Visium-class: The 'Visium' - Class
In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Visium-class

R Documentation

The `Visium` - Class

Description

Abstracts the concept of 10X Visium spatial biology experiments.

Slots

capture_area: list. List of length two. Provides standardized measures of the active region where tissue can be placed on a Visium slide.
ccd: character. The center to center distance of the barcoded spots provided in a valid SPATA2 spatial measure.
fiducial_frame: list. List of length two. Provides standardized measures of spots help the sample microscopist see where to place tissue and are also used by Space Ranger to determine where the capture area is in an image.
info: list. List of miscellaneous meta data for the method.
name: character. The name of the spatial method.
observational_unit: character. Single word that describes the observational unit of the experiment.

Distance measures

Several functions in SPATA2 have arguments that take distance input. To specifically refer to a distance the unit must be specified. There are three ways to create valid input for these arguments.

1. In pixel:

There are two valid input options to specify the distance in pixel:

numeric: Single numeric values, e.g. arg_input = c(2, 3.554, 69, 100.67). If no unit is specified the input will be interpreted as pixels.
character: Suffixed with 'px', e.g. arg_input = c('2px', '3.554px', '69px', '100.67px')

Note: The unit pixel (px) is used for distances as well as for areas. If pixel refers to a distance the pixel side length is meant. If pixel refers to an area the number of pixels is meant.

2. According to the Systeme international d'unites (SI):

Specifying distances in SI units e.g. arg_input = c('2mm', '4mm') etc. requires the input to be a character as the unit must be provided as suffix. Between the numeric value and the unit must be no empty space! Valid suffixes can be obtained using the function validUnitsOfLengthSI().

3. As vectors of class unit:

Behind the scenes SPATA2 works with the units package. Input is converted into vectors of class units. Therefore, input can be directly provided this way: arg_input = units::set_unit(x = c(2,4), value = 'mm') Note that pixel is not a valid unit in the units package. If you want to specify the input in pixel you have to use input option 1. In pixel.