slanted_reorder {slanter} | R Documentation |
Reorder data rows and columns to move high values close to the diagonal.
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 |
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)))