*
*/
+/* This class library coverage at the given distances of the Cramer-von Mises statistic.
+ you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries"
+ paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0
+ DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
+
+
#include "coverage.h"
//**********************************************************************************************************************
numUserGroups = globaldata->Groups.size();
numGroups = globaldata->gGroupmap->getNumGroups();
}
+
//**********************************************************************************************************************
-void Coverage::getValues(FullMatrix* matrix, float d, vector< vector<float> >& data) {
+void Coverage::getValues(FullMatrix* matrix, vector< vector< vector<float> > >& data, vector<float> dist) {
try {
vector<float> min;
vector<string> groups;
//initialize data
- data.resize(numUserGroups);
+ data.resize(dist.size());
for (int l = 0; l < data.size(); l++) {
- data[l].push_back(0.0);
+ data[l].resize(numGroups);
+ for (int k = 0; k < data[l].size(); k++) {
+ data[l][k].push_back(0.0);
+ }
}
/**************************************/
//get the minimums for each comparision
/**************************************/
int count = 0;
- int a = 0;
- int b = 0;
+
for (int i = 0; i < numGroups; i++) {
for (int j = 0; j < numGroups; j++) {
-
- //is this "box" one hte user wants analyzed?
+
+ //is this "box" one the user wants analyzed?
if ((inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups) == true) && (inUsersGroups(globaldata->gGroupmap->namesOfGroups[j], globaldata->Groups) == true)) {
- min = matrix->getMins(count); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
-
+ min = matrix->getMins(count); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
+
//find the coverage at this distance
sort(min.begin(), min.end());
-//cout << "minvector for : " << globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[j] << endl;
-//for(int h = 0; h<min.size(); h++) {
-// cout << min[h] << " ";
-//}
-//cout << endl;
- int index = -1;
- //find index in min where value is higher than d
- for (int m = 0; m < min.size(); m++) {
- if (min[m] > d) { index = m; break; }
- }
- // if you don't find one than all the mins are less than d
- if (index == -1) { index = min.size(); }
+ //loop through each distance and fill data
+ for (int k = 0; k < data.size(); k++) {
+
+ int index = -1;
+ //find index in min where value is higher than d
+ for (int m = 0; m < min.size(); m++) {
+ if (min[m] > dist[k]) { index = m; break; }
+ }
- //save value in data
- data[a][b] = 1.0 - ((min.size()-index)/(float)min.size());
-//cout << "D = " << d << "data " << a << b << " = " << data[a][b] << endl;
- if (b < numUserGroups-1) { b++; }
- else{ //you are moving to a new row of "boxes"
- b = 0;
- a++;
+ // if you don't find one than all the mins are less than d
+ if (index == -1) { index = min.size(); }
+
+ //save value in data
+ data[k][i][j] = 1.0 - ((min.size()-index)/(float)min.size());
+
}
}
count++;
}
}
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+
//**********************************************************************************************************************
-//For the random matrices
-void Coverage::getValues(FullMatrix* matrix, float d, vector< vector<float> >& data, string r) {
+void Coverage::getValues(FullMatrix* matrix, vector< vector< vector<float> > >& data, vector<float> dist, string mode) {
try {
- vector<float> min;
+ vector<float> min1;
+ vector<float> min2;
vector<string> groups;
//initialize data
- data.resize(numUserGroups);
+ data.resize(dist.size());
for (int l = 0; l < data.size(); l++) {
- data[l].push_back(0.0);
+ data[l].resize(numGroups);
+ for (int k = 0; k < data[l].size(); k++) {
+ data[l][k].push_back(0.0);
+ }
}
-
- /**************************************/
- //get the minimums for each comparision
- /**************************************/
+
int count = 0;
- int a = 0;
- int b = 0;
+ int count2 = 0;
+
+ //for each box
for (int i = 0; i < numGroups; i++) {
for (int j = 0; j < numGroups; j++) {
-
- //is this "box" one hte user wants analyzed?
- if ((inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups) == true) && (inUsersGroups(globaldata->gGroupmap->namesOfGroups[j], globaldata->Groups) == true)) {
-cout << "combo " << a << b << endl;
-cout << "original matrix mins4rows " << endl;
-matrix->printMinsForRows(cout);
- //create random matrix for this comparison
- matrix->shuffle(count);
-
- min = matrix->getMins(count); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
-cout << "shuffled matrix mins4rows " << endl;
-matrix->printMinsForRows(cout);
+
+ if (i != j) {
+ //is this "box" one the user wants analyzed?
+ if ((inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups) == true) && (inUsersGroups(globaldata->gGroupmap->namesOfGroups[j], globaldata->Groups) == true)) {
+
+ matrix->shuffle(globaldata->gGroupmap->namesOfGroups[i], globaldata->gGroupmap->namesOfGroups[j]);
+
+ min1 = matrix->getMins(count); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
+ min2 = matrix->getMins(count2); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
- //find the coverage at this distance
- sort(min.begin(), min.end());
+ //find the coverage at this distance
+ sort(min1.begin(), min1.end());
- int index = -1;
- //find index in min where value is higher than d
- for (int m = 0; m < min.size(); m++) {
- if (min[m] > d) { index = m; break; }
- }
+ //find the coverage at this distance
+ sort(min2.begin(), min2.end());
+
+ float distDiff = 0;
+
+ //loop through each distance and fill data
+ for (int k = 0; k < data.size(); k++) {
+ //****** coverage of AA **********//
+ int index = -1;
+ //find index in min where value is higher than d
+ for (int m = 0; m < min1.size(); m++) {
+ if (min1[m] > dist[k]) { index = m; break; }
+ }
- // if you don't find one than all the mins are less than d
- if (index == -1) { index = min.size(); }
+ // if you don't find one than all the mins are less than d
+ if (index == -1) { index = min1.size(); }
+
+ //****** coverage of AB **********//
+ int index2 = -1;
+ //find index in min where value is higher than d
+ for (int m = 0; m < min2.size(); m++) {
+ if (min2[m] > dist[k]) { index2 = m; break; }
+ }
- //save value in data
- data[a][b] = 1.0 - ((min.size()-index)/(float)min.size());
-cout << "D = " << d << "data " << a << b << " = " << data[a][b] << endl;
- if (b < numUserGroups-1) { b++; }
- else{ //you are moving to a new row of "boxes"
- b = 0;
- a++;
+ // if you don't find one than all the mins are less than d
+ if (index2 == -1) { index2 = min2.size(); }
+
+ //coverage of ii
+ float covII = 1.0 - ((min1.size()-index)/(float)min1.size());
+
+ //coverage of ij
+ float covIJ = 1.0 - ((min2.size()-index2)/(float)min2.size());
+
+ //save value in data (Caa - Cab)^2 * distDiff
+ data[k][i][j] = ((covII-covIJ) * (covII-covIJ)) * distDiff;
+
+ //update distDiff
+ if (k < data.size() - 1) {
+ distDiff = dist[k+1] - dist[k];
+ }
+ }
+
+ //put matrix back to original
+ matrix->restore();
}
}
- count++;
-
- //restore matrix to original form for next shuffle
- matrix->restore();
-min = matrix->getMins(count-1);
-cout << "restored matrix mins4rows " << endl;
-matrix->printMinsForRows(cout);
+ count2++;
}
+ count += numGroups+1; //go from AA to BB to CC
}
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
+
}
-//**********************************************************************************************************************
-
\ No newline at end of file
projects / mothur.git / blobdiff