*
*/
+/* This class is designed to implement an integral form 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 "libshuffcommand.h"
+#include "libshuff.h"
+#include "slibshuff.h"
+#include "dlibshuff.h"
//**********************************************************************************************************************
-
-LibShuffCommand::LibShuffCommand(){
+LibShuffCommand::LibShuffCommand(string option){
try {
+
globaldata = GlobalData::getInstance();
- convert(globaldata->getCutOff(), cutOff);
- convert(globaldata->getIters(), iters);
- matrix = globaldata->gMatrix;
- coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
- summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
- openOutputFile(coverageFile, out);
- openOutputFile(summaryFile, outSum);
+ abort = false;
+ Groups.clear();
- //set the groups to be analyzed
- setGroups();
-
- //file headers for coverage file
- out << "D" << '\t';
- for (int i = 0; i < groupComb.size(); i++) {
- out << "C" + groupComb[i] << '\t';
- }
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't output AA to AA
- if (i != j) {
- out << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"iters","groups","step","form","cutoff"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //make sure the user has already run the read.dist command
+ if ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL)) {
+ mothurOut("You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. "); mothurOutEndLine(); abort = true;;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; savegroups = groups; }
+ else {
+ savegroups = groups;
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
+ convert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
+ convert(temp, cutOff);
+
+ temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
+ convert(temp, step);
+
+ userform = validParameter.validFile(parameters, "form", false); if (userform == "not found") { userform = "integral"; }
+
+ if (abort == false) {
+
+ matrix = globaldata->gMatrix; //get the distance matrix
+ setGroups(); //set the groups to be analyzed
+
+ if(userform == "discrete"){
+ form = new DLibshuff(matrix, iters, step, cutOff);
+ }
+ else{
+ form = new SLibshuff(matrix, iters, cutOff);
}
}
+
}
- out << endl;
-
- numComp = numGroups*numGroups;
-
- coverage = new Coverage();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "LibShuffCommand", "LibShuffCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
-
//**********************************************************************************************************************
-LibShuffCommand::~LibShuffCommand(){
- delete coverage;
+void LibShuffCommand::help(){
+ try {
+ mothurOut("The libshuff command can only be executed after a successful read.dist command including a groupfile.\n");
+ mothurOut("The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required.\n");
+ mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
+ mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix.\n");
+ mothurOut("The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form.\n");
+ mothurOut("The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete.\n");
+ mothurOut("The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n");
+ mothurOut("Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n");
+ mothurOut("The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01.\n");
+ mothurOut("The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "LibShuffCommand", "help");
+ exit(1);
+ }
}
//**********************************************************************************************************************
int LibShuffCommand::execute(){
try {
- //deltaValues[0] = scores for the difference between AA and AB.
- //cValues[0][0] = AA, cValues[0][1] = AB, cValues[0][2] = AC, cValues[1][0] = BA, cValues[1][1] = BB...
- sumDelta.resize(numComp-numGroups, 0.0);
-
- float D = 0.0;
+ if (abort == true) { return 0; }
- /*****************************/
- //get values for users matrix
- /*****************************/
- matrix->getMinsForRowsVectors();
+ savedDXYValues = form->evaluateAll();
+ savedMinValues = form->getSavedMins();
- //get values for users matrix
- while (D <= cutOff) {
- cValues = coverage->getValues(matrix, D);
-
- //find delta values
- int count = 0;
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't save AA to AA
- if (i != j) {
- //(Caa - Cab)^2
- deltaValues.push_back( (abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j])) );
- sumDelta[count] += deltaValues[count];
- count++;
- }
- }
- }
-
- D += 0.01;
-
- printCoverageFile(D);
-
- //clear out old Values
- cValues.clear();
- deltaValues.clear();
+ pValueCounts.resize(numGroups);
+ for(int i=0;i<numGroups;i++){
+ pValueCounts[i].assign(numGroups, 0);
}
- /*******************************************************************************/
- //create and score random matrixes finding the sumDelta values for summary file
- /******************************************************************************/
-
- //initialize rsumDelta
- rsumDelta.resize(numComp-numGroups);
- for (int l = 0; l < rsumDelta.size(); l++) {
- for (int w = 0; w < iters; w++) {
- rsumDelta[l].push_back(0.0);
- }
- }
+ Progress* reading = new Progress();
- for (int m = 0; m < iters; m++) {
- //generate random matrix in getValues
- //values for random matrix
- while (D <= cutOff) {
- cValues = coverage->getValues(matrix, D);
-
- //find delta values
- int count = 0;
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't save AA to AA
- if (i != j) {
- //(Caa - Cab)^2
- rsumDelta[count][m] += (abs(cValues[i][i]-cValues[i][j]) * abs(cValues[i][i]-cValues[i][j]));
- count++;
- }
- }
+ for(int i=0;i<numGroups-1;i++) {
+ for(int j=i+1;j<numGroups;j++) {
+ reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
+ for(int p=0;p<iters;p++) {
+ form->randomizeGroups(i,j);
+ if(form->evaluatePair(i,j) >= savedDXYValues[i][j]) { pValueCounts[i][j]++; }
+ if(form->evaluatePair(j,i) >= savedDXYValues[j][i]) { pValueCounts[j][i]++; }
+ reading->update(p);
}
-
- D += 0.01;
-
- //clear out old Values
- cValues.clear();
+ form->resetGroup(i);
+ form->resetGroup(j);
}
}
-
- /**********************************************************/
- //find the signifigance of the user matrix' sumdelta values
- /**********************************************************/
-
- for (int t = 0; t < rsumDelta.size(); t++) {
- //sort rsumDelta t
- sort(rsumDelta[t].begin(), rsumDelta[t].end());
-
- //the index of the score higher than yours is returned
- //so if you have 1000 random matrices the index returned is 100
- //then there are 900 matrices with a score greater then you.
- //giving you a signifigance of 0.900
- int index = findIndex(sumDelta[t], t);
-
- //the signifigance is the number of trees with the users score or higher
- sumDeltaSig.push_back((iters-index)/(float)iters);
+ reading->finish();
+ delete reading;
- }
-
+ mothurOutEndLine();
printSummaryFile();
+ printCoverageFile();
//clear out users groups
globaldata->Groups.clear();
+ delete form;
+
+ //delete globaldata's copy of the gmatrix to free up memory
+ delete globaldata->gMatrix; globaldata->gMatrix = NULL;
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "LibShuffCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
+
//**********************************************************************************************************************
-void LibShuffCommand::printCoverageFile(float d) {
+
+void LibShuffCommand::printCoverageFile() {
try {
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ ofstream outCov;
+ summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.coverage";
+ openOutputFile(summaryFile, outCov);
+ outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
+ //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
- out << setprecision(globaldata->getIters().length()) << d << '\t';
+ map<double,vector<int> > allDistances;
+ map<double,vector<int> >::iterator it;
+
+ vector<vector<int> > indices(numGroups);
+ int numIndices = numGroups * numGroups;
- //print out coverage values
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- out << cValues[i][j] << '\t';
+ int index = 0;
+ for(int i=0;i<numGroups;i++){
+ indices[i].assign(numGroups,0);
+ for(int j=0;j<numGroups;j++){
+ indices[i][j] = index++;
+ for(int k=0;k<savedMinValues[i][j].size();k++){
+ if(allDistances[savedMinValues[i][j][k]].size() != 0){
+ allDistances[savedMinValues[i][j][k]][indices[i][j]]++;
+ }
+ else{
+ allDistances[savedMinValues[i][j][k]].assign(numIndices, 0);
+ allDistances[savedMinValues[i][j][k]][indices[i][j]] = 1;
+ }
+ }
}
}
+ it=allDistances.begin();
+
+ //cout << setprecision(8);
+
+ vector<int> prevRow = it->second;
+ it++;
- //print out delta values
- for (int i = 0; i < deltaValues.size(); i++) {
- out << deltaValues[i] << '\t';
+ for(;it!=allDistances.end();it++){
+ for(int i=0;i<it->second.size();i++){
+ it->second[i] += prevRow[i];
+ }
+ prevRow = it->second;
}
- out << endl;
-
+ vector<int> lastRow = allDistances.rbegin()->second;
+ outCov << setprecision(8);
+
+ outCov << "dist";
+ for (int i = 0; i < numGroups; i++){
+ outCov << '\t' << groupNames[i];
+ }
+ for (int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
+ outCov << groupNames[j] << '-' << groupNames[i];
+ }
+ }
+ outCov << endl;
+
+ for(it=allDistances.begin();it!=allDistances.end();it++){
+ outCov << it->first << '\t';
+ for(int i=0;i<numGroups;i++){
+ outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
+ }
+ for(int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
+ outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
+ }
+ }
+ outCov << endl;
+ }
+ outCov.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "LibShuffCommand", "printCoverageFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
+
//**********************************************************************************************************************
+
void LibShuffCommand::printSummaryFile() {
try {
- //format output
+
+ ofstream outSum;
+ summaryFile = getRootName(globaldata->getPhylipFile()) + "libshuff.summary";
+ openOutputFile(summaryFile, outSum);
+
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
- for (int i = 0; i < numGroups; i++) {
- for (int j = 0; j < numGroups; j++) {
- //don't output AA to AA
- if (i != j) {
- outSum << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
+ cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+ mothurOutJustToLog("Comparison\tdCXYScore\tSignificance"); mothurOutEndLine();
+ outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+
+ int precision = (int)log10(iters);
+ for(int i=0;i<numGroups;i++){
+ for(int j=i+1;j<numGroups;j++){
+ if(pValueCounts[i][j]){
+ cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+ mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[i][j]) + "\t" + toString((pValueCounts[i][j]/(float)iters))); mothurOutEndLine();
+ outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+ }
+ else{
+ cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+ mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[i][j]) + "\t" + toString((1/(float)iters))); mothurOutEndLine();
+ outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[i][j] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+ }
+ if(pValueCounts[j][i]){
+ cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+ mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[j][i]) + "\t" + toString((pValueCounts[j][i]/(float)iters))); mothurOutEndLine();
+ outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+ }
+ else{
+ cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
+ mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[j][i]) + "\t" + toString((1/(float)iters))); mothurOutEndLine();
+ outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[j][i] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
}
}
}
- outSum << endl;
-
- //print out delta values
- for (int i = 0; i < sumDelta.size(); i++) {
- outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
- }
- outSum << endl;
-
+ outSum.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "LibShuffCommand", "printSummaryFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
+
void LibShuffCommand::setGroups() {
try {
//if the user has not entered specific groups to analyze then do them all
for (int i=0; i < numGroups; i++) {
globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
}
- }else {
- if (globaldata->getGroups() != "all") {
+ } else {
+ if (savegroups != "all") {
//check that groups are valid
for (int i = 0; i < globaldata->Groups.size(); i++) {
if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+ mothurOut(globaldata->Groups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
// erase the invalid group from globaldata->Groups
- globaldata->Groups.erase (globaldata->Groups.begin()+i);
+ globaldata->Groups.erase(globaldata->Groups.begin()+i);
}
}
for (int i=0; i < numGroups; i++) {
globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
}
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- }else { numGroups = globaldata->Groups.size(); }
- }else { //users wants all groups
+ mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+ } else { numGroups = globaldata->Groups.size(); }
+ } else { //users wants all groups
numGroups = globaldata->gGroupmap->getNumGroups();
globaldata->Groups.clear();
for (int i=0; i < numGroups; i++) {
}
}
}
+
+ //sort so labels match
+ sort(globaldata->Groups.begin(), globaldata->Groups.end());
- // number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
- for (int i=0; i<numGroups; i++) {
- for (int l = 0; l < numGroups; l++) {
- //set group comparison labels
- groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
- }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************/
-int LibShuffCommand::findIndex(float score, int index) {
- try{
- for (int i = 0; i < rsumDelta[index].size(); i++) {
- if (rsumDelta[index][i] >= score) { return i; }
- }
- return rsumDelta[index].size();
+ //sort
+ sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
+
+ groupNames = globaldata->Groups;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the LibShuffCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "LibShuffCommand", "setGroups");
exit(1);
}
}
/***********************************************************/
-
projects / mothur.git / blobdiff