plotImageGgplot: Plot histology image (ggplot2)

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

Plot histology image (ggplot2)

Description

Plots the histology image with ggplot2.

Usage

plotImageGgplot(
  object,
  unit = getSpatialMethod(object)@unit,
  frame_by = "image",
  xrange = NULL,
  yrange = NULL,
  ...
)

Arguments

object	An object of class spata2.
unit	Character value. Units of x- and y-axes. Defaults to 'px'.
xrange, yrange	Vector of length two or NULL. If not NULL, specifies the x- and y-range to which the output image is cropped. E.g. xrange = c(200, 500) results in the image being cropped from x-coordinate 200px up to x-coordinate 500px. If NULL, the original image ranges are taken. This argument works within the SPATA2 distance framework. If values are specified in European units of length the input is immediately converted to pixel units. See info section Distance measures for more information.
...	Additional arguments given to ggpLayerAxesSI() if unit is not 'px'.

Value

A ggplot.

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.

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