A function for generating a consistent file system for data files and visualizations. If none of the parameters are set the full path generated by this function will be root_path/output
output_dir(start_path = NULL, experiment = NULL, plot_type = NULL, end_path = NULL, root_path = NULL, custom_path = NULL, overwrite = FALSE, mkdir = TRUE)
| start_path | With the start_path set, the full path generated by this function will be root_path/start_path/?experiment?/?plot_type?/end_path. Default: NULL |
|---|---|
| experiment | (optional) This will add a second level to the start_path file system. Default: NULL |
| plot_type | (optional) This will add a third level to the start_path file system. With ONLY the plot_type set the full path generated by this function will be root_path/plot_type. Default: NULL |
| end_path | (optional) This will add the final directory to the start_path file system Default: A formatted date-time string. |
| root_path | The root of the new file system (start_path or not). Default: The working directory. |
| custom_path | This is an absolute path that overrides everything else. Default: NULL |
| overwrite | A logical denoting that overwriting is acceptable. Default: FALSE |
| mkdir | A logical denoting weather or not the directory should be created or not. Default: TRUE |
Creates a directory for output and returns the path as a string.
This function is incredibly useful on it's own but also for various other plotting/saving functions within the package. It helps keep data organized using a standard workflow.
# NOT RUN { if(interactive()){ # Get the path to an output directory without creating library(MicrobiomeR) output_dir <- output_dir(start_path="output", experiment="microbiome-proj", mkdir=FALSE) print(output_dir) # Create a folder for your plot types output_dir <- output_dir(plot_type="scatter-plots") print(output_dir) } # }