createGiottoInstructions: createGiottoInstructions

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

createGiottoInstructions

Description

Function to set global instructions for giotto functions

Usage

createGiottoInstructions(
  python_path = NULL,
  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
)

Arguments

python_path	path to python binary to use
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)

Details

## This is a simple guide to help explain the different Giotto instructions:

• Instructions can be set at the beginning of each workflow with createGiottoInstructions

• The provided instructions for a giotto object can be viewed with showGiottoInstructions

• One or more parameters can be changed with changeGiottoInstructions

• All instructions can be replaced with the replaceGiottoInstructions function

## The following list of parameters can be provided to save_param:

• python_path: here you can provide the path to your custom python binary (only at beginning of script)

• show_plot: TRUE or FALSE, show the plot to the console

• return_plot: TRUE or FALSE, return the ggplot object (e.g. to further modify or save the plot)

• save_plot: TRUE or FALSE, automatically save the plot to your designated save_dir

• save_dir: directory to save the plot to

• plot_format: default picture format to use, default is .png

• dpi: default dpi for each plot if plot is in raster format

• units: default plotting units (e.g. in)

• height: default height of plot

• width: default width of plot

#' Specific saving instructions can also be directly provided for each plotting function. See showSaveParameters for more details

Value

named vector with giotto instructions

See Also

More online information can be found here https://rubd.github.io/Giotto_site/articles/instructions_and_plotting.html

Examples

instructions <- createGiottoInstruction(python_path = '/path/to/python',
                                        save_plot = TRUE,
                                        save_dir = '/path/to/working/dir')


giotto_object <- createGiottoObject(raw_exprs = '/path/to/expression/matrix',
                                    spatial_locs = '/path/to/spatial/locations',
                                    instructions = instructions)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.