sclero (version 0.2)

assign.size: Assign spot sizes to 'rawDist' objects for estimating spatial extent of sample averaging error.

Description

Assigns spot sizes to rawDist objects for estimating averaging error.

Usage

assign.size(rawDist, file = NULL, path = NULL, names = "generate.invalid", types = c("oval", "freehand", "rect"))

Arguments

rawDist

rawDist object to which the values should be assigned.

file

optional. ImageJ .zip file containing the spot size information. If NULL (default), the file name is assumed to be the same than from where rawDist data was read from.

path

optional. A character argument specifying the location of the file. If NULL (default), the file is assumed to be located in the working directory. See dir for further information.

names

optional. A character argument specifying how the names of spots should be generated. See read.ijdata for details. Defaults to "generate.invalid".

types

optional. A character vector specifying the strType of ROI objects to be considered as sample spots (see plot.ijroi for possible pattern types). Defaults to c("oval", "freehand", "rect") meaning that oval and freehand selections, as well as rectangle tool selections will be used to calculate the spatial extent of sample spots.

Value

Returns a list of class 'rawDist' with a list of ppp objects containing locations of sample spot centroids and a list of hyperframes containing spot size information.

Details

If the .zip file containing spot size information is the same than from which the rawDist object was derived from and located in your working directory, assignment of spot sizes is simply specified by assign.size(rawDist). Otherwise, use the path argument to specify the folder where the file is located.

See Also

read.ijdata spot.dist assign.value plot.spotDist

Examples

data(shellspots)
shell <- convert.ijdata(shellspots)
path <- file.path(system.file("extdata", package = "sclero"))
sizes <- assign.size(shell, path = path)
sizes$spot.area