Function to set global instructions for giotto functions
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
)path to python binary to use
print plot to console, default = TRUE
return plot as object, default = TRUE
automatically save plot, dafault = FALSE
path to directory where to save plots
format of plots (defaults to png)
resolution for raster images
units of format (defaults to in)
height of plots
width of plots
using docker implementation of Giotto (defaults to FALSE)
named vector with giotto instructions
## 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
More online information can be found here https://rubd.github.io/Giotto_site/articles/instructions_and_plotting.html
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)