The Giotto instructions slot contains values that homogenize and facilitate the behavior of the Giotto object, such as whether the plots should be stored locally, shown, or returned, where to save the plots, what python path to use, etc.
If you don’t provide specific instructions, some default values will be automatically added.
Create new instructions and save them in a variable to pass them to the Giotto object later.
results_folder <- "path/to/results"
python_path <- NULL
instructions <- createGiottoInstructions(save_dir = results_folder,
save_plot = TRUE,
show_plot = FALSE,
return_plot = FALSE,
python_path = python_path)
createGiottoObject(expression = my_expression,
spatial_locs = my_spatial_locs,
instructions = instructions)
# Ensure Giotto Suite is installed
if(!"Giotto" %in% installed.packages()) {
pak::pkg_install("drieslab/Giotto")
}
# Ensure Giotto Data is installed
if(!"GiottoData" %in% installed.packages()) {
pak::pkg_install("drieslab/GiottoData")
}
library(Giotto)
# Ensure the Python environment for Giotto has been installed
genv_exists <- checkGiottoEnvironment()
if(!genv_exists){
# The following command need only be run once to install the Giotto environment
installGiottoEnvironment()
}
# load the object
g <- GiottoData::loadGiottoMini("visium")
instructions(g)
instructions(g, "return_plot") <- TRUE
instructions(g, c("return_plot", "save_plot")) <- c(TRUE, TRUE)R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin20
Running under: macOS Sequoia 15.0.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Giotto_4.1.4 GiottoClass_0.4.3
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 viridisLite_0.4.2
[3] dplyr_1.1.4 GiottoVisuals_0.2.7
[5] fastmap_1.2.0 SingleCellExperiment_1.26.0
[7] lazyeval_0.2.2 digest_0.6.37
[9] lifecycle_1.0.4 terra_1.7-78
[11] magrittr_2.0.3 compiler_4.4.2
[13] rlang_1.1.4 tools_4.4.2
[15] igraph_2.0.3 utf8_1.2.4
[17] yaml_2.3.10 data.table_1.16.0
[19] knitr_1.48 S4Arrays_1.4.1
[21] htmlwidgets_1.6.4 reticulate_1.39.0
[23] DelayedArray_0.30.1 abind_1.4-8
[25] withr_3.0.1 purrr_1.0.2
[27] BiocGenerics_0.50.0 grid_4.4.2
[29] stats4_4.4.2 fansi_1.0.6
[31] colorspace_2.1-1 ggplot2_3.5.1
[33] scales_1.3.0 gtools_3.9.5
[35] SummarizedExperiment_1.34.0 cli_3.6.3
[37] rmarkdown_2.28 crayon_1.5.3
[39] generics_0.1.3 rstudioapi_0.16.0
[41] httr_1.4.7 rjson_0.2.23
[43] zlibbioc_1.50.0 parallel_4.4.2
[45] XVector_0.44.0 matrixStats_1.4.1
[47] vctrs_0.6.5 Matrix_1.7-1
[49] jsonlite_1.8.9 GiottoData_0.2.15
[51] IRanges_2.38.1 S4Vectors_0.42.1
[53] ggrepel_0.9.6 scattermore_1.2
[55] magick_2.8.5 GiottoUtils_0.2.0
[57] plotly_4.10.4 tidyr_1.3.1
[59] pak_0.8.0 glue_1.8.0
[61] codetools_0.2-20 cowplot_1.1.3
[63] gtable_0.3.5 GenomeInfoDb_1.40.1
[65] GenomicRanges_1.56.1 UCSC.utils_1.0.0
[67] munsell_0.5.1 tibble_3.2.1
[69] pillar_1.9.0 htmltools_0.5.8.1
[71] GenomeInfoDbData_1.2.12 R6_2.5.1
[73] evaluate_1.0.0 lattice_0.22-6
[75] Biobase_2.64.0 png_0.1-8
[77] backports_1.5.0 SpatialExperiment_1.14.0
[79] Rcpp_1.0.13 SparseArray_1.4.8
[81] checkmate_2.3.2 colorRamp2_0.1.0
[83] xfun_0.47 MatrixGenerics_1.16.0
[85] pkgconfig_2.0.3