slanted_reorder: Reorder data rows and columns to move high values close to...

In tanaylab/slanter: Slanted Matrices and Ordered Clustering

Description

Given a matrix expressing the cross-similarity between two (possibly different) sets of entities, this uses slanted_orders to compute the "best" order for visualizing the matrix, then returns the reordered data. Commonly used in pheatmap(slanted_reorder(data), ...), and of course sheatmap does this internally for you.

Usage

slanted_reorder(
  data,
  order_data = NULL,
  order_rows = TRUE,
  order_cols = TRUE,
  squared_order = TRUE,
  same_order = FALSE,
  discount_outliers = TRUE
)

Arguments

data	A rectangular matrix to reorder, of non-negative values (unless order_data is specified).
order_data	An optional matrix of non-negative values of the same size to use for computing the orders.
order_rows	Whether to reorder the rows.
order_cols	Whether to reorder the columns.
squared_order	Whether to reorder to minimize the l2 norm (otherwise minimizes the l1 norm).
same_order	Whether to apply the same order to both rows and columns.
discount_outliers	Whether to do a final order phase discounting outlier values far from the diagonal.

Value

A matrix of the same shape whose rows and columns are a permutation of the input.

Examples

slanter::slanted_reorder(cor(t(mtcars)))

tanaylab/slanter documentation built on May 12, 2021, 11:21 a.m.