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
andscale_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 ifFALSE
- verbose
be verbose
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
#> [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