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 'missing,missing'
instructions(gobject, param, ...)
# S4 method for class 'giotto,missing'
instructions(gobject)
# S4 method for class 'giotto,character'
instructions(gobject, param)
# S4 method for class 'giottoInstructions,character'
instructions(gobject, param)
# 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,missing'
instructions(gobject, param, initialize) <- value
# S4 method for class 'giotto,character,logical'
instructions(gobject, param, initialize) <- value
# S4 method for class 'giottoInstructions,character,ANY'
instructions(gobject, param) <- valueArguments
- python_path
path to python binary to use or directory one level up from the
envdirectory (similar to output ofreticulate::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
- param
Specific param in instructions to access or modify
- ...
params to pass to
createGiottoInstructions()- initialize
(boolean, default = TRUE) whether to initialize the giotto object
- value
value to set
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"
# create instructions
ins <- instructions()
#> 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 an 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