createGiottoImage#

Last Updated: Mar 11, 2023

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#

`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, xmin_adj, ymax_adj, y m in_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, xmax_set, ymin_set, y m ax_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) [flip_y_axis] flip y-axis (image_flip) Example: image_transformations = c(flip_x_axis, flip_y_axis); first flip x-axis and then y-axis

Value#

a giottoImage object