Layout: The Layout class
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Details Fields and Methods Note Author(s) See Also Examples

Package: aroma
Class Layout

Object
~~|
~~+--Layout

Directly known subclasses:
GalLayout

public static class Layout
extends Object

The Layout class describes the layout of a microarray slide, such as the number of spots and the layout of the grids etc. A microarray slide is layout in a number of grids, where each grid is refered to by its row and its column. Within each grid, each spot is refered to by its row and its column within that grid. For example, a microarray slide with 4*3 grids and where each grid has 12*10 spots, has in total 4*3*12*10 = 12*120 = 1440 spots. The spot in the top left corner is located at grid (1,1) and spot (1,1) and we say it has the location (1,1,1,1). In the above example, the spot in the lower right corner of the slide has the location (4,3,12,10). Further more, each spot on a microarray slide has a unique index. This index starts counting starts with grid 1, moves along row 1 from column 1 until the last column, then advances to the next row. After all rows in grid 1 are indexed, counting proceeds to grid 2 and so on. This way of indexing the spots is used by for instance GenePix, Spot and ScanAlyze. Continuing the example above, the spot at location (1,1,1,1) has index 1, the spot at location (4,3,12,10) has index 1440. The spot at location (2,2,11,3) has index ((2-1)*3+(2-1))*12*10+(11-1)*10+3 = 483. To get the index from a location one do getIndex(layout, 2,2,11,3) where layout <- Layout(4,3,12,10). To get the location from a index one do getLocation(layout, 483), which gives the vector (2, 2, 11, 3). To get the position, i.e. the overall row and column of a spot on the microarray slide one can do getPosition(483) which give the position (23,13).

All spots are refered to by their unique indices.

1	Layout(ngrid.r=0, ngrid.c=0, nspot.r=0, nspot.c=0, geneSpotMap=NULL, name=NULL, id=NULL, plate=NULL, printorder=NULL)

`nspot.r`	The number of rows of spots per grid. This first argument can also be a list containing the fields nspot.r, nspot.c, ngrid.r, and ngrid.c.
`nspot.c`	The number of columns of spots per grid.
`ngrid.r`	The number of rows of grids per slide.
`ngrid.c`	The number of columns of grids per slide.
`name`	A `vector` of names for the spot. optional.
`id`	A `vector` of ids for the spot. optional.
`printorder`	A `matrix` or a `character` string specifying the order that spots where printed. For more details `*setPrintorder()`.
`geneSpotMap`	.
`plate`	.

GenBank Accession numbers, SwissProt/TrEMBL Accession numbers or Entry Names.

Fields

	`ngrid.r`	The number of rows of grids per slide.
	`ngrid.c`	The number of columns of grids per slide.
	`nspot.r`	The number of rows of spots in each grid.
	`nspot.c`	The number of columns of spots in each grid.
	`name`	A `vector` of strings which specified the name of each gene.
	`id`	A `vector` of strings which specified the id of each gene.

Methods:

	`anonymize`	-
	`as.character`	-
	`as.data.frame`	-
	`as`	-
	`as.Layout`	-
	`equals`	Checks if a Layout object is equals to some other object.
	`fromDataFrame`	-
	`getBlank`	-
	`getGeneGroups`	-
	`getId`	Gets the id of one or more spots.
	`getIndex`	Gets the index of a spot given its location.
	`getIndices`	Gets the indices of the spots at the given locations.
	`getLayoutGroupsByName`	-
	`getLocation`	Gets the location of a spot given its index.
	`getName`	Gets the name of one or more spots.
	`getPlate`	-
	`getPlateGroups`	-
	`getPlateNumber`	-
	`getPosition`	Gets the position of a set of spots given their indices.
	`getPrintdipGroups`	-
	`getPrintorder`	Gets the order of the spots in which they were printed.
	`getPrinttipGroups`	-
	`getSlideColumnGroups`	-
	`getSlideRowGroups`	-
	`gridSize`	Gets the number of spots in each grid.
	`hasIds`	-
	`hasNames`	-
	`hasPlates`	-
	`indexOf`	Gets the index of one or more spots from their name or id.
	`nbrOfColumns`	Gets the number of columns on a microarray.
	`nbrOfGrids`	Gets the number of grids on a microarray.
	`nbrOfPlates`	-
	`nbrOfReplicates`	-
	`nbrOfRows`	Gets the number of rows on a microarray.
	`nbrOfSpots`	Gets the size of a microarray.
	`put`	-
	`read`	Reads layout information from a tab-delimited file.
	`rename`	-
	`set`	Sets the layout.
	`setGeneGroups`	-
	`setId`	Sets the id of one or more spots.
	`setName`	Sets the name of one or more spots.
	`setPlate`	-
	`setPlateGroups`	-
	`setPrintdipGroups`	-
	`setPrintorder`	-
	`setPrinttipGroups`	-
	`setSlideColumnGroups`	-
	`setSlideRowGroups`	-
	`size`	Gets the size of a microarray.
	`toXYMatrix`	Layouts out values in the same way as the spots are layout.
	`write`	Writes the layout information to a tab-delimited file.

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save

There are several functions that returns a Layout object. It is only in very special cases that you have to create one yourself.

In the sma package some functions are related to this class. This, class might be backward compatible with these functions, but the reverse is not true. The following functions are known be related to this class: init.grid, id2image (and image2id).

Henrik Bengtsson (http://www.braju.com/R/)

MicroarrayData.getLayout.

  layout <- Layout(ngrid.r=4, ngrid.c=4, nspot.r=18, nspot.c=18)

  SMA$loadData("mouse.setup")
  layout <- Layout(mouse.setup)
  # or, equivalent...
  layout <- as.Layout(mouse.setup)