5 * Created by Sarah Westcott on 3/9/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 /* This class is designed to implement an integral form of the Cramer-von Mises statistic.
11 you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries"
12 paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0
13 DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
16 #include "libshuffcommand.h"
18 #include "slibshuff.h"
19 #include "dlibshuff.h"
21 //**********************************************************************************************************************
23 LibShuffCommand::LibShuffCommand(string option){
25 globaldata = GlobalData::getInstance();
30 //allow user to run help
31 if(option == "help") { help(); abort = true; }
34 //valid paramters for this command
35 string Array[] = {"iters","groups","step","form","cutoff","outputdir","inputdir"};
36 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
38 OptionParser parser(option);
39 map<string, string> parameters = parser.getParameters();
41 ValidParameters validParameter;
43 //check to make sure all parameters are valid for command
44 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
45 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
48 //if the user changes the output directory command factory will send this info to us in the output parameter
49 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
51 outputDir += hasPath(globaldata->getPhylipFile()); //if user entered a file with a path then preserve it
54 //make sure the user has already run the read.dist command
55 if ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL)) {
56 mothurOut("You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. "); mothurOutEndLine(); abort = true;;
59 //check for optional parameter and set defaults
60 // ...at some point should added some additional type checking...
61 groups = validParameter.validFile(parameters, "groups", false);
62 if (groups == "not found") { groups = ""; savegroups = groups; }
65 splitAtDash(groups, Groups);
66 globaldata->Groups = Groups;
70 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
73 temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
74 convert(temp, cutOff);
76 temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
79 userform = validParameter.validFile(parameters, "form", false); if (userform == "not found") { userform = "integral"; }
83 matrix = globaldata->gMatrix; //get the distance matrix
84 setGroups(); //set the groups to be analyzed and sorts them
86 /********************************************************************************************/
87 //this is needed because when we read the matrix we sort it into groups in alphabetical order
88 //the rest of the command and the classes used in this command assume specific order
89 /********************************************************************************************/
90 matrix->setGroups(globaldata->gGroupmap->namesOfGroups);
92 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { sizes.push_back(globaldata->gGroupmap->getNumSeqs(globaldata->gGroupmap->namesOfGroups[i])); }
93 matrix->setSizes(sizes);
96 if(userform == "discrete"){
97 form = new DLibshuff(matrix, iters, step, cutOff);
100 form = new SLibshuff(matrix, iters, cutOff);
107 catch(exception& e) {
108 errorOut(e, "LibShuffCommand", "LibShuffCommand");
112 //**********************************************************************************************************************
114 void LibShuffCommand::help(){
116 mothurOut("The libshuff command can only be executed after a successful read.dist command including a groupfile.\n");
117 mothurOut("The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required.\n");
118 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");
119 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");
120 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");
121 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");
122 mothurOut("The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n");
123 mothurOut("Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n");
124 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");
125 mothurOut("The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n");
126 mothurOut("Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n\n");
128 catch(exception& e) {
129 errorOut(e, "LibShuffCommand", "help");
134 //**********************************************************************************************************************
136 int LibShuffCommand::execute(){
139 if (abort == true) { return 0; }
141 savedDXYValues = form->evaluateAll();
142 savedMinValues = form->getSavedMins();
144 pValueCounts.resize(numGroups);
145 for(int i=0;i<numGroups;i++){
146 pValueCounts[i].assign(numGroups, 0);
149 Progress* reading = new Progress();
151 for(int i=0;i<numGroups-1;i++) {
152 for(int j=i+1;j<numGroups;j++) {
153 reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
154 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
155 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
157 for(int p=0;p<iters;p++) {
158 form->randomizeGroups(spoti,spotj);
159 if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj]) { pValueCounts[i][j]++; }
160 if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti]) { pValueCounts[j][i]++; }
163 form->resetGroup(spoti);
164 form->resetGroup(spotj);
174 //clear out users groups
175 globaldata->Groups.clear();
178 //delete globaldata's copy of the gmatrix to free up memory
179 delete globaldata->gMatrix; globaldata->gMatrix = NULL;
183 catch(exception& e) {
184 errorOut(e, "LibShuffCommand", "execute");
189 //**********************************************************************************************************************
191 void LibShuffCommand::printCoverageFile() {
195 summaryFile = outputDir + getRootName(getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
196 openOutputFile(summaryFile, outCov);
197 outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
198 //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
200 map<double,vector<int> > allDistances;
201 map<double,vector<int> >::iterator it;
203 vector<vector<int> > indices(numGroups);
204 int numIndices = numGroups * numGroups;
207 for(int i=0;i<numGroups;i++){
208 indices[i].assign(numGroups,0);
209 for(int j=0;j<numGroups;j++){
210 indices[i][j] = index++;
212 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
213 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
215 for(int k=0;k<savedMinValues[spoti][spotj].size();k++){
216 if(allDistances[savedMinValues[spoti][spotj][k]].size() != 0){
217 allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]]++;
220 allDistances[savedMinValues[spoti][spotj][k]].assign(numIndices, 0);
221 allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]] = 1;
226 it=allDistances.begin();
228 //cout << setprecision(8);
230 vector<int> prevRow = it->second;
233 for(;it!=allDistances.end();it++){
234 for(int i=0;i<it->second.size();i++){
235 it->second[i] += prevRow[i];
237 prevRow = it->second;
240 vector<int> lastRow = allDistances.rbegin()->second;
241 outCov << setprecision(8);
244 for (int i = 0; i < numGroups; i++){
245 outCov << '\t' << groupNames[i];
247 for (int i=0;i<numGroups;i++){
248 for(int j=i+1;j<numGroups;j++){
249 outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
250 outCov << groupNames[j] << '-' << groupNames[i];
255 for(it=allDistances.begin();it!=allDistances.end();it++){
256 outCov << it->first << '\t';
257 for(int i=0;i<numGroups;i++){
258 outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
260 for(int i=0;i<numGroups;i++){
261 for(int j=i+1;j<numGroups;j++){
262 outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
263 outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
270 catch(exception& e) {
271 errorOut(e, "LibShuffCommand", "printCoverageFile");
276 //**********************************************************************************************************************
278 void LibShuffCommand::printSummaryFile() {
282 summaryFile = outputDir + getRootName(getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
283 openOutputFile(summaryFile, outSum);
285 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
286 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
288 cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
289 mothurOutJustToLog("Comparison\tdCXYScore\tSignificance"); mothurOutEndLine();
290 outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
292 int precision = (int)log10(iters);
293 for(int i=0;i<numGroups;i++){
294 for(int j=i+1;j<numGroups;j++){
295 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
296 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
298 if(pValueCounts[i][j]){
299 cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
300 mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((pValueCounts[i][j]/(float)iters))); mothurOutEndLine();
301 outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
304 cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
305 mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((1/(float)iters))); mothurOutEndLine();
306 outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
308 if(pValueCounts[j][i]){
309 cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
310 mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((pValueCounts[j][i]/(float)iters))); mothurOutEndLine();
311 outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
314 cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
315 mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((1/(float)iters))); mothurOutEndLine();
316 outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
323 catch(exception& e) {
324 errorOut(e, "LibShuffCommand", "printSummaryFile");
329 //**********************************************************************************************************************
331 void LibShuffCommand::setGroups() {
333 //if the user has not entered specific groups to analyze then do them all
334 if (globaldata->Groups.size() == 0) {
335 numGroups = globaldata->gGroupmap->getNumGroups();
336 for (int i=0; i < numGroups; i++) {
337 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
340 if (savegroups != "all") {
341 //check that groups are valid
342 for (int i = 0; i < globaldata->Groups.size(); i++) {
343 if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
344 mothurOut(globaldata->Groups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
345 // erase the invalid group from globaldata->Groups
346 globaldata->Groups.erase(globaldata->Groups.begin()+i);
350 //if the user only entered invalid groups
351 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
352 numGroups = globaldata->gGroupmap->getNumGroups();
353 for (int i=0; i < numGroups; i++) {
354 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
356 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();
357 } else { numGroups = globaldata->Groups.size(); }
358 } else { //users wants all groups
359 numGroups = globaldata->gGroupmap->getNumGroups();
360 globaldata->Groups.clear();
361 for (int i=0; i < numGroups; i++) {
362 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
367 //sort so labels match
368 sort(globaldata->Groups.begin(), globaldata->Groups.end());
371 sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
373 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { globaldata->gGroupmap->groupIndex[globaldata->gGroupmap->namesOfGroups[i]] = i; }
375 groupNames = globaldata->Groups;
378 catch(exception& e) {
379 errorOut(e, "LibShuffCommand", "setGroups");
384 /***********************************************************/