create_subdir	Create subfolder within out for saving results	false
verbose	Print debugging messages	true
encode_url	Encode all input URLsĘ	false
splitby_field	Field name or list of field names to for which data should be separated	cell_id
experimental_param	Field names of parameters in which a head to head comparison should be made. Most useful for optimizing parameters	x_density
annot_field	List of fields to include in annotation box. Shows all unique values of each field to point to causes of variability in each boxplot.	pert_type
num_decimals	Number of decimal places to show in x-variable value ticks	3
save_plot	Boolean. Save figures to output directory as PNG files	true
save_fig	Boolean. Save plots in FIG format. Useful if formatting plots need to be resized or reformatted.	false
heatmap_ctls	Show controls in heatmap	false
save_gct	Save subset of GUTC matrix containing treatment signature connections	true
show_figure	Show figure windows	false