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In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

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Area measures

Several functions in SPATA2 have arguments that take area input. To specifically refer to an area 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 an area 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 areas in SI units e.g. arg_input = c('2mm2', '4mm2') 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 validUnitsOfAreaSI().

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 = 'mm2') 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.

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.

Expansion of cropped image sections

The argument expand is a versatile way, to specify how a cropped image section is extracted. If you want the cropped image as is, specify expand = 0. Else, there are multiple options. In general, expand takes three kinds of values, namely percentages, distances and distance exclamations.

• Percentage: A string suffixed with %. E.g. expand = '50%' adds 50% of the distance from the center to the border of the image annotation to the image frame.

• Distance measures: In pixel or European units of length. E.g. expand = list(x = '1mm') expands the x-axis on both sides with 1mm. ⁠expand = list(x = c('0.5mm', 1.5mm')⁠ expands the x-axis on the left side with 0.5mm and on the right side with 1.5mm.

• Exclam distance measures: Distance measure with an exclamation mark suffix. E.g. expand = '1mm!' centers the image and forces an axis length of 1 millimeter. (Example 5)

Depending on how the values are specified different parts of the image can be expanded.

Single values, like expand = 50, are recycled: Every end of each image axis is expanded by 50 pixel. (Example 2)

Vectors of length two, like expand = c('1mm', '2mm'), are recycled: The beginning of each axis is expanded by 1 millimeter. The end of each axis is expanded by 2mm. (Example 3)

Named lists can be more precise. expand = list(x = c('1mm', '0.5mm'), y = c('0.25mm', '1mm')). Applies the vectors to expand the corresponding axis. (Example 4)

Using exclam input the side of the axis must not be specified as the axis is fixed as a whole. E.g expand = list(x = '1mm!', y = '2mm!') results in the same output as ⁠expand = list(x = c('1mm!', '1mm!'), y = c('2mm!', '2mm!')⁠.

Selection of image annotations with tags

Input for argument tags specifies the tags of interest. Argument test decides about how the specified tags are used to select the image annotations of interest. There are multiple options:

1. Argument test set to 'any' or 1: To be included, an image annotation must be tagged with at least one of the input tags.

2. Argument test set to 'all' or 2: To be included, an image annotation must be tagged with all of the input tags. Can contain tags that are not specified.

3. Argument test set to 'identical' or 3: To be included, an image annotation must be tagged with all of the input tags. Can not be tagged with anything else.

4. Argument test set to not_identical or 4: To be included, an image annotation must not be tagged with the combination of input tags.

5. Argument test set to 'none' or 5: To be included, an image annotation must not contain any of the input tags.

Note that the filtering process happens after the filtering by input for argument ids. You can first select a group of image annotations by naming their IDs and then select among them via tags and test. If ids is NULL, you select among all image annotations via tags and test. And if tags is also NULL, the function uses all image annoations.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.