reconnect a gobject's dead image pointers using filepaths to the original source image files
Usage
reconnectGiottoImage(
gobject,
auto_reconnect = TRUE,
reconnect_type = c("all", "image", "largeImage"),
image_name = NULL,
largeImage_name = NULL,
image_path = NULL,
largeImage_path = NULL,
verbose = TRUE
)Arguments
- gobject
giotto object
- auto_reconnect
automatically reconnect images if TRUE. manual if FALSE
- reconnect_type
type of image to reconnect when auto_reconnect = TRUE
- image_name
names of images to reconnect
- largeImage_name
name of large images to reconnect
- image_path
named list of paths to images to reconnect to giottoImages
- largeImage_path
named list of paths to images to reconnect to giottoLargeImages
- verbose
be verbose
Details
Inputs can either be given as both image
name (image_name/largeImage_name) and
filepath (image_path/largeImage_path) args or as only a named
list through a filepath argument alone. If auto_reconnect = TRUE then
no additional params need to be supplied. As long as giotto image objects
were directly created using filepaths, those filepaths are stored within
the image objects and will be referenced during reconnection. Issues will
only arise if giotto image objects were created directly from the underlying
image handling package objects (magick or raster objects) or
if image files have been moved since the the giotto image object was
generated. In such cases, use manual reconnection by
setting auto_reconnect = FALSE.
See also
Other basic image functions:
addGiottoImage(),
plotGiottoImage(),
updateGiottoImage()
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"
reconnectGiottoImage(g, reconnect_type = "largeImage")
#> Attempting automatic reconnection...
#> largeImage(s) discovered...
#> --> alignment : filepath found
#>
#> --> image : filepath found
#>
#>
#> done
#> 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