updateGiottoImageMG: updateGiottoImageMG

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

updateGiottoImageMG

Description

Updates the boundaries of a giotto image object attached to a giotto object if both gobject and image_name params are given. Alternatively can directly accept and return as image

Usage

updateGiottoImageMG(
  gobject = NULL,
  image_name = NULL,
  giottoImage = NULL,
  xmax_adj = 0,
  xmin_adj = 0,
  ymax_adj = 0,
  ymin_adj = 0,
  x_shift = 0,
  y_shift = 0,
  scale_factor = NULL,
  scale_x = 1,
  scale_y = 1,
  order = c("first_adj", "first_scale"),
  xmin_set = NULL,
  xmax_set = NULL,
  ymin_set = NULL,
  ymax_set = NULL,
  return_gobject = TRUE,
  verbose = TRUE
)

Arguments

gobject	giotto object containing giotto image object
image_name	name of giotto image object
giottoImage	image object to directly update
xmax_adj, xmin_adj, ymax_adj, ymin_adj	adjust image boundaries by increasing maximum and decreasing minimum bounds respectively of xy bounds
x_shift, y_shift	shift entire image along xy axes
scale_factor	set scale_x and scale_y params at the same time
scale_x, scale_y	independently scale x or y axis image mapping from coordinate origin
order	order of operations between fine adjustments (adjustment and shift parameters) and scaling
xmin_set	set image xmin boundary. Applied before adjustments
xmax_set	set image xmax boundary. Applied before adjustments
ymin_set	set image ymin boundary. Applied before adjustments
ymax_set	set image ymax boundary. Applied before adjustments
return_gobject	return a giotto object if TRUE, a giotto image object if FALSE
verbose	be verbose

Value

a giotto object or an updated giotto image object if return_gobject = FALSe

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