ggpLayerZoom: Set plot limits manually

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Set plot limits manually

Description

Sets the limits on the x- and y-axis of a ggplot based on manual input.

Usage

ggpLayerZoom(
  object = NULL,
  xrange = NULL,
  yrange = NULL,
  expand_x = c(0, 0),
  expand_y = c(0, 0),
  round = 2,
  n_breaks = 5,
  unit = NULL,
  img_name = activeImage(object)
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
xrange, yrange	Distance vector of length two or NULL. If not NULL, specifies the x- and y-range to which the spatial output is cropped. E.g. xrange = c(200, 500) results in the two dimensional space being cropped from x-coordinate 200px up to x-coordinate 500px. If NULL, the original range is used.
expand_x, expand_y	Given to expand of ggplot2::scale_x/y_continuous().
unit	Character value. Overwrites the unit of the x- and y-axis. (If NULL, the defalt, the unit for the respective axis is taken from xrange and yrange input.)
img_name	Character value. The name of the image of interest. If NULL, the active image is chosen by default. Either way, must be one of getImageNames().

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.

Examples

library(SPATA2)
library(patchwork)

object <- loadExampleObject("UKF275T")

object <-
 createNumericAnnotations(
   object = object,
   variable = "HM_HYPOXIA",
   threshold = "kmeans_high",
   id = "hypoxia_ann",
   inner_borders = FALSE,
   force1 = TRUE
   )

# range of hypoxia annotation
hr <- getSpatAnnRange(object, id = "hypoxia_ann")

hr_ggpL <- ggpLayerSpatAnnOutline(object, ids = "hypoxia_ann")

plotSurface(object, "HM_HYPOXIA") + hr_ggpL

p_rect <-
 plotImage(object) +
 hr_ggpL +
 ggpLayerRect(object, xrange = hr$x, yrange = hr$y)

p_zoomed <-
 plotImage(object) +
 ggpLayerZoom(object, xrange = hr$x, yrange = hr$y)

p_rect + p_zoomed

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.