createGiottoInstructions | R Documentation |
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
)
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) |
## 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
named vector with giotto instructions
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)
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