extractAssaySubmatrix: Extract assay submatrix

In csoneson/SEE: Interactive SummarizedExperiment Explorer

Extract assay submatrix

Description

Extract an assay submatrix based on the multiple row/column selection and any custom specifications from .createCustomDimnamesModalObservers.

Usage

.extractAssaySubmatrix(
  x,
  se,
  envir,
  use_custom_row_slot,
  custom_row_text_slot,
  cap_row_selection_slot = NULL,
  as_matrix = TRUE
)

Arguments

x	A Panel instance that uses the row selection modal.
se	The current SummarizedExperiment object.
envir	The evaluation environment. This assumes that .processMultiSelections has already been run.
use_custom_row_slot	String specifying the name of the slot indicating whether to use custom rows.
custom_row_text_slot	String specifying the name of the slot holding the custom row names. This is expected to be of the same format as described in ?.createCustomDimnamesModalObservers.
cap_row_selection_slot	String specifying the name of the slot containing the cap on the number of selected rows.
as_matrix	Logical scalar indicating whether to coerce the submatrix into an ordinary matrix. If FALSE, the existing matrix representation is preserved.

Details

This is designed to extract a matrix of assay values for a subset of rows/columns of interest, most typically for a ComplexHeatmapPlot. It assumes that the class of x contains a slot indicating whether custom rows should be used, plus a slot to hold the selected custom row names (usually from a modal, see .createCustomDimnamesModalObservers).

If a multiple row selection is present in envir and custom rows are not to be used, that selection is used to define the rows of the submatrix. All columns are returned in the submatrix unless a multiple column selection is present in envir and the SelectEffect in x is “Restrict”, in which case only the selected columns are returned.

Value

A character vector of commands to set up the assay submatrix. The submatrix itself is generated within envir as the plot.data variable.

Author(s)

Kevin Rue-Albrecht

csoneson/SEE documentation built on Dec. 13, 2024, 6:43 p.m.