X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=kruskalwalliscommand.cpp;h=805d21e51d5331576185f6d28128af8dad7cbae3;hp=bf4fafa950f2f180227f61ab41e1377008927c82;hb=b25ede2ad307ae76f8a610443e0ec3ec69621ce7;hpb=b8ff3bca0560a53832723f4621fcddef7ec4e499 diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp index bf4fafa..805d21e 100644 --- a/kruskalwalliscommand.cpp +++ b/kruskalwalliscommand.cpp @@ -6,14 +6,19 @@ */ #include "kruskalwalliscommand.h" +#include "linearalgebra.h" //********************************************************************************************************************** -vector KruskalWallisCommand::setParameters(){ +vector KruskalWallisCommand::setParameters(){ try { + CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared); + CommandParameter pclass("class", "String", "", "", "", "", "","",false,false); parameters.push_back(pclass); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pclasses("classes", "String", "", "", "", "", "","",false,false); parameters.push_back(pclasses); + //every command must have inputdir and outputdir. This allows mothur users to redirect input and output files. CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); - CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups); - CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -25,12 +30,16 @@ vector KruskalWallisCommand::setParameters(){ } } //********************************************************************************************************************** -string KruskalWallisCommand::getHelpString(){ +string KruskalWallisCommand::getHelpString(){ try { string helpString = ""; - helpString += "The kruskalwallis command parameter options are \n"; - helpString += "Kruskal–Wallis one-way analysis of variance is a non-parametric method for testing whether samples originate from the same distribution."; - return helpString; + helpString += "The kruskal.wallis command allows you to ....\n"; + helpString += "The kruskal.wallis command parameters are: shared, design, class, label and classes.\n"; + helpString += "The class parameter is used to indicate the which category you would like used for the Kruskal Wallis analysis. If none is provided first category is used.\n"; + helpString += "The classes parameter is used to indicate the classes you would like to use. Clases should be inputted in the following format: classes=label-label. For example to include groups from treatment with value early or late and age= young or old. class=treatment-age.\n"; + helpString += "The label parameter is used to indicate which distances in the shared file you would like to use. labels are separated by dashes.\n"; + helpString += "The kruskal.wallis command should be in the following format: kruskal.wallis(shared=final.an.shared, design=final.design, class=treatment).\n"; + return helpString; } catch(exception& e) { m->errorOut(e, "KruskalWallisCommand", "getHelpString"); @@ -42,7 +51,7 @@ string KruskalWallisCommand::getOutputPattern(string type) { try { string pattern = ""; - if (type == "summary") { pattern = "[filename],cooccurence.summary"; } + if (type == "kruskall-wallis") { pattern = "[filename],[distance],kruskall_wallis"; } else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } return pattern; @@ -53,13 +62,12 @@ string KruskalWallisCommand::getOutputPattern(string type) { } } //********************************************************************************************************************** -KruskalWallisCommand::KruskalWallisCommand(){ +KruskalWallisCommand::KruskalWallisCommand(){ try { - abort = true; calledHelp = true; + abort = true; calledHelp = true; setParameters(); vector tempOutNames; - outputTypes["summary"] = tempOutNames; - + outputTypes["kruskall-wallis"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand"); @@ -67,68 +75,95 @@ KruskalWallisCommand::KruskalWallisCommand(){ } } //********************************************************************************************************************** -KruskalWallisCommand::KruskalWallisCommand(string option) { +KruskalWallisCommand::KruskalWallisCommand(string option) { try { - abort = false; calledHelp = false; - + abort = false; calledHelp = false; + allLines = 1; + //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { + //valid paramters for this command vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); - map::iterator it; ValidParameters validParameter; - + map::iterator it; //check to make sure all parameters are valid for command - for (it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + + vector tempOutNames; + outputTypes["kruskall-wallis"] = tempOutNames; - //get shared file - sharedfile = validParameter.validFile(parameters, "shared", true); - if (sharedfile == "not open") { sharedfile = ""; abort = true; } - else if (sharedfile == "not found") { - //if there is a current shared file, use it - sharedfile = m->getSharedFile(); - if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } - else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; } - }else { m->setSharedFile(sharedfile); } - - //if the user changes the output directory command factory will send this info to us in the output parameter - outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sharedfile); } - - groups = validParameter.validFile(parameters, "groups", false); - if (groups == "not found") { groups = ""; } - else { - m->splitAtDash(groups, Groups); - } - m->setGroups(Groups); - - //if the user changes the input directory command factory will send this info to us in the output parameter - string inputDir = validParameter.validFile(parameters, "inputdir", false); + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; } else { - string path; - it = parameters.find("shared"); + + string path; + it = parameters.find("design"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["desing"] = inputDir + it->second; } + } + + it = parameters.find("shared"); //user has given a template file - if(it != parameters.end()){ + if(it != parameters.end()){ path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["shared"] = inputDir + it->second; } } + } + + //get shared file, it is required + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setSharedFile(sharedfile); } + + //get shared file, it is required + designfile = validParameter.validFile(parameters, "design", true); + if (designfile == "not open") { designfile = ""; abort = true; } + else if (designfile == "not found") { + //if there is a current shared file, use it + designfile = m->getDesignFile(); + if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setDesignFile(designfile); } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = m->hasPath(sharedfile); //if user entered a file with a path then preserve it } - - vector tempOutNames; - outputTypes["summary"] = tempOutNames; - - + + string label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + mclass = validParameter.validFile(parameters, "class", false); + if (mclass == "not found") { mclass = ""; } + + classes = validParameter.validFile(parameters, "classes", false); + if (classes == "not found") { classes = ""; } + } - + } catch(exception& e) { m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand"); @@ -136,128 +171,165 @@ KruskalWallisCommand::KruskalWallisCommand(string option) { } } //********************************************************************************************************************** + int KruskalWallisCommand::execute(){ try { + if (abort == true) { if (calledHelp) { return 0; } return 2; } - InputData* input = new InputData(sharedfile, "sharedfile"); - vector lookup = input->getSharedRAbundVectors(); - string lastLabel = lookup[0]->getLabel(); - - - //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. - set processedLabels; - set userLabels = labels; - - ofstream out; - map variables; - variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); - string outputFileName = getOutputFileName("summary",variables); - m->openOutputFile(outputFileName, out); - outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName); - out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); - out << "H\tpvalue\n"; - - //math goes here + DesignMap designMap(designfile); + //if user set classes set groups=those classes + if (classes != "") { + map > thisClasses = m->parseClasses(classes); + vector groups = designMap.getNamesUnique(thisClasses); + if (groups.size() != 0) { m->setGroups(groups); } + else { m->mothurOut("[ERROR]: no groups meet your classes requirement, quitting.\n"); return 0; } + } - int N = m->getNumGroups(); - double H; - double tmp = 0.0; - vector vec; - vector groups = m->getGroups(); - string group; - int count; - double sum; - - //merge all groups into a vector + //if user did not select class use first column + if (mclass == "") { mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); } + InputData input(sharedfile, "sharedfile"); + vector lookup = input.getSharedRAbundVectors(); + string lastLabel = lookup[0]->getLabel(); + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = labels; - //rank function here - assignRank(vec); - //populate counts and ranSums vectors - for (int i=0;icontrol_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + process(lookup, designMap); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); } - counts[i] = count; - rankSums[i] = sum; + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input.getSharedRAbundVectors(lastLabel); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + + process(lookup, designMap); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + } + + lastLabel = lookup[0]->getLabel(); + //prevent memory leak + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } + + if (m->control_pressed) { return 0; } + + //get next line to process + lookup = input.getSharedRAbundVectors(); } - //test statistic - for (int i=0;icontrol_pressed) { return 0; } - //H = ss / ( (N * (N + 1))/12 ); - - //correction for ties? + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; + }else { + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); + } + } - //p-value calculation + //run last label if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input.getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + process(lookup, designMap); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } - return 0; - } + + //output files created by command + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + return 0; + + } catch(exception& e) { m->errorOut(e, "KruskalWallisCommand", "execute"); exit(1); } } //********************************************************************************************************************** -void KruskalWallisCommand::assignRank(vector &vec) { - try { - double rank = 1; - double numRanks, avgRank, j; - vector::iterator it, oldit; - - sort (vec.begin(), vec.end(), comparevalue); - - it = vec.begin(); - - while ( it != vec.end() ) { - j = rank; - oldit = it; - if (!equalvalue(*it, *(it+1))) { - (*it).rank = rank; - rank = rank+1; - it++; } - else { - while(equalrank(*it, *(it+1))) { - j = j + (j+1); - rank++; - it++; - } - numRanks = double (distance(oldit, it)); - avgRank = j / numRanks; - while(oldit != it) { - (*oldit).rank = avgRank; - oldit++; - } - } +int KruskalWallisCommand::process(vector& lookup, DesignMap& designMap) { + try { + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[distance]"] = lookup[0]->getLabel(); + string outputFileName = getOutputFileName("kruskall-wallis",variables); + + ofstream out; + m->openOutputFile(outputFileName, out); + outputNames.push_back(outputFileName); outputTypes["kruskall-wallis"].push_back(outputFileName); + out << "OTULabel\tKW\tPvalue\n"; + + int numBins = lookup[0]->getNumBins(); + //sanity check to make sure each treatment has a group in the shared file + set treatments; + for (int j = 0; j < lookup.size(); j++) { + string group = lookup[j]->getGroup(); + string treatment = designMap.get(group, mclass); //get value for this group in this category + treatments.insert(treatment); } + if (treatments.size() < 2) { m->mothurOut("[ERROR]: need at least 2 things to classes to compare, quitting.\n"); m->control_pressed = true; } - + LinearAlgebra linear; + for (int i = 0; i < numBins; i++) { + if (m->control_pressed) { break; } + + vector values; + for (int j = 0; j < lookup.size(); j++) { + string group = lookup[j]->getGroup(); + string treatment = designMap.get(group, mclass); //get value for this group in this category + spearmanRank temp(treatment, lookup[j]->getAbundance(i)); + values.push_back(temp); + } + + double pValue = 0.0; + double H = linear.calcKruskalWallis(values, pValue); + + //output H and signifigance + out << m->currentBinLabels[i] << '\t' << H << '\t' << pValue << endl; + } + out.close(); + + return 0; } - catch(exception& e) { - m->errorOut(e, "KruskalWallisCommand", "getRank"); + catch(exception& e) { + m->errorOut(e, "KruskalWallisCommand", "process"); exit(1); } - -} -//********************************************************************************************************************** -void KruskalWallisCommand::assignValue(vector &vec) { - } //********************************************************************************************************************** -//********************************************************************************************************************** -//********************************************************************************************************************** +