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createGiottoImage
createGiottoImage.Rd
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 (e.g. "cell")
- 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
(default = FALSE) 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