extractAssaySubmatrix: Extract assay submatrix
In iSEE: Interactive SummarizedExperiment Explorer

Description Usage Arguments Details Value Author(s)

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

1	.extractAssaySubmatrix(x, se, envir, use_custom_row_slot, custom_row_text_slot)

`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`.

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.

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

Kevin Rue-Albrecht

iSEE documentation built on Feb. 3, 2021, 2:01 a.m.