map.color

Function map a numeric vector of a property to a vector of colors for that property according to that property value.

Processes data from Molecular Dynamics simulations using
Self Organising Maps. Features include the ability to read different
input formats. Trajectories can be analysed to identify groups of important
frames. Output visualisation can be generated for maps and pathways.
Methodological details can be found in Motta S et al (2022)
<doi:10.1021/acs.jctc.1c01163>.
I/O functions for xtc format files were implemented using the 'xdrfile'
library available under open source license. The relevant information can
be found in inst/COPYRIGHT.

Stefano Motta

SOMMD

Self Organising Maps for the Analysis of Molecular Dynamics Data

Alessandro Pandini

Erik Lindahl

David van der Spoel

map.color function

<dl><dt>x</dt>
<dd>a numeric vector</dd>
<dt>pal</dt>
<dd>a color palette</dd>
<dt>limits</dt>
<dd>the values of the extremes for the colorscale</dd>
<dt>na.col</dt>
<dd>the color that will be assigned to the na.values of the vector</dd></dl>

Arguments

Map the property vector to colours — map.color

<dl>

<dt>x</dt>
<dd>a numeric vector</dd>


<dt>pal</dt>
<dd>a color palette</dd>


<dt>limits</dt>
<dd>the values of the extremes for the colorscale</dd>


<dt>na.col</dt>
<dd>the color that will be assigned to the na.values of the vector</dd>

</dl>

map.color: Map the property vector to colours

Description

Usage

Value

Arguments