = FALSE, name = NULL)

Value

A new Align object.

Arguments

centers

either the number of clusters, say \(k\), or a set of initial (distinct) cluster centres. If a number, a random set of (distinct) rows in x is chosen as the initial centres.

...

Arguments passed on to stats::kmeans

iter.max

the maximum number of iterations allowed.

nstart

if centers is a number, how many random sets should be chosen?

algorithm

character: may be abbreviated. Note that "Lloyd" and "Forgy" are alternative names for one algorithm.

trace

logical or integer number, currently only used in the default method ("Hartigan-Wong"): if positive (or true), tracing information on the progress of the algorithm is produced. Higher values may produce more tracing information.

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().

Examples

ggheatmap(matrix(rnorm(81), nrow = 9)) +
    hmanno("t") +
    align_kmeans(3L)