% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/colours.R
\name{GENOVA_colours}
\alias{GENOVA_colours}
\title{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.
}
\section{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.

\preformatted{

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

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

}

\subsection{Hot}{

\if{html}{
  \out{<div style="text-align: center">}\figure{colour-hot.png}{options: style="width:255px;max-width:100\%;"}\out{</div>}
  }
\if{latex}{
  \out{\begin{center}}\figure{colour-hot.png}\out{\end{center}}
  }
}

\subsection{White-Red}{

\if{html}{
  \out{<div style="text-align: center">}\figure{colour-whitered.png}{options: style="width:255px;max-width:100\%;"}\out{</div>}
  }
\if{latex}{
  \out{\begin{center}}\figure{colour-whitered.png}\out{\end{center}}
  }
}
}

\section{Diverent palettes}{


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

\subsection{Divergent}{

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

\if{html}{
  \out{<div style="text-align: center">}\figure{colour-divergent.png}{options: style="width:255px;max-width:100\%;"}\out{</div>}
  }
\if{latex}{
  \out{\begin{center}}\figure{colour-divergent.png}\out{\end{center}}
  }
}

\subsection{Green-Pink}{

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

\if{html}{
  \out{<div style="text-align: center">}\figure{colour-greenpink.png}{options: style="width:255px;max-width:100\%;"}\out{</div>}
  }
\if{latex}{
  \out{\begin{center}}\figure{colour-greenpink.png}\out{\end{center}}
  }
}
}

\section{Details}{
 
The colours in ggplot based visualisations, such as 
\code{\link[GENOVA]{visualise}()} and \code{\link[GENOVA]{pyramid}()}, are 
based on the 
\code{\link[=GENOVA_colour_scales]{scale_(colour|fill)_GENOVA}()} and 
\code{\link[=GENOVA_colour_scales]{scale_(colour|fill)_GENOVA_div}()}
functions.

For visualisations in base R, such as \code{\link[GENOVA]{hic_matrixplot}()} 
and \code{\link[GENOVA:GENOVA_image]{image()}},
the \code{\link[grDevices]{colorRampPalette}()} 
function is used.
}

