loadGiotto

Saves a Giotto object to a specific folder structure

Usage

loadGiotto(
  path_to_folder,
  load_params = list(),
  reconnect_giottoImage = TRUE,
  python_path = NULL,
  init_gobject = TRUE,
  verbose = TRUE
)

Arguments

path_to_folder

path to folder where Giotto object was stored with saveGiotto

load_params

additional parameters for loading or reading giotto object

reconnect_giottoImage

(default = TRUE) whether to attempt reconnection of magick based image objects

python_path

(optional) manually set your python path

init_gobject

logical. Whether to initialize the giotto object after loading. (default = TRUE)

verbose

be verbose

Value

Giotto object

Details

Works together with saveGiotto to save and re-load Giotto objects. Additional load_params need to be provided as a list and will go to readRDS or qread You can set the python path, alternatively it will look for an existing Giotto python environment.

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"
td <- tempdir()
saveGiotto(gobject = g, dir = td)
#> 1. Start writing feature information
#> 2. Start writing spatial information
#> For spatial information: cell
#> 3. Start writing image information
#> For image information: alignment
#> For image information: image

loadGiotto(path_to_folder = paste0(td, "/saveGiottoDir"))
#> 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"
#> 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