.extractAssaySubmatrix {iSEE} | R Documentation

## 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)

### 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`.

### 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

[Package iSEE version 2.4.0 Index]