createGiottoImage: createGiottoImage

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

createGiottoImage

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, 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, xmax_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) [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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.