Plot histology images (ggplot2)

Reads in and plots all images known to the SPATA2 object.

plotImagesGgplot(
  object,
  names = NULL,
  verbose = NULL,
  nrow = NULL,
  ncol = NULL,
  ...
)

Arguments

object

An object of class spata2.

names

Character vector or NULL. If character, specifies the images by name. If NULL, all images are plotted.

verbose

Logical. If set to TRUE informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)

nrow, ncol

Numeric values or NULL. Used to arrange multiple plots.

...

Additionel arguments given to plotImageGgplot().

Value

A ggplot assembled with via patchwork::wrap_plots().

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.