createGiottoImage#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/images.R#L35

Description#

Creates a giotto image that can be added to a Giotto object and/or used to add an image to the spatial plotting functions

Usage#

createGiottoImage(
  gobject = NULL,
  spat_unit = NULL,
  spatial_locs = NULL,
  spat_loc_name = NULL,
  mg_object,
  name = "image",
  image_transformations = NULL,
  negative_y = TRUE,
  do_manual_adj = FALSE,
  xmax_adj = 0,
  xmin_adj = 0,
  ymax_adj = 0,
  ymin_adj = 0,
  scale_factor = 1,
  x_shift = NULL,
  y_shift = NULL,
  scale_x = NULL,
  scale_y = NULL,
  order = c("first_scale", "first_adj"),
  xmin_set = NULL,
  xmax_set = NULL,
  ymin_set = NULL,
  ymax_set = NULL,
  verbose = TRUE
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

spatial_locs

spatial locations (alternative if gobject = NULL )

spat_loc_name

name of spatial locations within gobject

mg_object

magick image object

name

name for the image

image_transformations

vector of sequential image transformations

negative_y

Map image to negative y spatial values if TRUE during automatic alignment. Meaning that origin is in upper left instead of lower left.

do_manual_adj

flag to use manual adj values instead of automatic alignment when given a gobject or spatlocs

xmax_adj, x min_adj, ymax_adj, ymin_adj

adjustment of the maximum or maximum x or y-value to align the image

scale_factor

scaling of image dimensions relative to spatial coordinates

x_shift, y_shift

shift image along x or y axes

scale_x, scale_y

independently scale image in x or y direction

order

perform scaling or adjustments and shifts first

xmin_set, x max_set, ymin_set, ymax_set

values to override image minmax spatial anchors when doing adjustments

verbose

be verbose

Details#

image_transformations: transformation options from magick library [ flip_x_axis ] flip x-axis ( `image_flop <#imageflop>`__ ) [ flip_y_axis ] flip y-axis ( `image_flip <#imageflip>`__ ) Example: image_transformations = c(flip_x_axis, flip_y_axis); first flip x-axis and then y-axis

Value#

a giottoImage object