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regenerate subobjects and clean up code
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Package: GiottoData | ||
Type: Package | ||
Title: Datasets for Giotto | ||
Version: 0.2.11.0 | ||
Author: c( | ||
Version: 0.2.12.0 | ||
Authors@R: c( | ||
person("Ruben", "Dries", email = "[email protected]", | ||
role = c("aut", "cre")) | ||
) | ||
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Imports: | ||
data.table (>= 1.14.0), | ||
GiottoUtils (>= 0.1.7), | ||
rprojroot | ||
Suggests: | ||
devtools, | ||
GiottoVisuals, | ||
Giotto, | ||
reticulate, | ||
terra (>= 1.5-12) | ||
Remotes: | ||
drieslab/GiottoClass, | ||
|
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# GiottoData 0.2.12.0 (2024/05/22) | ||
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## Bug fixes | ||
- fix onload image subobject reconnection when generated from dev directory as opposed to lib directory | ||
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## Breaking changes | ||
- `gDataDir()` has been made an internal | ||
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## Enhancements | ||
- Additional params can now be passed to `GiottoClass::loadGiotto()` from `loadGiottoMini()` through `...` | ||
- `init_gobject` param for `loadGiottoMini()` | ||
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## New | ||
- `generate_mini_subobjects()` for rebuilding the mini subobjects | ||
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# GiottoData 0.2.11.0 (2024/05/21) | ||
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## Changes | ||
- Mini CosMx rebuilt for GiottoClass 0.3.1 | ||
- Mini Visium rebuilt for GiottoClass 0.3.1. Added both the "alignment" and "image" (H&E) images. "image" was also spatially re-aligned | ||
- Mini starmap rebuilt for GiottoClass 0.3.1 |
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#' @name generate_mini_subobjects | ||
#' @title Generate mini subobjects | ||
#' @description | ||
#' Generate the GiottoData mini subobjects based on Mini_objects_script.R | ||
#' in `/inst/Mini_objects/` subdirectory. | ||
#' @returns NULL invisibly | ||
#' @export | ||
generate_mini_subobjects <- function() { | ||
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script_path <- file.path( | ||
gdata_devdir(), "inst", "Mini_objects", "Mini_objects_script.R" | ||
) | ||
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source(script_path, echo = TRUE) | ||
return(invisible()) | ||
} |
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#' @title Get GiottoData library path | ||
#' @name gDataDir | ||
#' @description Utility function to find library install location of the GiottoData | ||
#' package. Provided as shorthand to make loading files easier. | ||
#' @export | ||
gDataDir = function() { | ||
system.file(package = 'GiottoData') | ||
#' @title Get GiottoData paths | ||
#' @name giottodata_paths | ||
#' @description Utility functions to get helpful filepaths within the | ||
#' \pkg{GiottoData} package. | ||
#' @param \dots passed to `file.path()` | ||
NULL | ||
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# library paths #### | ||
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#' @describeIn giottodata_paths Get the library install path | ||
#' of the package. Should not be used in contexts where package is loaded with | ||
#' `devtools::load_all()` | ||
#' @keywords internal | ||
gdata_libdir = function(...) { | ||
file.path(system.file(package = 'GiottoData'), ...) | ||
} | ||
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#' @describeIn giottodata_paths Get the library path to the mini | ||
#' subobjects directory | ||
#' @keywords internal | ||
gdata_subobject_libdir <- function(...) { | ||
gdata_libdir("Mini_objects", ...) | ||
} | ||
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#' @describeIn giottodata_paths Get the library path to the mini | ||
#' datasets directory | ||
#' @keywords internal | ||
gdata_dataset_libdir <- function(...) { | ||
gdata_libdir("Mini_datasets", ...) | ||
} | ||
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# development paths #### | ||
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#' @describeIn giottodata_paths Get the development root path | ||
#' @keywords internal | ||
gdata_devdir <- function(...) { | ||
file.path(rprojroot::find_package_root_file(), ...) | ||
} | ||
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#' @describeIn giottodata_paths Get the development path to the mini | ||
#' subobjects directory | ||
#' @keywords internal | ||
gdata_subobject_devdir <- function(...) { | ||
gdata_devdir("inst", "Mini_objects", ...) | ||
} | ||
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#' @describeIn giottodata_paths Get the development path to the mini | ||
#' datasets directory | ||
#' @keywords internal | ||
gdata_dataset_devdir <- function(...) { | ||
gdata_devdir("inst", "Mini_datasets", ...) | ||
} | ||
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# https://stackoverflow.com/questions/7963898/extracting-the-last-n-characters-from-a-string-in-r | ||
str_tail <- function(x, n){ | ||
substr(x, nchar(x)-n+1, nchar(x)) | ||
} |
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