Display axes with SI units of length

Performs necessary transformations to display axes of surface plots and STS/IAS line- or ridgeplots with SI units of length.

ggpLayerAxesSI(
  object,
  unit = getSpatialMethod(object)@unit,
  which = c("x", "y"),
  breaks = NULL,
  expand = NULL,
  add_labs = FALSE,
  round = 2,
  xlim = NULL,
  ylim = NULL,
  ...
)

Arguments

object

An object of class spata2.

unit

The desired unit. Defaults to the unit in which the original size of the image of the spatial method is provided. Obtain valid input options with validUnitsOfLengthSI().

which

One or two of 'x' and 'y'. Specifies for which axes the transformation is performed. Defaults to both.

breaks

Specifies where the breaks are set. Labels are plotted in the unit specified in unit. Valid input:

  • NULL: No specification. Five breaks are set equally distributed. Does not work with STS/IAS related plots as the range is taken from the whole image.

  • vector: Vector of distance measures. Breaks are set for axes denoted in which. (Defaults to both, x and y.)

  • list: List with slots x and y. Vector of distance measures to set each axis specifically.

expand

Specifies how the axis are expanded. Using expand of ggplot2::scale_x/y_continuous(). Valid input:

  • NULL: No specification. Default is used.

  • vector: Numeric vector of length two. Input is set for axes denoted in which. (Defaults to both, x and y.)

  • list: List with slots x and y. Numeric vector of length two, used for each axis specifically.

add_labs

Logical. If TRUE, adds x- and y-labs to the plot.

round

Numeric value or FALSE. If numeric, given to digits of base::round(). Rounds transformed values before they are returned.

xlim, ylim

Vectors of length two. Distance measures that set the limits on the respective axes.

...

Used to absorb deprecated arguments or functions.

breaks_x, breaks_y

Deprecated in favor of breaks.

frame_by

Deprecated. Use ggplayerFrame*() - functions.

Value

ggpLayer*()-functions return lists of ggproto objects that can be added to ggplots via the + operator. In most of the cases they are supposed to be added to plots created with the plotSurface*()

family.

Details

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.

Examples


 library(tidyverse)

 object <- downloadPubExample("313_T")

 object <- setDefault(object, pt_clrsp = "BuGn", display_image = FALSE)

 # ------ for surface plots

 # no axes specification
 plotSurface(object, color_by = "FN1") +
  ggpLayerThemeCoords()

 # in millimeters
 plotSurface(object, color_by = "FN1") +
  ggpLayerThemeCoords() +
  ggpLayerAxesSI(object, unit = "mm")


 # in millimeters set specifically
 my_breaks <- str_c(1:7, "mm")

 print(my_breaks)

 plotSurface(object, color_by = "FN1") +
  ggpLayerThemeCoords() +
  ggpLayerAxesSI(object, unit = "mm", breaks = my_breaks, add_labs = TRUE)

 plotSurface(object, color_by = "FN1") +
  ggpLayerThemeCoords() +
  ggpLayerAxesSI(object, unit = "mm", breaks = list(x = my_breaks, y = str_c(2:5, "mm")), add_labs = TRUE)


 # ----- for gradient plots

 plotSurface(object, color_by = "FN1") +
  ggpLayerHorizonIAS(object, id = "necrotic_center", distance = "2.25mm", binwidth = "112.5um")

 # no axis specification
 plotIasLineplot(object, id = "necrotic_center", distance = "2.25mm", variables = "FN1")

 # with axis specification, make sure to set which = "x" as y is used for expression!
 plotIasLineplot(object, id = "necrotic_center", distance = "2.25mm", variables = "FN1") +
  ggpLayerAxesSI(object, unit = "mm", breaks = str_c(c(0.5, 1, 1.5, 2), "mm"), which = "x")