reconnectGiottoImage: Reconnect images with dead pointers

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Reconnect images with dead pointers

Description

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 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.

Value

a giotto object with updated image pointer

See Also

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.