GENOVA_colours: Colours in GENOVA

In robinweide/GENOVA: GENOVA: expore the Hi-C

Colours in GENOVA

Description

GENOVA comes with a few built-in colour palettes. The gradients in GENOVA's palettes have been carefully chosen to be perceptually linear, which is great for Hi-C visualisations.

Sequential palettes

The sequential palettes are used for displaying absolute values, such as the (normalised) contacts values in Hi-C matrices, or the average of aggregates. The default palette is the 'Hot' palette. The default sequential palette can be changed by setting the global options.

options("GENOVA.colour.palette" = "whitered")

options("GENOVA.colour.palette" = "hot")

Hot

White-Red

Diverent palettes

The divergent palettes are used for displaying relative values, such as Z-score normalised contacts, differences and fold changes.

Divergent

The default divergent palette is called "divergent" and goes from a blue at low values, to a light grey at the midpoint to red at high values.

Green-Pink

A secondary divergent palette, "greenpink" is only used when two objects in a plot require divergent palettes, but need to be discriminated from oneanother.

Details

The colours in ggplot based visualisations, such as visualise() and pyramid(), are based on the scale_(colour|fill)_GENOVA() and scale_(colour|fill)_GENOVA_div() functions.

For visualisations in base R, such as hic_matrixplot() and image(), the colorRampPalette() function is used.

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.