ArrayGrid-class {DelayedArray} | R Documentation

## ArrayGrid and ArrayViewport objects

### Description

ArrayGrid and ArrayViewport objects are used internally to support block processing of array-like objects.

### Usage

    ## Constructor functions:
    ArbitraryArrayGrid(tickmarks)
    RegularArrayGrid(refdim, spacings=refdim)

    downsample(x, ratio=1L)

### Arguments

`tickmarks` | A list of integer vectors, one along each dimension of the reference array, representing the tickmarks along that dimension. Each integer vector must be sorted in ascending order. NAs or negative values are not allowed.
`refdim` | An integer vector containing the dimensions of the reference array.
`spacings` | An integer vector specifying the grid spacing along each dimension.
`x` | An ArrayGrid object.
`ratio` | An integer vector specifying the ratio of the downsampling along each dimension. Can be of length 1, in which case the same ratio is used along all the dimensions.

### Value

- For `ArbitraryArrayGrid()`: An ArbitraryArrayGrid instance.

- For `RegularArrayGrid()`: A RegularArrayGrid instance.

- For `downsample()`: An ArrayGrid object on the same reference array than `x`.

### See Also

- `read_block`.

- `blockApply` for more information about block processing of array-like objects.

- `mapToGrid` for mapping reference array positions to grid positions and vice-versa.

- `chunkGrid`.

- DelayedArray objects.

- array objects in base R.

### Examples

    ## ---------------------------------------------------------------------
    ## A. ArrayGrid OBJECTS
    ## ---------------------------------------------------------------------

    ## Create a regularly-spaced grid on top of a 3700 x 100 x 33 array:
    grid1 <- RegularArrayGrid(c(3700, 100, 33), c(250, 100, 10))

    ## Dimensions of the reference array:
    refdim(grid1)

    ## Number of grid elements along each dimension of the reference array:
    dim(grid1)

    ## Total number of grid elements:
    length(grid1)

    ## First element in the grid:
    grid1[[1L]]             # same as grid1[[1L, 1L, 1L]]

    ## Last element in the grid:
    grid1[[length(grid1)]]  # same as grid1[[15L, 1L, 4L]]

    ## Dimensions of the grid elements:
    dims(grid1)             # one row per grid element

    ## Lengths of the grid elements:
    lengths(grid1)          # same as rowProds(dims(grid1))
    stopifnot(sum(lengths(grid1)) == prod(refdim(grid1)))

    maxlength(grid1)        # does not need to compute lengths(grid1)) first
                            # so is more efficient than max(lengths(grid1))
    stopifnot(maxlength(grid1) == max(lengths(grid1)))

    ## Create an arbitrary-spaced grid on top of a 15 x 9 matrix:
    grid2 <- ArbitraryArrayGrid(list(c(2L, 7:10, 13L, 15L), c(5:6, 6L, 9L)))

    refdim(grid2)
    dim(grid2)
    length(grid2)
    grid2[[1L]]             # same as grid2[[1L, 1L]]
    grid2[[length(grid2)]]  # same as grid2[[15L, 9L]]

    dims(grid2)
    lengths(grid2)
    array(lengths(grid2), dim(grid2))  # display the grid element lengths in
                                       # an array of same shape as grid2

    stopifnot(sum(lengths(grid2)) == prod(refdim(grid2)))

    maxlength(grid2)        # does not need to compute lengths(grid2)) first
                            # so is more efficient than max(lengths(grid2))
    stopifnot(maxlength(grid2) == max(lengths(grid2)))

    ## Max (i.e. highest) resolution grid:
    Hgrid <- RegularArrayGrid(6:4, c(1, 1, 1))
    Hgrid
    dim(Hgrid)              # same as refdim(Hgrid)
    stopifnot(identical(dim(Hgrid), refdim(Hgrid)))
    stopifnot(all(lengths(Hgrid) == 1))

    ## Min (i.e. lowest) resolution grid:
    Lgrid <- RegularArrayGrid(6:4, 6:4)
    Lgrid
    stopifnot(all(dim(Lgrid) == 1))
    stopifnot(identical(dim(Lgrid[[1L]]), refdim(Lgrid)))
    stopifnot(identical(dims(Lgrid), matrix(refdim(Lgrid), nrow=1)))

    ## ---------------------------------------------------------------------
    ## B. ArrayViewport OBJECTS
    ## ---------------------------------------------------------------------

    ## Grid elements are ArrayViewport objects:
    grid1[[1L]]
    class(grid1[[1L]])
    grid1[[2L]]
    grid1[[2L, 1L, 1L]]
    grid1[[15L, 1L, 4L]]

    ## Construction of a standalong ArrayViewport object:
    m0 <- matrix(1:30, ncol=5)
    block_dim <- c(4, 3)
    viewport1 <- ArrayViewport(dim(m0), IRanges(c(3, 2), width=block_dim))
    viewport1

    dim(viewport1)     # 'block_dim'
    length(viewport1)  # number of array elements in the viewport
    ranges(viewport1)

    ## ---------------------------------------------------------------------
    ## C. GRIDS CAN BE TRANSPOSED
    ## ---------------------------------------------------------------------

    tgrid2 <- t(grid2)
    dim(tgrid2)
    refdim(tgrid2)

    ## Use aperm() if the grid has more than 2 dimensions:
    tgrid1 <- aperm(grid1)
    dim(tgrid1)
    refdim(tgrid1)

    aperm(grid1, c(3, 1, 2))
    aperm(grid1, c(1, 3, 2))
    aperm(grid1, c(3, 1))     # some dimensions can be dropped
    aperm(grid1, c(3, 2, 3))  # and some can be repeated

    ## ---------------------------------------------------------------------
    ## D. DOWNSAMPLING AN ArrayGrid OBJECT
    ## ---------------------------------------------------------------------
    ## The elements (ArrayViewport) of an ArrayGrid object can be replaced
    ## with bigger elements obtained by merging adjacent elements. How many
    ## adjacent elements to merge along each dimension is specified via the
    ## 'ratio' vector (one integer per dimension). We call this operation
    ## "downsampling. It can be seen as reducing the "resolution" of a grid
    ## by the specified ratio (if we think of the grid elements as pixels).
    downsample(grid2, 2)
    downsample(grid2, 3)
    downsample(grid2, 4)

    ## Downsampling preserves the dimensions of the reference array:
    stopifnot(identical(refdim(downsample(grid2, 2)), refdim(grid2)))
    stopifnot(identical(refdim(downsample(grid2, 3)), refdim(grid2)))
    stopifnot(identical(refdim(downsample(grid2, 4)), refdim(grid2)))

    ## A big enough ratio will eventually produce the coarsest possible grid
    ## i.e. a grid with a single grid element covering the entire reference
    ## array:
    grid3 <- downsample(grid2, 7)
    length(grid3)
    grid3[[1L]]
    stopifnot(identical(dim(grid3[[1L]]), refdim(grid3)))

    ## Downsampling by a ratio of 1 is a no-op:
    stopifnot(identical(downsample(grid2, 1), grid2))

    ## Using one ratio per dimension:
    downsample(grid2, c(2, 1))

    ## Downsample a max resolution grid:
    refdim <- c(45, 16, 20)
    grid4 <- RegularArrayGrid(refdim, c(1, 1, 1))
    ratio <- c(6, 1, 3)
    stopifnot(identical(
        downsample(grid4, ratio),
        RegularArrayGrid(refdim, ratio)
    ))

[Package DelayedArray version 0.13.12 Index]