ggpLayerSpatAnnPointer: Add pointer towards spatial annotations
In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

ggpLayerSpatAnnPointer

R Documentation

Add pointer towards spatial annotations

Description

Adds segments and, if desired, labels to the surface plot that point towards and highlight the position of spatial annotations.

Usage

ggpLayerSpatAnnPointer(
  object,
  ids = NULL,
  tags = NULL,
  test = "any",
  color_by = NULL,
  ptr_angles = 45,
  ptr_labels = NULL,
  ptr_lengths = "250um",
  ptr_alpha = 0.9,
  ptr_arrow = NULL,
  ptr_color = "black",
  ptr_size = 1,
  text_alpha = 0.9,
  text_color = "black",
  text_dist = 0,
  text_nudge_x = 0,
  text_nudge_y = 0,
  text_size = 4,
  point_at = "center",
  seed = NULL,
  clrp = NULL,
  clrp_adjust = NULL
)

Arguments

`object`	An object of class `SPATA2` or, in case of S4 generics, objects of classes for which a method has been defined.
`tags`	Character vector or `NULL`. If character, the tags for the image annotation selection. See section Selection of spatial annotations for more information.
`test`	Character value. One of c('any'. 'all', 'identical', 'not_identical', 'none'). Specifies how input for `tags` is used to select spatial annotations. See section Selection of spatial annotations for more information.
`color_by`	Character value or `NULL`. If character, one of 'id' or 'label' which colors the the pointers accordingly.
`ptr_angles`, `ptr_lengths`	Numeric value of length 1 or of length equal to the number of spatial annotations. Specifies the angle from which the segments points towards the spatial annotation as well as their length. `ptr_lengths` works within the SPATA2 distance framework. See section Distance measures for more information.
`ptr_labels`	Specifies if and how the pointers are labeled. If `NULL`, the default, the spatial annotations are labeled by their ID. If character, specifies the exact label of each spatial annotation and should be of length 1 or of length equal to the number of spatial annotations. If `FALSE`, no text is displayed.
`ptr_alpha`	Numeric value. Specifies the transparency of the pointers.
`ptr_arrow`	`NULL` or `arrow` as displayed by `grid::arrow()`.
`ptr_color`	Character value. Specifies the color of the pointers if `color_by` is not a character.
`ptr_size`	Numeric value. Specifies the size (thickness) of the pointers.
`text_dist`	Distance measure. Specifies the distance from the text to the pointer.
`point_at`	Character value. If 'center', the pointer is directed at the center of the spatial annotation. If 'border', the pointer points at a random point of the spatial annotation border - recommended if the spatial annotation is big.
`seed`	Numeric value or `NULL`. If numeric, sets seed before picking a random point of the spatial annotation border if `point_at = 'border'`.
`clrp`	Character value. Specifies the color palette to be used to represent groups of discrete variables. Run `validColorPalettes()` to obtain valid input options.
`clrp_adjust`	Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.

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.