DelayedSetDimnames-class: DelayedSetDimnames objects

In Bioconductor/DelayedArray: A unified framework for working transparently with on-disk and in-memory array-like datasets

DelayedSetDimnames objects

Description

NOTE: This man page is about DelayedArray internals and is provided for developers and advanced users only.

The DelayedSetDimnames class provides a formal representation of a delayed "set dimnames" operation. It is a concrete subclass of the DelayedUnaryIsoOp virtual class, which itself is a subclass of the DelayedUnaryOp virtual class, which itself is a subclass of the DelayedOp virtual class:

                          DelayedOp
                              ^
                              |
                       DelayedUnaryOp
                              ^
                              |
                      DelayedUnaryIsoOp
                              ^
                              |
                      DelayedSetDimnames
  

DelayedSetDimnames objects are used inside a DelayedArray object to represent the delayed "set dimnames" operations carried by the object. They're never exposed to the end user and are not intended to be manipulated directly.

Usage

## S4 method for signature 'DelayedSetDimnames'
is_noop(x)

## S4 method for signature 'DelayedSetDimnames'
summary(object, ...)

## ~ ~ ~ Seed contract ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

## DelayedSetDimnames objects inherit the default dim()
## and extract_array() methods defined for DelayedUnaryIsoOp
## derivatives, but overwite their dimnames() method.

## S4 method for signature 'DelayedSetDimnames'
dimnames(x)

## ~ ~ ~ Propagation of sparsity ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

## DelayedSetDimnames objects inherit the default
## is_sparse() and extract_sparse_array() methods defined
## for DelayedUnaryIsoOp derivatives.

Arguments

x, object	A DelayedSetDimnames object.
...	Not used.

See Also

• DelayedOp objects.

• showtree to visualize the nodes and access the leaves in the tree of delayed operations carried by a DelayedArray object.

Examples

## DelayedSetDimnames extends DelayedUnaryIsoOp, which extends
## DelayedUnaryOp, which extends DelayedOp:
extends("DelayedSetDimnames")

## ---------------------------------------------------------------------
## BASIC EXAMPLE
## ---------------------------------------------------------------------
m0 <- matrix(1:30, ncol=5, dimnames=list(letters[1:6], NULL))
M2 <- M1 <- M0 <- DelayedArray(m0)
showtree(M0)

dimnames(M1) <- list(NULL, LETTERS[1:5])
showtree(M1)
class(M1@seed)      # a DelayedSetDimnames object

colnames(M2) <- LETTERS[1:5]
showtree(M2)
class(M2@seed)      # a DelayedSetDimnames object

## ---------------------------------------------------------------------
## PROPAGATION OF SPARSITY
## ---------------------------------------------------------------------
## DelayedSetDimnames objects always propagate sparsity.

sm0 <- sparseMatrix(i=c(1, 4), j=c(1, 3), x=c(11, 43), dims=4:3)
SM <- SM0 <- DelayedArray(sm0)
showtree(SM0)
is_sparse(SM0)      # TRUE

dimnames(SM) <- list(letters[1:4], LETTERS[1:3])
showtree(SM)
class(SM@seed)      # a DelayedSetDimnames object
is_sparse(SM@seed)  # TRUE

## ---------------------------------------------------------------------
## SANITY CHECKS
## ---------------------------------------------------------------------
stopifnot(class(M1@seed) == "DelayedSetDimnames")
stopifnot(class(M2@seed) == "DelayedSetDimnames")
stopifnot(class(SM@seed) == "DelayedSetDimnames")
stopifnot(is_sparse(SM@seed))

Bioconductor/DelayedArray documentation built on Aug. 8, 2024, 5:01 a.m.