reconnectGiottoImage#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/images.R#L2456

Description#

reconnect a gobject’s dead image pointers using filepaths to the original source image files

Usage#

reconnectGiottoImage(
  gobject,
  auto_reconnect = TRUE,
  image_name = NULL,
  largeImage_name = NULL,
  image_path = NULL,
  largeImage_path = NULL,
  verbose = TRUE
)

Arguments#

Argument

Description

gobject

giotto object

auto_reconnect

automatically reconnect images if TRUE. manual if FALSE

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