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plot_chr_winboost.cpp
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/* this function plots single-marker/window-marker (boost) allele frequency along a chromosome */
/* Date : 2013-Apr-24 */
/* Date : 2014-Feb-20 : test 3D-plot with quality score on markers */
/* Date : 2014-Mar-18 : test k-means for ranking markers */
/* Date : 2014-May-05 : use af=alt/(alt+ref+error) for winAF2new */
/* Date : 2014-Sep-05 : only pull down boost-values of a chromosome when no confident peak */
/* Date : 2015-Jun-15 : add PCI plotting for backcrossing data */
#include <stddef.h>
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string>
#include <string.h>
#include <assert.h>
#include <map>
#include <vector>
#include <fstream>
#include <sstream>
#include <iostream>
#include "globals.h"
#include "print_plot_info.h"
#include "split_string.h"
#include "kmeans.h"
#include "find_z_value.h"
#include "Calc_Wilson_score_interval.h"
// visualization
#include "dislin/dislin_d.h"
using namespace std;
struct WININFO
{
double pos; // window center
double val; // window average/std
double beg; // window begin
double end; // window end
};
bool plot_chr_winboost(std::string chrID,
unsigned long plot_ith_chr,
map<unsigned long, TRIPLE> interData,
map<unsigned long, TRIPLE> filtered)
{
double interest_regPos[2];
double interest_regHET[2];
char iregion[1024];
double avg_threshold = interval_min_mean;
double cv_threshold = interval_max_cvar;
//
double max_quality = 0.0;
double miax_bg1_cov[2];
double cluster_avg_cov_bg1;
double cluster_dim_cov_bg1;
double miax_bg2_cov[2];
double cluster_avg_cov_bg2;
double cluster_dim_cov_bg2;
//
unsigned long dtSize = interData.size();
double* myPosiSet = (double*)malloc((dtSize+1)*sizeof(double));
double* myFreqSet = (double*)malloc((dtSize+1)*sizeof(double));
double* myScorSet = (double*)malloc((dtSize+1)*sizeof(double));
// PCI plot - 2015-Jun-15 17:52
double* PciPosiSet;
double* PciFreqSet;
double* PciEuppSet;
double* PciElowSet;
double oberveredAFMean = 0.0;
if(pci && pci_chr.compare(chrID)==0)
{
PciPosiSet = (double*)malloc((dtSize+1)*sizeof(double));
PciFreqSet = (double*)malloc((dtSize+1)*sizeof(double));
PciEuppSet = (double*)malloc((dtSize+1)*sizeof(double));
PciElowSet = (double*)malloc((dtSize+1)*sizeof(double));
percentile_z = find_z_value(z_table, pci_cfd);
}
/* prepare for clustering of markers..........................................................*/
unsigned long n = dtSize;
unsigned long m = 0;
unsigned long k = (clusterK>dtSize)?dtSize:clusterK;
double t = 0.01;
double** markerData;
double** centroids;
unsigned long* cluster_counts;
assert(myPosiSet && myFreqSet && myScorSet);
// test condition: when k>=2 ...................................................................
if(k >= 2)
if(strcatCMD.find("SHOREmap outcross") != std::string::npos)
{
std::vector<string> quainfo = split_string((*(QUALITY1.begin())).second, ',');
if(quainfo.size() == 11) // caution! generated format by SHOREmap create function
{
m = 8;
}
else if(quainfo.size() <= 5) // caution! generated format by SHORE variant calling
{
m = 2;
}
}
else if(strcatCMD.find("SHOREmap backcross") != std::string::npos)
{
if(!bg_ref_filter && strcatCMD.find("--bg")==std::string::npos)
{
/* clustering..with..foreground..quality..and.....coverage.....of.....mutant.....base */
m = 2;
}
else if(!bg_ref_filter && strcatCMD.find("--bg")!= std::string::npos)
{
/* clutering..with..foreground+background.quality and..coverage...of...mutant....base */
m = 4;
}
else if(bg_ref_filter)
{
/* clustering with fg quality, coverage of mutbase, bg quality and cov, af of refbase */
m = 5;
}
}
else
{
printf("ERROR: dimension of markerData is unknown??? Exited.\n");
exit(1);
}
if(k >= 2)
{
markerData = (double**)malloc((dtSize+1)*sizeof(double*));
centroids = (double**)malloc((k+1)*sizeof(double*));
cluster_counts = (unsigned long*)malloc((k+1)*sizeof(unsigned long));
assert(markerData && centroids && cluster_counts);
for(int mali = 0; mali < dtSize+1; mali ++)
{
markerData[mali] = (double*)malloc(m*sizeof(double));
assert(markerData[mali]);
if(mali <= k)
{
centroids[mali] = (double*)malloc(m*sizeof(double));
assert(centroids[mali]);
}
}
}
/* prepare...xray:position....and.....yray....(and zray):....frequency...for.........plotting */
miax_bg1_cov[0] = INF;
miax_bg1_cov[1] = 0;
miax_bg2_cov[0] = INF;
miax_bg2_cov[1] = 0;
map<unsigned long, TRIPLE>::iterator mkr_itr = interData.begin();
map<unsigned long, TRIPLE>::iterator mkr_itr_end = interData.end();
unsigned long ipos = 0;
unsigned long ipci = 0;
while(mkr_itr != mkr_itr_end)
{
/* this (position, frequency): caution with error ........................................*/
double icov = (double)(*mkr_itr).second.Ci[0]+(*mkr_itr).second.Ci[1]+(*mkr_itr).second.Ci[2];
*(myPosiSet+ipos) = (double)(*mkr_itr).first;
*(myFreqSet+ipos) = (double)(*mkr_itr).second.Ci[1]/icov; // ref/icov or mut/icov
if(pci && pci_chr.compare(chrID)==0)
{
if((*mkr_itr).first>=pci_start && (*mkr_itr).first<=pci_end)
{
*(PciPosiSet+ipci) = (double)(*mkr_itr).first;
*(PciFreqSet+ipci) = (double)(*mkr_itr).second.Ci[1]/icov;
double interval[2];
Calc_Wilson_score_interval(icov, (*mkr_itr).second.Ci[1], percentile_z, interval);
*(PciEuppSet+ipci) = interval[1] - *(PciFreqSet+ipci);
*(PciElowSet+ipci) = *(PciFreqSet+ipci) - interval[0];
oberveredAFMean += *(PciFreqSet+ipci);
ipci ++;
}
}
// new.....2014-02-20: find chr+".#."+pos and assign quality/rank score ..................*/
// m = 2;
if(k >= 2)
{
markerData[ipos][0] = (double)(*mkr_itr).second.Ci[1]; // fg-mut-cov...........
std::stringstream posTmp;
posTmp << (unsigned long)(*mkr_itr).first;
string qkey("");
qkey += chrID;
qkey += ".#.";
qkey += posTmp.str();
map<std::string, std::string>::iterator qitr = QUALITY1.find(qkey);
string qua = (*qitr).second.c_str(); // like qua = eop002,40.
std::vector<string> qinfo = split_string(qua, ',');
markerData[ipos][1] = atof(qinfo[1].c_str()); // fg-mut-qua...........
if(markerData[ipos][1] > max_quality)
{
max_quality = markerData[ipos][1];
}
if(strcatCMD.find("SHOREmap outcross") != std::string::npos && m==8)
{
// qinfo <- FLAG4parentA,(40,20,0.571429,1),(40,36,1),(40,29,1).....................
markerData[ipos][2] = atof(qinfo[5].c_str()); // qua
markerData[ipos][3] = atof(qinfo[6].c_str()); // cov
markerData[ipos][4] = atof(qinfo[7].c_str()); // af
markerData[ipos][5] = atof(qinfo[8].c_str()); // qua
markerData[ipos][6] = atof(qinfo[9].c_str()); // cov
markerData[ipos][7] = atof(qinfo[10].c_str()); // af
if(miax_bg1_cov[0] > markerData[ipos][3]) miax_bg1_cov[0] = markerData[ipos][3];
if(miax_bg1_cov[1] < markerData[ipos][3]) miax_bg1_cov[1] = markerData[ipos][3];
if(miax_bg2_cov[0] > markerData[ipos][6]) miax_bg2_cov[0] = markerData[ipos][6];
if(miax_bg2_cov[1] < markerData[ipos][6]) miax_bg2_cov[1] = markerData[ipos][6];
}
else if(strcatCMD.find("SHOREmap backcross")!=std::string::npos && m==4)
{
/*fg-cov, fg-qua, bg-cov, bg-cov................................................. */
map<std::string, std::string>::iterator bgmkr_itr = bgMARKER.find(qkey);
std::vector<string> bgmkr_info = split_string((*bgmkr_itr).second, '#');
markerData[ipos][2] = atof(bgmkr_info[1].c_str()); // bg-mut-cov
markerData[ipos][3] = atof(bgmkr_info[0].c_str()); // bg-mut-sco
}
else if (strcatCMD.find("SHOREmap backcross")!=std::string::npos && m==5)
{
/* clustering with fg quality, cov of mutbase, bg quality and cov, af of ref base */
map<std::string, std::string>::iterator bgref_itr = bgREF.find(qkey);
std::vector<string> bgref_info = split_string((*bgref_itr).second, '#');
markerData[ipos][2] = atof(bgref_info[1].c_str()); // bg-ref-cov
markerData[ipos][3] = atof(bgref_info[0].c_str()); // bg-ref-sco
markerData[ipos][4] = atof(bgref_info[2].c_str()); // bg-ref-ccd
}
else
{
;
}
}
/* next..........................................................................position */
ipos ++;
mkr_itr ++;
}
oberveredAFMean = oberveredAFMean/ipci;
/* scale the factors: column 0 and 2 (if bg-mut): (cov-mean)/mean, column 1 and 3: quality/40 */
//fg-cov, fg-qua
if(verbose && k>=2)
{
cout << "\t" << m << " items will be used for clustering markers with " << endl;
cout << "\t\tfgmut_avg_cov=" << cluster_avg_coverage << ", ";
cout << "fgmut_dim_cov=" << cluster_dim_coverage << endl;
}
double bgref_cdim; // caution: further accessed when re-scaling
double bgref_cmean;
unsigned long oni;
if(k >= 2)
if(m == 2)
{
oni = 0;
while(oni < interData.size())
{
////printf("%ld: %.0f %.0f --> ", oni, markerData[oni][0], markerData[oni][1]);
markerData[oni][0] = 1-0.5*fabs(markerData[oni][0]-(double)cluster_avg_coverage)/(double)cluster_dim_coverage;
markerData[oni][1] = markerData[oni][1]/max_quality;
////printf("%.2f %.0f \n", markerData[oni][0], markerData[oni][1]);
oni++;
}
}
else if(strcatCMD.find("SHOREmap outcross")!=std::string::npos && m==8)
{
assert(miax_bg1_cov[0] <= miax_bg1_cov[1] && miax_bg1_cov[0]>0);
cluster_avg_cov_bg1 = (miax_bg1_cov[1] + miax_bg1_cov[0])/2.0;
cluster_dim_cov_bg1 = (miax_bg1_cov[1] - miax_bg1_cov[0])/2.0;
if(cluster_dim_cov_bg1 == 0) cluster_dim_cov_bg1 = 1; // caution!
assert(miax_bg2_cov[0] <= miax_bg2_cov[1] && miax_bg2_cov[0]>0);
cluster_avg_cov_bg2 = (miax_bg2_cov[1] + miax_bg2_cov[0])/2.0;
cluster_dim_cov_bg2 = (miax_bg2_cov[1] - miax_bg2_cov[0])/2.0;
if(cluster_dim_cov_bg2 == 0) cluster_dim_cov_bg2 = 1; // caution!
if(verbose)
{
cout << "\t\tbg1_avg_cov=" << cluster_avg_cov_bg1 << ", ";
cout << "bg1_dim_cov=" << cluster_dim_cov_bg1 << endl;
cout << "\t\tbg2_avg_cov=" << cluster_avg_cov_bg2 << ", ";
cout << "bg2_dim_cov=" << cluster_dim_cov_bg2 << endl;
}
oni = 0;
while(oni < interData.size())
{
////printf("\t%.0f %.0f %.0f %.0f %.0f %.0f %.0f %.0f -> ",
//// markerData[oni][0], markerData[oni][1],
//// markerData[oni][2], markerData[oni][3], markerData[oni][4],
//// markerData[oni][5], markerData[oni][6], markerData[oni][7]);
markerData[oni][0] = 1-0.5*fabs(markerData[oni][0]-(double)cluster_avg_coverage)/(double)cluster_dim_coverage;
markerData[oni][1] = markerData[oni][1]/max_quality;
markerData[oni][2] = markerData[oni][2]/max_quality;
markerData[oni][3] = 1-0.5*fabs(markerData[oni][3]-(double)cluster_avg_cov_bg1)/(double)cluster_dim_cov_bg1;
// markerData[ipos][4] = markerData[ipos][4];
markerData[oni][5] = markerData[oni][5]/max_quality;
markerData[oni][6] = 1-0.5*fabs(markerData[oni][6]-(double)cluster_avg_cov_bg2)/(double)cluster_dim_cov_bg2;
// markerData[ipos][7] = markerData[ipos][7];
////printf("%.2f %.2f %.2f %.2f %.2f %.2f %.2f %.2f \n",
//// markerData[oni][0], markerData[oni][1],
//// markerData[oni][2], markerData[oni][3], markerData[oni][4],
//// markerData[oni][5], markerData[oni][6], markerData[oni][7]);
oni ++;
}
}
else if(strcatCMD.find("SHOREmap backcross")!=std::string::npos && m>=4 && m<=5)
{
// fg-cov, fg-qua, bg-cov, bg-cov
if(m == 5)
{
if(strcatCMD.find("--bg-ref-cov-max") == std::string::npos &&
strcatCMD.find("--bg-ref-cov") == std::string::npos)
{
printf("Warning: no coverage constraints on bg-ref bases, default will apply!\n");
}
else if(strcatCMD.find("--bg-ref-cov-max") == std::string::npos &&
strcatCMD.find("--bg-ref-cov") != std::string::npos)
{
printf("Warning: only constraint on min-cov of ref base, default will apply!\n");
}
else if (strcatCMD.find("--bg-ref-cov-max")!=std::string::npos &&
strcatCMD.find("--bg-ref-cov") ==std::string::npos)
{
printf("Warning: no min-cove constraint on bg-ref bases, default will apply!\n");
}
else ;
bgref_cdim = (bg_ref_cov_max - bg_ref_cov)/2.0;
bgref_cmean = (bg_ref_cov_max + bg_ref_cov)/2.0;
if(bgref_cdim == 0.0) bgref_cdim = 1.0;//caution!
if(verbose)
printf("\tbgref_avg_coverage=%.0f, bgref_dim_coverage=%.0f\n", bgref_cmean, bgref_cdim);
}
oni = 0;
while(oni < interData.size())
{
////printf("\t%.0f %.0f %.0f %.0f",
//// markerData[oni][0], markerData[oni][1],
//// markerData[oni][2], markerData[oni][3]);
////if(m == 5)
////{
//// printf(" %.2f\t\t -->\t", markerData[oni][4]);
////}
////else
////{
//// printf("\t\t -->\t");
////}
markerData[oni][0] = 1-0.5*fabs(markerData[oni][0]-(double)cluster_avg_coverage)/(double)cluster_dim_coverage;
markerData[oni][1] = markerData[oni][1]/max_quality;
if(m == 4)
{
markerData[oni][2] = 1-markerData[oni][2]/(double)bg_read; // lower - better
markerData[oni][3] = (max_quality-markerData[oni][3])/max_quality; // bg-mut/lower - better
}
else // if (m == 5)
{
markerData[oni][2] = 1-0.5*fabs(markerData[oni][2]-bgref_cmean)/bgref_cdim; // higher - better
markerData[oni][3] = markerData[oni][3]/max_quality; // bg-ref-higher - better
}
////printf("%.2f %.2f %.2f %.2f",
//// markerData[oni][0], markerData[oni][1],
//// markerData[oni][2], markerData[oni][3]);
////if(m == 5)
////{
//// printf(" %.2f\n", markerData[oni][4]);
////}
////else
////{
//// printf("\n");
////}
oni ++;
}
}
else
{
;
}
char** real_value_centeroids;
if(k >= 2)
{
if(verbose) printf("\tScaling of factors for %ld markers done.\n", dtSize);
real_value_centeroids = (char**)malloc((k+1)*sizeof(char*));
assert(real_value_centeroids);
for(int irvc=0; irvc<k+1; irvc++)
{
real_value_centeroids[irvc] = (char*)malloc(256*sizeof(char));//caution!
assert(real_value_centeroids[irvc]);
}
k_means(markerData, n, m, k, t, centroids, cluster_counts, myScorSet);
if(verbose)
printf("\t%ld markers ==> %ld (actual; %ld expected) clusters. ", dtSize, k, clusterK);
/* recover re-scaled values of centroids to real ones.....................................*/
if(strcatCMD.find("SHOREmap outcross")!=std::string::npos && (m==2 || m==8))
{
if(verbose) printf("Non-scaled centers of clusters given in PDF.\n");
double cen_fg_cov_low, cen_fg_cov_high, cen_fg_qua;
double cen_bg1_cov_low, cen_bg1_cov_high, cen_bg1_cov, cen_bg1_qua;
double cen_bg2_cov_low, cen_bg2_cov_high, cen_bg2_cov, cen_bg2_qua;
/*
markerData[oni][0] => fg-cov
markerData[oni][1] => fg-qua
markerData[oni][2] => bg1-qua
markerData[oni][3] => bg1-cov
markerData[ipos][4]=> bg1-af
markerData[oni][5] => bg2-qua
markerData[oni][6] => bg2-cov
markerData[ipos][7]=> bg2-af
*/
for(int ki=k-1; ki>=0; ki --)
{
printf("\t%.2f %.2f ",
centroids[ki][0],
centroids[ki][1]);
if(m == 8)
printf("%.2f %.2f %.2f %.2f %.2f %.2f -> ",
centroids[ki][2],
centroids[ki][3],
centroids[ki][4],
centroids[ki][5],
centroids[ki][6],
centroids[ki][7]);
else
printf(" -> ");
cen_fg_cov_low = (1-centroids[ki][0])*(double)cluster_dim_coverage;
cen_fg_cov_low = cen_fg_cov_low*2.0;
cen_fg_cov_high = (double)cluster_avg_coverage + cen_fg_cov_low;
cen_fg_cov_low = (double)cluster_avg_coverage - cen_fg_cov_low;
if(cen_fg_cov_low < (double)filter_min_coverage)
{
cen_fg_cov_low = cen_fg_cov_high;
}
cen_fg_qua = centroids[ki][1]*max_quality;
if(m == 8)
{
cen_bg1_qua = centroids[ki][2]*max_quality;
cen_bg1_cov_low = (1-centroids[ki][3])*(double)cluster_dim_cov_bg1;
cen_bg1_cov_low = cen_bg1_cov_low*2.0;
cen_bg1_cov_high = (double)cluster_avg_cov_bg1 + cen_bg1_cov_low;
cen_bg1_cov_low = (double)cluster_avg_cov_bg1 - cen_bg1_cov_low;
if(cen_bg1_cov_low < (double)miax_bg1_cov[0])
{
cen_bg1_cov_low = cen_bg1_cov_high;
}
cen_bg2_qua = centroids[ki][5]*max_quality;
cen_bg2_cov_low = (1-centroids[ki][6])*(double)cluster_dim_cov_bg2;
cen_bg2_cov_low = cen_bg2_cov_low*2.0;
cen_bg2_cov_high = (double)cluster_avg_cov_bg2 + cen_bg2_cov_low;
cen_bg2_cov_low = (double)cluster_avg_cov_bg2 - cen_bg2_cov_low;
if(cen_bg2_cov_low < (double)miax_bg2_cov[0])
{
cen_bg2_cov_low = cen_bg2_cov_high;
}
}
////
if(cluster_counts[ki] > 0)
{
sprintf(real_value_centeroids[ki],
" cluster %2d: (%-3.1f, %3.1f) %2.1f", ki,
cen_fg_cov_low, cen_fg_cov_high, cen_fg_qua);
if(m == 8)
sprintf(real_value_centeroids[ki],
"%s %2.1f (%-3.1f, %3.1f) %.2f %2.1f (%-3.1f, %3.1f) %.2f %8ld\0",
real_value_centeroids[ki],
cen_bg1_qua, cen_bg1_cov_low, cen_bg1_cov_high, centroids[ki][4],
cen_bg2_qua, cen_bg2_cov_low, cen_bg2_cov_high, centroids[ki][7],
cluster_counts[ki]);
}
else
{
sprintf(real_value_centeroids[ki], " cluster %2d:", ki);
for(int noni=0; noni<m; noni++)
{
sprintf(real_value_centeroids[ki], "%s ~~~", real_value_centeroids[ki]);
}
sprintf(real_value_centeroids[ki], "%s %ld\0",
real_value_centeroids[ki],
cluster_counts[ki]);
}
printf("\t%s \n", real_value_centeroids[ki]);
}
}
else if(strcatCMD.find("SHOREmap backcross")!=std::string::npos && m>=2 && m<=5)
{
if(verbose) printf("Non-scaled centers of clusters given in PDF.\n");
double cen_fg_cov_low, cen_fg_cov_high, cen_fg_qua;
double cen_bg_cov_low, cen_bg_cov_high, cen_bg_cov, cen_bg_qua;
for(int ki=k-1; ki>=0; ki --)
{
cen_fg_cov_low = (1-centroids[ki][0])*(double)cluster_dim_coverage;
cen_fg_cov_low = cen_fg_cov_low*2.0;
cen_fg_cov_high = (double)cluster_avg_coverage + cen_fg_cov_low;
cen_fg_cov_low = (double)cluster_avg_coverage - cen_fg_cov_low;
if(cen_fg_cov_low < (double)filter_min_coverage)
{
cen_fg_cov_low = cen_fg_cov_high;
}
cen_fg_qua = centroids[ki][1]*max_quality;
if(m == 4)
{
cen_bg_cov = (1-centroids[ki][2])*(double)bg_read;
cen_bg_qua = max_quality-centroids[ki][3]*max_quality;
}
else if(m == 5)
{
cen_bg_cov_low = (1-centroids[ki][2])*bgref_cdim;
cen_bg_cov_low = cen_bg_cov_low*2.0;
cen_bg_cov_high = bgref_cmean + cen_bg_cov_low;
cen_bg_cov_low = bgref_cmean - cen_bg_cov_low;
if((int)round(cen_bg_cov_low) < bg_ref_cov)
{
cen_bg_cov_low = cen_bg_cov_high;
}
cen_bg_qua = centroids[ki][3]*max_quality;
}
else ;
if(cluster_counts[ki] > 0)
{
sprintf(real_value_centeroids[ki], " cluster %2d: (L:%3.1f, H:%3.1f) %3.1f", ki,
cen_fg_cov_low, cen_fg_cov_high, cen_fg_qua);
if(m == 5)
{
sprintf(real_value_centeroids[ki],"%s (L:%3.1f, H:%3.1f) %3.1f %3.2f %8ld\0",
real_value_centeroids[ki],
cen_bg_cov_low, cen_bg_cov_high, cen_bg_qua, centroids[ki][4],
cluster_counts[ki]);
}
else if(m ==4 )
{
sprintf(real_value_centeroids[ki], "%s %3.1f %3.1f %8ld\0",
real_value_centeroids[ki],
cen_bg_cov, cen_bg_qua,
cluster_counts[ki]);
}
else if(m == 2)
{
sprintf(real_value_centeroids[ki], "%s %8ld\0",
real_value_centeroids[ki],
cluster_counts[ki]);
};
}
else
{
sprintf(real_value_centeroids[ki], " cluster %2d:", ki);
for(int noni=0; noni<m; noni++)
{
sprintf(real_value_centeroids[ki], "%s ~~~", real_value_centeroids[ki]);
}
sprintf(real_value_centeroids[ki], "%s %ld\0",
real_value_centeroids[ki],
cluster_counts[ki]);
}
////printf("\t%s \n", real_value_centeroids[ki]);
}
}
else
{
;
}
}
/* figure out range of chromosome to plot ....................................................*/
double ci_start = 0.0;
double ci_end = 0.0;
double ci_step = 0.0;
if(strcatCMD.find("--chromosome") != std::string::npos)
{
ci_start = reg_begin;
ci_end = reg_end;
ci_step = (ci_end-ci_start+1)/5;
}
else
{
ci_start = 0.0;
ci_end = (double)(CHR2SIZE[chrID]);
//ci_step = (double)ci_end/5;
//(double)chrsizes_max
//double ratio = (double)ci_end/(double)chrsizes_max;
ci_step = 3000000;
if((double)chrsizes_max/ci_step < 1)
while((double)chrsizes_max/ci_step < 5) // to avoid dense plotting of x-axis
{
ci_step -= 1000;
}
else
while((double)chrsizes_max/ci_step > 10) // to avoid dense plotting of x-axis
{
ci_step += 1000000;
}
}
/* prepare window-averaged allele frequency, boost value, coefficient of variation........... */
double winbeg; // position of window begin
double winend; // position of window end
double winctr; // position of window center
double avgfrq; // averaged window frequency 1
double avgbst; // boost value of window
double bstmax; // maximum of boost values
double mut_sum; // coverage of all mut-alleles in a window
double cov_sum; // coverage of all ref+mut alleles in a window
double sgl_frq; // allele frequency of a single SNP
double sgl_sco; // base quality score of a single mutant base
long mkr_sum; // number of SNPs in a window
bstmax = 0.0;
std::vector<WININFO> bstmax_pos; // positions of boost max
std::vector<WININFO> winAVGnew; // sum of counts(allele1) / sum of counts(allele1+allele2)
std::vector<WININFO> winAF2new; // sum of AFs(allele1+allele2) /num of markers in a window
std::vector<WININFO> winSTDnew; // std of AFs of the above calculation
std::vector<WININFO> winBSTnew; // boost value calculated from a window-freq of markers
std::vector<WININFO> winSCOnew; // score value calculated for a window-freq of markers
std::vector<double> winSGLnew; // AFs of single markers in a window
if(plot_window)
for(winbeg=(double)ci_start; winbeg<=(double)(ci_end-window_size+1); winbeg+=(double)window_step)
{
winend = winbeg + window_size - 1;
mut_sum = 0;
cov_sum = 0;
mkr_sum = 0;
sgl_frq = 0;
sgl_sco = 0;
winSGLnew.clear(); // clear tmp winSGLnew for next window....................
mkr_itr = interData.begin();
mkr_itr_end = interData.end();
while(mkr_itr != mkr_itr_end)
{
double mkrp = (double)(*mkr_itr).first;
if(mkrp<winbeg)
{
mkr_itr++;
continue;
}
if(mkrp>=winbeg && mkrp<=winend)
{
std::stringstream posTmp;
posTmp << (unsigned long)(*mkr_itr).first;
string qkey("");
qkey += chrID;
qkey += ".#.";
qkey += posTmp.str();
map<std::string, std::string>::iterator qitr = QUALITY1.find(qkey);
string qua = (*qitr).second.c_str(); // like qua = eop002,40.......
std::vector<string> quainfo = split_string(qua, ',');
if((double)atol(quainfo[1].c_str()) < quality_min &&
strcatCMD.find("SHOREmap backcross")!=std::string::npos)
{
mkr_itr ++;
continue;
}
sgl_sco += (double)(atol(quainfo[1].c_str()));
TRIPLE cntTmp = (*mkr_itr).second;
mut_sum += (double)(cntTmp.Ci[1]);
cov_sum += (double)(cntTmp.Ci[0] + cntTmp.Ci[1] + cntTmp.Ci[2]);//caution 2014-05-05: with error
mkr_sum += 1;
double tmp_sglfeq;
tmp_sglfeq = (double)(cntTmp.Ci[1])/(double)(cntTmp.Ci[0]+ cntTmp.Ci[1]+ cntTmp.Ci[2]);
sgl_frq += tmp_sglfeq;
winSGLnew.push_back(tmp_sglfeq);
mkr_itr ++;
}
if( mkr_itr==mkr_itr_end || mkrp>winend )
{
if(mkr_sum>=filter_min_marker)
{
winctr = (winend+winbeg)/2;
avgfrq = mut_sum/cov_sum;
WININFO iwin;
iwin.pos = winctr;
iwin.beg = winbeg; //// is starting from the pos of the 1st snp?
iwin.end = winend;
iwin.val = avgfrq;
/* window average 1 */
winAVGnew.push_back(iwin);
/* std for winAF2new */
std::vector<double>::iterator sglfrq_itr;
std::vector<double>::iterator sglfrq_itr_end;
sglfrq_itr = winSGLnew.begin();
sglfrq_itr_end = winSGLnew.end();
double x_xi_sq = 0;
while(sglfrq_itr != sglfrq_itr_end)
{
x_xi_sq += pow(*sglfrq_itr - iwin.val, 2);
sglfrq_itr ++;
}
iwin.val = sqrt(x_xi_sq/(winSGLnew.size()-1));
winSTDnew.push_back(iwin);
/* mean == winAF2new */
iwin.val = sgl_sco/(double)mkr_sum;
winSCOnew.push_back(iwin);
iwin.val = sgl_frq/(double)mkr_sum;
winAF2new.push_back(iwin);
/* boost */
if(plot_boost)
{
avgfrq = sgl_frq/(double)mkr_sum;
avgbst = fabs(1 - max(expect, 1-expect)/max(avgfrq, 1-avgfrq));
if(avgbst == 0)
{
avgbst = (double)INF;
}
else
{
avgbst = 1/avgbst;
}
if(avgbst!=INF && avgbst>bstmax)
{
bstmax = avgbst;
if(bstmax_pos.size() > 0) bstmax_pos.clear();
iwin.val = bstmax;
bstmax_pos.push_back(iwin);
}
else if(avgbst==bstmax)
{
iwin.val = bstmax;
bstmax_pos.push_back(iwin);
}
else ;
iwin.val = avgbst;
winBSTnew.push_back(iwin);
}
}
break;
}
}
}
/* check if windows exist to plot ............................................................*/
//if(winAF2new.size() == 0 && strcatCMD.find("SHOREmap outcross")!=std::string::npos)
if(plot_window && winAF2new.size() == 0)
{
printf("Warning: window-plot is asked, but it is cancelled (no boost-plot neither). \n");
printf("Reason: there is not any window with min-window-markers=%ld. \n",
filter_min_marker);
printf("Hint: increase window size or decrease min-window-markers from the cmd line.\n");
plot_window = false;
}
else
if(plot_window && verbose)
{
printf("\tregion to plot: (chr_start, chr_end) = %.0f, %.0f \n", ci_start+1, ci_end);
printf("\tnumber of windows-of-markers: %ld, ", winAF2new.size());
printf("1st-center: %.0f, ", (*winAF2new.begin()).pos);
std::vector<WININFO>::iterator avg_itr = --winAF2new.end();
printf("last-center: %.0f\n", (*avg_itr).pos);
}
////
////
/* plot window-averaged frequency */
unsigned long awinSize;
double* winPosiSet = NULL;
double* winFreqSet = NULL;
double* winAFr2Set = NULL;
double* winABSTSet = NULL;
double* winSTDnew2 = NULL;
double* winScorSet = NULL;
if(plot_window)
{
/* prepare.........double*.........variables.........required............by........dislin */
awinSize = winAVGnew.size();
winPosiSet = (double*)malloc((awinSize+1)*sizeof(double));
winFreqSet = (double*)malloc((awinSize+1)*sizeof(double));
winAFr2Set = (double*)malloc((awinSize+1)*sizeof(double));
winSTDnew2 = (double*)malloc((awinSize+1)*sizeof(double));
winScorSet = (double*)malloc((awinSize+1)*sizeof(double));
if(plot_boost)
{
winABSTSet = (double*)malloc((awinSize+1)*sizeof(double));
}
if(winPosiSet==NULL || winFreqSet==NULL || (plot_boost && winABSTSet==NULL) ||
winScorSet==NULL)
{
printf("Malloc error 2 in plot_chr_winboost(...). Exited.\n");
exit(1);
}
/* prepare........xray:position.......and.......yray:frequency........for.........plotting */
/* window-averaged.............................................................frequency 1 */
std::vector<WININFO>::iterator win_itr = winAVGnew.begin();
std::vector<WININFO>::iterator win_itr_end = winAVGnew.end();
unsigned long winpos = 0;
while(win_itr != win_itr_end)
{
/* this position */
*(winPosiSet+winpos) = (*win_itr).pos;
*(winFreqSet+winpos) = (*win_itr).val;
/* next position */
win_itr ++;
winpos ++;
}
/* std.........related............to.............window-averaged..............frequency 2 */
win_itr = winSTDnew.begin();
win_itr_end = winSTDnew.end();
winpos = 0;
while(win_itr != win_itr_end)
{
winSTDnew2[winpos] = (*win_itr).val;
win_itr ++;
winpos ++;
}
/* window-averaged............................................................frequency 2 */
win_itr = winAF2new.begin();
win_itr_end = winAF2new.end();
winpos = 0;
while(win_itr != win_itr_end)
{
*(winAFr2Set+winpos) = (*win_itr).val;
win_itr ++;
winpos ++;
}
// winABSTSet //
/* window-averaged..................................................................score */
win_itr = winSCOnew.begin();
win_itr_end = winSCOnew.end();
winpos = 0;
while(win_itr != win_itr_end)
{
*(winScorSet+winpos) = (*win_itr).val;
win_itr ++;
winpos ++;
}
/* finding....a....region....around.......the.......lowest.......cv=std/mean.......values */
if(strcatCMD.find("SHOREmap outcross")!=std::string::npos)
{
interest_regPos[0] = INF;
interest_regPos[1] = 0;
interest_regHET[0] = 0.025;
interest_regHET[1] = 0.025;
win_itr = winSTDnew.begin();
win_itr_end = winSTDnew.end();
unsigned long gi = 0;
while(win_itr != win_itr_end)
{
if((*win_itr).val <= cv_threshold)
if(winAFr2Set[gi] >= avg_threshold && winAFr2Set[gi] <= interval_max_mean)
{
/* record....minimum.....window....begin....and....maximum....window......end */
if((*win_itr).beg < interest_regPos[0]) interest_regPos[0] = (*win_itr).beg;
if((*win_itr).end > interest_regPos[1]) interest_regPos[1] = (*win_itr).end;
}
gi ++;
win_itr ++;
}
/* if.........there............is..............a.............valid.............region */
if(interest_regPos[1] > interest_regPos[0])
{
printf("\tMAPPING INTERVAL PREDICTED FROM %.0f ", interest_regPos[0]);
printf("TO %.0f, ", interest_regPos[1]);
if((unsigned long)(interest_regPos[1]-interest_regPos[0]+1)/1000000 > 0)
{
sprintf(iregion, "*Predicted mapping interval of size %.2f Mbp (large): %.0f ~ %.0f\0",
(interest_regPos[1]-interest_regPos[0]+1)/1000000.0,
interest_regPos[0], interest_regPos[1]);
printf("REGION SIZE = %.0f Mbp.\n",(interest_regPos[1]-interest_regPos[0]+1)/1000000.0);
}
else
{
sprintf(iregion, "*Predicted mapping interval of size %.2f Kbp (normal): %.0f ~ %.0f\0",
(interest_regPos[1]-interest_regPos[0]+1)/1000.0,
interest_regPos[0], interest_regPos[1]);
printf("REGION SIZE = %.0f Kbp.\n",(interest_regPos[1]-interest_regPos[0]+1)/1000.0);
}
}
}
}
/* replace boost values of INF as the maixmum boost value */
if(plot_window && plot_boost && strcatCMD.find("SHOREmap outcross")!=std::string::npos)
{
std::vector<WININFO>::iterator bst_itr;
std::vector<WININFO>::iterator bst_itr_end;
bst_itr = winBSTnew.begin();
bst_itr_end = winBSTnew.end();
while(bst_itr != bst_itr_end)
{
if((*bst_itr).val == INF)
{
(*bst_itr).val = bstmax;
WININFO iwin;
iwin.pos = (*bst_itr).pos;
iwin.val = bstmax;
bstmax_pos.push_back(iwin);
}
(*bst_itr).val = (*bst_itr).val/(bstmax+MARGIN);// normalized.........as...........[0,1]
bst_itr ++;
}
/* new on 2013-07-16 18:22 */
/* if the minimum boost value is around 0.5, then boost value is not informative */
/* then we can pull the values down a little bit according to the minimum boost value */
double bst_min = 1.0;
bst_itr = winBSTnew.begin();
while(bst_itr != bst_itr_end)
{
if(bst_min > (*bst_itr).val)
{
bst_min = (*bst_itr).val;
}
bst_itr ++;
}
if(bst_min >= 0.25 && interest_regPos[1] < interest_regPos[0])
{
// CAUTION: only pull down boost-values of a chromosome indicating no confident peak
// TODO: also consider mean of AFs; only when AF_max < say 0.6
bst_itr = winBSTnew.begin();
while(bst_itr != bst_itr_end)
{
(*bst_itr).val -= bst_min;
bst_itr ++;
}
}
/* window-boost.....................................................................value */
if(plot_boost)
{
std::vector<WININFO>::iterator win_itr;
std::vector<WININFO>::iterator win_itr_end;
win_itr = winBSTnew.begin();
win_itr_end = winBSTnew.end();
unsigned long winpos = 0;
while(win_itr != win_itr_end)
{
*(winABSTSet+winpos) = (*win_itr).val;
win_itr ++;
winpos ++;
}
}
}
/* output.......statistical.......info.......if.........required.........--........2013-12-23 */
if(plot_record)
{
print_plot_info(chrID, myPosiSet, myFreqSet, dtSize,
winPosiSet, winAFr2Set, winSTDnew2, winABSTSet,
awinSize);
}
/* setting of page format, file forma and file name in the parent-function */
/* set axis system */
double unit_color;
double base_color;
double peak_color;
if(strcatCMD.find("SHOREmap outcross")!=std::string::npos && k >= 2)
{
////base_color = 254.0*0.35;
////peak_color = 254.0*0.55;
base_color = 1.0;
peak_color = 254.0;
unit_color = (peak_color-base_color)/(k-1);
}
else if(k >= 2)
{
base_color = 1.0;
peak_color = 254.0;
unit_color = (peak_color-base_color)/(k-1);
}
else ;
axspos(700,3500); // level 1 - determines position of an axis system
int xaxisLen = 9700;
int yaxisLen = 2200;
int zaxisLen = 2200;
if(strcatCMD.find("--chromosome") != std::string::npos)
{
ax3len(xaxisLen, yaxisLen, zaxisLen);
if(k >= 2) colran (base_color, peak_color);
}
else // scale with the maximum length of chromosomes
{
if(plot_scale)
{
double ratio = (double)ci_end/(double)chrsizes_max;
////axslen((int)(10100.0*ratio),2200);
ax3len((int)(xaxisLen*ratio), yaxisLen, zaxisLen);
if(k >= 2) colran (base_color, peak_color);
}
else
{
////axslen(10100,2200);
ax3len(xaxisLen, yaxisLen, zaxisLen);
if(k >= 2) colran (base_color, peak_color);
}
}
shdmod ("SYMB", "CURVE");
//setscl(myPosiSet, dtSize, "x"); // level 1 - sets the scale of axis
//setscl(myFreqSet, dtSize, "y"); // level 1
pagera(); // level 1/2/3 - plot a border around the page
complx(); // level - complex font
int ic0 = intrgb(0,0,0); // level 1/2/3 - creates explicit color value from RGB
frmclr(ic0); // level 1/2/3 - defines color of frames
axclrs(ic0, "ALL", "XYZ"); // ’LINE’, ’TICKS’, ’LABELS’, ’NAME’, ’ALL’
height(80); // level 1/2/3 - defines height of characters in plot
// (names of title&axis not included)
helve();
psfont("Helvetica");
name("Chromosome Position", "x"); // level 1/2/3 - defines axis titles
if(plot_boost && plot_window) //
name("Allele Frequency (with boost)", "y");
else
name("Allele Frequency", "y");