TranscriptomiC/colocalisation.cpp at main · LorenzoTarricone/TranscriptomiC · GitHub

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// this object will wrap all functionalities needed to compute the colocalisation matrix

#include "colocalisation.h"
#include "colocalization_matrix.h"


colocalisation::~colocalisation(){
    delete expression;
}


// run steps to compute colocalisation matrix
void colocalisation::compute(){

    // compute colocalisation matrix
    step1();
    std::cout << "[Progress] Step 1 finished successfully ..." << std::endl;
    step2();
    std::cout << "[Progress] Step 2 finished successfully ..." << std::endl;
    step3();
    std::cout << "[Progress] Step 3 finished successfully ..." << std::endl;
    step4();
    std::cout << "[Progress] Step 4 finished successfully ..." << std::endl;
    step5();
    std::cout << "[Progress] Step 5 finished successfully ..." << std::endl;

}

// save colocalisation matrix to file
void colocalisation::saveToFile(std::string filename){
    std::cout << "[Progress] Saving File ..." << std::endl;
    expression_raw.writeToFile(filename,*A_colocalisation,expression_raw.getcurrentGenes());
    delete A_colocalisation;
}

// Individual steps to compute the colocalisation matrix

void colocalisation::step1(){
    // step 1 - create distance matrix
    std::cout << "[Progress] Running step 1 ..." << std::endl;
    A_distance = new Eigen::MatrixXd;
    *A_distance = matrix_distance(A_spatial);
    std::cout<<(*A_distance).block(0,0,std::min((int)A_distance->rows(),10),std::min((int)A_distance->cols(),10))<<std::endl;
    std::cout<<"\nDistance matrix shape: (" << (*A_distance).rows() << ", " << (*A_distance).cols() << ")"<<std::endl;
}

void colocalisation::step2(){
    // step 2 - linkage matrix with parameters m and p
    std::cout << "[Progress] Running step 2 ..." << std::endl;
    A_linkage = new Eigen::MatrixXd;
    *A_linkage = matrix_linkage(*A_distance, m, p);

    delete A_distance;

    std::cout<<(*A_linkage).block(0,0,std::min((int)A_linkage->rows(),10),std::min((int)A_linkage->cols(),10))<<std::endl;
    std::cout<<"\nLinkage matrix shape: (" << (*A_linkage).rows() << ", " << (*A_linkage).cols() << ")"<<std::endl;

}

void colocalisation::step3(){
    //  step 3 - apply linkage to expression matrix -> neighbouring matrix
    std::cout << "[Progress] Running step 3 ..." << std::endl;


    A_combine = new Eigen::MatrixXd;
    *A_combine = combine_linkage(*A_linkage,*expression);

    delete A_linkage;

    std::cout<<A_combine->block(0,0,std::min((int)A_combine->rows(),10),std::min((int)A_combine->cols(),10))<<std::endl;
    std::cout<<"\n Comparison matrix shape: (" << A_combine->rows() << ", " << A_combine->cols() << ")"<<std::endl;
}

void colocalisation::step4(){
    //  step 4 - compare expression and neighbouring matrices (with default parameters
    std::cout << "[Progress] Running step 4 ..." << std::endl;
    A_compare = new Eigen::MatrixXd;
    *A_compare = comparison_old(*expression, *A_combine);

    std::cout<<A_compare->block(0,0,std::min((int)A_compare->rows(),10),std::min((int)A_compare->cols(),10))<<std::endl;
    std::cout<<"\n Comparison matrix shape: (" << A_compare->rows() << ", " << A_compare->cols() << ")"<<std::endl;


    delete A_combine;
}

void colocalisation::step5(){
    // step 5 - compute enrichement score
    std::cout << "[Progress] Running step 5 ..." << std::endl;
    A_colocalisation = new Eigen::MatrixXd;
    *A_colocalisation = enrichment(*A_compare);


    std::cout<<A_colocalisation->block(0,0,std::min((int)A_colocalisation->rows(),10),std::min((int)A_colocalisation->cols(),10))<<std::endl;
    std::cout<<"\n Colocalisation matrix shape: (" << A_colocalisation->rows() << ", " << A_colocalisation->cols() << ")"<<std::endl;

}