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updateGiottoImage

Source: R/images.R
updateGiottoImage.Rd

Updates the spatial positioning and sizing of a giotto image or largeImage attached to a giotto object.

Usage

updateGiottoImage(
  gobject = NULL,
  image_name = NULL,
  largeImage_name = 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"),
  xmax_set = NULL,
  xmin_set = NULL,
  ymax_set = NULL,
  ymin_set = NULL,
  return_gobject = TRUE,
  verbose = TRUE
)

Arguments

gobject

gobject containing desired image object

image_name

name of giotto image object

largeImage_name

name of giotto largeImage object

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, xmax_set, ymin_set, ymax_set

directly set xy image boundaries. Overrides minmax values as spatial anchor.

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

Details

This function works for all image objects associated with Giotto.

See also

Other basic image functions: addGiottoImage(), plotGiottoImage(), reconnectGiottoImage()

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"

updateGiottoImage(g, largeImage_name = "image")
#> An object of class giotto 
#> >Active spat_unit:  cell 
#> >Active feat_type:  rna 
#> dimensions    : 634, 624 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons      : cell 
#> [AGGREGATE INFO]
#> expression -----------------------
#>   [cell][rna] raw normalized scaled
#> spatial locations ----------------
#>   [cell] raw
#> spatial networks -----------------
#>   [cell] Delaunay_network spatial_network
#> spatial enrichments --------------
#>   [cell][rna] cluster_metagene DWLS
#> dim reduction --------------------
#>   [cell][rna] pca custom_pca umap custom_umap tsne
#> nearest neighbor networks --------
#>   [cell][rna] sNN.pca custom_NN
#> attached images ------------------
#> images      : alignment image 
#> 
#> 
#> Use objHistory() to see steps and params used