createGiottoInstructions

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

Argument

Description

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` <#creategiottoinstructions>`_

  • The provided instructions for a giotto object can be viewed with ``showGiottoInstructions` <#showgiottoinstructions>`_

  • One or more parameters can be changed with ``changeGiottoInstructions` <#changegiottoinstructions>`_

  • All instructions can be replaced with the ``replaceGiottoInstructions` <#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` <#showsaveparameters>`_ for more details

Value

named vector with giotto instructions

Seealso

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)