placement/formats/edge_color.cpp

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/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2023 Lucas Czech
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/placement/formats/edge_color.hpp"
 
#include "genesis/placement/function/helper.hpp"
#include "genesis/placement/function/functions.hpp"
#include "genesis/placement/placement_tree.hpp"
#include "genesis/placement/sample.hpp"
#include "genesis/utils/color/color.hpp"
#include "genesis/utils/color/functions.hpp"
 
#include <cmath>
 
namespace genesis {
namespace placement {
 
// =================================================================================================
//     Placement Edge Color Functions
// =================================================================================================
 
std::vector<utils::Color> placement_color_count_gradient( Sample const& smp, bool linear )
{
    // Init the result vector with grey color for each edge.
    auto ret = std::vector<utils::Color>( smp.tree().edge_count(), utils::Color(0.5,0.5,0.5) );
 
    // Get the highest number of placements on any edge.
    // If this is zero, there are no placements, so we can immediately return.
    auto const max_placements_per_edge = placement_count_max_edge(smp).second;
    if (max_placements_per_edge == 0) {
        return ret;
    }
 
    auto place_map = placements_per_edge( smp );
 
    // Calculate the heat gradient color based on the number of placements for each edge.
    for( auto const& edge : smp.tree().edges() ) {
        auto const placements_on_edge = place_map[ edge.index() ].size();
 
        if( placements_on_edge > 0) {
            double val;
            if (linear) {
                val = placements_on_edge / max_placements_per_edge;
            } else {
                val = log( placements_on_edge ) / log( max_placements_per_edge );
            }
            ret[edge.index()] = utils::heat_gradient(val);
        }
 
        // LOG_DBG <<  edge.placements.size() << " --> "
        //         << 100 * edge.placements.size() / max_placements_per_edge_
        //         << " = " << edge_color.dump();
    }
 
    return ret;
}
 
} // namespace placement
} // namespace genesis