Appendix E — YAML Parameters

All reports are run from a Parent.qmd file, which has a yaml header with a params section.

The various parameters of this section are described below.

E.1 Explanation of YAML Parameters

Parameter	Default Value	Description
adcode	false	Whether to show R code.
analyse_type	null <QC,DA,DS>	Specify analysis type.
annotation_column	null	Column used for annotation; defaults to none.
batch	null	Batch metadata column name for the analysis, if applicable.
cluster_id	"cluster_id"	Default identifier for clusters.
col_block	null	block_id’s diffcyt parameter.
cols_design_GLMM_random	null	Columns used in GLMM for random effects.
conditions	null	Conditions metadata column name under which the analysis is performed.
conditions_reference	null	Reference condition for comparison in analyses.
contrast	null	Contrast condition for analysis, each is compare to conditions_reference .
fc	1	Fold change threshold for significance.
log_bar	false	Whether to use logarithmic scaling on bar plots.
min_cells	1	Minimum number of cells required per sample.
min_samples	null	Minimum number of samples required for analysis.
path	<file path>	Path to the data file.
p_value	0.05	P-value threshold for statistical significance.
plot_legends	null	Metadata column name to add on graphs.
project	null	Project description if provided.
rds	<.rds>	RDS file name.
show_parameters	true	Whether to show parameters in outputs.
show_summary	true	Whether to display summary information tables.
show_heatmap_on_off	true	Whether to show or hide the number of cells per fcs heatmaps.
sorted	false	Whether data should be sorted on graph by conditions.
transform	false	Whether data should be transformed on Differential analysis.
subset_column	null	Column used for subsetting data, if applicable.