DelayedUnaryIsoOpStack-class: DelayedUnaryIsoOpStack objects

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

DelayedUnaryIsoOpStack objects

Description

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

The DelayedUnaryIsoOpStack class provides a formal representation of a stack of delayed unary isometric operations, that is, of a group of delayed unary isometric operations stacked (a.k.a. piped) together. 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
                              ^
                              |
                    DelayedUnaryIsoOpStack
  

DelayedUnaryIsoOpStack objects are used inside a DelayedArray object to represent groups of delayed unary isometric 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 'DelayedUnaryIsoOpStack'
summary(object, ...)

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

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

## S4 method for signature 'DelayedUnaryIsoOpStack'
extract_array(x, index)

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

## S4 method for signature 'DelayedUnaryIsoOpStack'
is_sparse(x)

## S4 method for signature 'DelayedUnaryIsoOpStack'
extract_sparse_array(x, index)

Arguments

x, object	A DelayedUnaryIsoOpStack object.
index	See ?extract_array in the S4Arrays package for a description of the index argument.
...	Not used.

Details

A DelayedUnaryIsoOpStack object is used to represent the delayed version of an operation of the form:

    out <- a |> OP1 |> OP2 |> ... |> OPk
  

where:

• OP1, OP2, ..., OPk are isometric array transformations i.e. operations that return an array with the same dimensions as the input array.

• a is the input array.

• The output (out) is an array of same dimensions as a.

In addition, each operation (OP) in the pipe must satisfy the property that each value in the output array must be determined **solely** by the corresponding value in the input array. In other words:

    a |> OP |> `[`(i_1, i_2, ..., i_n)   # i.e. OP(a)[i_1, i_2, ..., i_n]
  

must be equal to:

    a |> `[`(i_1, i_2, ..., i_n) |> OP   # i.e. OP(a[i_1, i_2, ..., i_n])
  

for any valid multidimensional index (i_1, i_2, ..., i_n).

We refer to this property as the locality principle.

Concrete examples:

1. Things like is.na(), is.finite(), logical negation (!), nchar(), tolower().

2. Most functions in the Math and Math2 groups e.g. log(), sqrt(), abs(), ceiling(), round(), etc... Notable exceptions are the cum*() functions (cummin(), cummax(), cumsum(), and cumprod()): they don't satisfy the locality principle.

3. Operations in the Ops group when one operand is an array and the other a scalar e.g. a + 10, 2 ^ a, a <= 0.5, etc...

See Also

• DelayedOp objects.

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

• extract_array in the S4Arrays package.

• extract_sparse_array in the SparseArray package.

Examples

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

## ---------------------------------------------------------------------
## BASIC EXAMPLE
## ---------------------------------------------------------------------
m0 <- matrix(runif(12), ncol=3)
M0 <- DelayedArray(m0)
showtree(M0)

M <- log(1 + M0) / 10
showtree(M)
class(M@seed)        # a DelayedUnaryIsoOpStack object

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

M1 <- SM0 - 11
showtree(M1)
class(M1@seed)       # a DelayedUnaryIsoOpStack object
is_sparse(M1@seed)   # FALSE

SM2 <- 10 * SM0
showtree(SM2)
class(SM2@seed)      # a DelayedUnaryIsoOpStack object
is_sparse(SM2@seed)  # TRUE

M3 <- SM0 / 0
showtree(M3)
class(M3@seed)       # a DelayedUnaryIsoOpStack object
is_sparse(M3@seed)   # FALSE

SM4 <- log(1 + SM0) / 10
showtree(SM4)
class(SM4@seed)      # a DelayedUnaryIsoOpStack object
is_sparse(SM4@seed)  # TRUE

SM5 <- 2 ^ SM0 - 1
showtree(SM5)
class(SM5@seed)      # a DelayedUnaryIsoOpStack object
is_sparse(SM5@seed)  # TRUE

## ---------------------------------------------------------------------
## SANITY CHECKS
## ---------------------------------------------------------------------
stopifnot(class(M@seed) == "DelayedUnaryIsoOpStack")
stopifnot(class(M1@seed) == "DelayedUnaryIsoOpStack")
stopifnot(!is_sparse(M1@seed))
stopifnot(class(SM2@seed) == "DelayedUnaryIsoOpStack")
stopifnot(is_sparse(SM2@seed))
stopifnot(class(M3@seed) == "DelayedUnaryIsoOpStack")
stopifnot(!is_sparse(M3@seed))
stopifnot(class(SM4@seed) == "DelayedUnaryIsoOpStack")
stopifnot(is_sparse(SM4@seed))
stopifnot(class(SM5@seed) == "DelayedUnaryIsoOpStack")
stopifnot(is_sparse(SM5@seed))

Bioconductor/DelayedArray documentation built on Dec. 7, 2024, 10:27 p.m.