saveGiotto

Saves a Giotto object to a specific folder structure

Usage

saveGiotto(
  gobject,
  foldername = "saveGiottoDir",
  dir = getwd(),
  method = c("RDS", "qs"),
  method_params = list(),
  overwrite = FALSE,
  export_image = TRUE,
  image_filetype = "PNG",
  include_feat_coord = TRUE,
  verbose = TRUE,
  ...
)

Arguments

gobject

Giotto object

foldername

Folder name

dir

Directory where to create the folder

method

method to save main object

method_params

additional method parameters for RDS or qs

overwrite

Overwrite existing folders

export_image

logical. Write out an image of the format specified by image_filetype when saving a giottoLargeImage. Future image loads and reconnects will point to this new file.

image_filetype

the image filetype to use, see writeRaster. Default is "PNG". For TIFF outputs, try "COG"

include_feat_coord

logical. Whether to keep the feature coordinates when saving. Dropping them can improve performance for large datasets.

verbose

be verbose

...

additional parameters for writeRaster

Value

Creates a directory with Giotto object information

Details

Works together with loadGiotto to save and re-load Giotto objects. Additional method_params need to be provided as a list and will go to saveRDS or qsave

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"

saveGiotto(gobject = g, dir = tempdir(), overwrite = TRUE)
#> Folder already exist and overwrite = TRUE,
#>  overwrite folder
#> 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
#> [1] TRUE