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Giotto instructions

Source: R/instructions.R, R/methods-instructions.R
giotto_instructions.Rd

Giotto instructions are default settings that are applied at the giotto object level. Once added to an object, they affect the way that the object behaves. You can create a giottoInstructions object using createGiottoInstructions() and add them to the giotto object during creation or using the instructions() generic. Specific settings can be replaced or retrieved using the param argument. Additionally, when using instructions<-() as a replacement function, initialize() will be called on the giotto object if initialize = TRUE.

If no giottoInstructions object is provided during giotto object creation, then a default one will be created during giotto object initialization.

Usage

createGiottoInstructions(
  python_path = getOption("giotto.py_path"),
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_dir = NULL,
  plot_format = NULL,
  dpi = NULL,
  units = NULL,
  height = NULL,
  width = NULL,
  is_docker = FALSE,
  plot_count = 0,
  fiji_path = NULL,
  no_python_warn = FALSE
)

# S4 method for class 'giotto,missing'
instructions(gobject)

# S4 method for class 'giotto,missing,missing'
instructions(gobject, initialize) <- value

# S4 method for class 'giotto,missing,logical'
instructions(gobject, initialize) <- value

# S4 method for class 'giotto,character'
instructions(gobject, param)

# S4 method for class 'giotto,character,missing'
instructions(gobject, param, initialize) <- value

# S4 method for class 'giotto,character,logical'
instructions(gobject, param, initialize) <- value

Arguments

python_path

path to python binary to use or directory one level up from the env directory (similar to output of reticulate::miniconda_path())

show_plot

print plot to console, default = TRUE

return_plot

return plot as object, default = TRUE

save_plot

automatically save plot, dafault = FALSE

save_dir

path to directory where to save plots

plot_format

format of plots (defaults to png)

dpi

resolution for raster images

units

units of format (defaults to in)

height

height of plots

width

width of plots

is_docker

using docker implementation of Giotto (defaults to FALSE)

plot_count

(global option) start count for creating automatic unique plots

fiji_path

path to fiji executable

no_python_warn

turn off warning that no compatible python env has been detected

gobject

giotto object

initialize

(boolean, default = TRUE) whether to initialize the giotto object

value

value to set

param

Specific param in instructions to access or modify

Value

giottoInstructions, instructions settings, or giotto objects with modified instructions

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"

# get instructions
instrs <- instructions(g)
force(instrs)
#> <giottoInstructions>
#> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python
#> show_plot        : TRUE
#> return_plot      : FALSE
#> save_plot        : FALSE
#> save_dir         : NA
#> plot_format      : png
#> dpi              : 300
#> units            : in
#> height           : 9
#> width            : 9
#> is_docker        : FALSE
#> active_spat_unit : cell
#> active_feat_type : rna

# get single instructions param
instructions(g, "show_plot")
#> [1] TRUE

# replace single instruction param
instructions(g, "show_plot") <- FALSE
instructions(g, "show_plot")
#> [1] FALSE

# replace multiple instruction params
instructions(g)
#> <giottoInstructions>
#> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python
#> show_plot        : FALSE
#> return_plot      : FALSE
#> save_plot        : FALSE
#> save_dir         : NA
#> plot_format      : png
#> dpi              : 300
#> units            : in
#> height           : 9
#> width            : 9
#> is_docker        : FALSE
#> active_spat_unit : cell
#> active_feat_type : rna
instructions(g, c("show_plot", "dpi")) <- list(TRUE, 600)
instructions(g)
#> <giottoInstructions>
#> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python
#> show_plot        : TRUE
#> return_plot      : FALSE
#> save_plot        : FALSE
#> save_dir         : NA
#> plot_format      : png
#> dpi              : 600
#> units            : in
#> height           : 9
#> width            : 9
#> is_docker        : FALSE
#> active_spat_unit : cell
#> active_feat_type : rna

# replace instructions
i <- createGiottoInstructions()
#> 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"
instructions(g) <- i
instructions(g)
#> <giottoInstructions>
#> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python
#> show_plot        : TRUE
#> return_plot      : TRUE
#> save_plot        : FALSE
#> save_dir         : /home/runner/work/GiottoClass/GiottoClass/docs/reference
#> plot_format      : png
#> dpi              : 300
#> units            : in
#> height           : 9
#> width            : 9
#> is_docker        : FALSE
#> active_spat_unit : cell
#> active_feat_type : rna