showtree: Visualize and access the leaves of a tree of delayed...

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

Visualize and access the leaves of a tree of delayed operations

Description

showtree can be used to visualize the tree of delayed operations carried by a DelayedArray object.

Use nseed, seed, or path to access the number of seeds, the seed, or the seed path of a DelayedArray object, respectively.

Use seedApply to apply a function to the seeds of a DelayedArray object.

Usage

showtree(x, show.node.dim=TRUE)

nseed(x)            # seed counter
seed(x)             # seed getter and setter
path(object, ...)   # path getter and setter

seedApply(x, FUN, ...)

Arguments

x, object	Typically a DelayedArray object but can also be a DelayedOp object or a list where each element is a DelayedArray or DelayedOp object.
show.node.dim	TRUE or FALSE. If TRUE (the default), the nodes dimensions and data type are displayed.
FUN	The function to be applied to each leaf in x.
...	Optional arguments to FUN for seedApply(). Additional arguments passed to methods for path().

Value

The number of seeds contained in x for nseed.

The seed contained in x for seed.

The path of the seed contained in object for path.

A list of length nseed(x) for seedApply.

See Also

• simplify to simplify the tree of delayed operations carried by a DelayedArray object.

• DelayedOp objects.

• DelayedArray objects.

Examples

## ---------------------------------------------------------------------
## showtree(), nseed(), and seed()
## ---------------------------------------------------------------------
m1 <- matrix(runif(150), nrow=15, ncol=10)
M1 <- DelayedArray(m1)
showtree(M1)
seed(M1)

M2 <- log(t(M1[5:1, c(TRUE, FALSE)] + 10))[-1, ]
showtree(M2)

## In the above example, the tree is linear i.e. all the operations
## are represented by unary nodes. The simplest way to know if a
## tree is linear is by counting its leaves with nseed():
nseed(M2)  # only 1 leaf means the tree is linear
seed(M2)

dimnames(M1) <- list(letters[1:15], LETTERS[1:10])
showtree(M1)

m2 <- matrix(1:20, nrow=10)
Y <- cbind(t(M1[ , 10:1]), DelayedArray(m2), M1[6:15, "A", drop=FALSE])
showtree(Y)
showtree(Y, show.node.dim=FALSE)
nseed(Y)  # the tree is not linear

Z <- t(Y[10:1, ])[1:15, ] + 0.4 * M1
showtree(Z)
nseed(Z)  # the tree is not linear

## ---------------------------------------------------------------------
## seedApply()
## ---------------------------------------------------------------------
seedApply(Y, class)
seedApply(Y, dim)

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