Formulas

Formulas

Formulas are composed of macros on both sides, which are connected by '~'. It looks like the formula syntax from R: Y ~ X. This basically determines how the plots are generated.

However, we don't support operators like it from R. So we only have Y ~ X, but not Y ~ X1 + X2. In order to implement this, we have to define a macro to add X1 and X2 up.

We have three types of macros:

1. continuous: extracts continues values from a variant, such as allele frequency, depth, etc.
2. categorical: extracts categorical values from a variant, such as variant type, genotype, etc.
3. aggregation: aggregates some values from a group of variants, such as mean of allele frequency from chromosome 1. You can also add a filter to aggregation by COUNT(1, filter=AAF[0.05, 0.95], group=CHROM)

See section Macros for details.

Tip

If you have both aggregations for Y and X, you can omit the group for either. The one without group will automatically use the group that is specified to the other one.

Predefined figure types for different combination of Y and X

Y	X	default figure type	other available figure types
aggregation	aggregation	scatter	-
aggregation	categorical	col	pie
aggregation	1	pie	col
anything other than aggregation	aggregation	not available	-
categorical	categorical	bar	pie
continuous	categorical	voilin	boxplot/histogram/density/freqpoly
categorical	1	pie	bar
categorical	continuous (not 1)	not available	-
continueous	continuous	scatter	-

geoms from ggplot2 used to plot for different figure types

figure type	geom
scatter	geom_point
col	geom_col
pie	geom_col with coord_polar
bar	geom_bar
violin	geom_violin
boxplot	geom_boxplot
density	geom_density
freqpoly	geom_freqpoly