*/
#include "kruskalwalliscommand.h"
+#include "linearalgebra.h"
//**********************************************************************************************************************
-vector<string> KruskalWallisCommand::setParameters(){
+vector<string> 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<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-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<value1|value2|value3>-label<value1|value2>. For example to include groups from treatment with value early or late and age= young or old. class=treatment<Early|Late>-age<young|old>.\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");
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;
}
}
//**********************************************************************************************************************
-KruskalWallisCommand::KruskalWallisCommand(){
+KruskalWallisCommand::KruskalWallisCommand(){
try {
- abort = true; calledHelp = true;
+ abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
-
+ outputTypes["kruskall-wallis"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "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<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
- map<string,string>::iterator it;
ValidParameters validParameter;
-
+ map<string,string>::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<string> 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<string> 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");
}
}
//**********************************************************************************************************************
+
int KruskalWallisCommand::execute(){
try {
+
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- InputData* input = new InputData(sharedfile, "sharedfile");
- vector<SharedRAbundVector*> 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<string> processedLabels;
- set<string> userLabels = labels;
-
- ofstream out;
- map<string,string> 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<string, vector<string> > thisClasses = m->parseClasses(classes);
+ vector<string> 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<groupRank> vec;
- vector<string> 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<SharedRAbundVector*> 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<string> processedLabels;
+ set<string> userLabels = labels;
- //rank function here
- assignRank(vec);
- //populate counts and ranSums vectors
- for (int i=0;i<N;i++) {
- count = 0;
- sum = 0;
- group = groups[i];
- for(int j;j<vec.size();j++) {
- if (vec[j].group == group) {
- count++;
- sum = sum + vec[j].rank;
- }
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_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;i<N;i++) { tmp = tmp + (pow(rankSums[i],2) / counts[i]); }
-
- H = (12 / (N*(N+1))) * tmp - (3*(N+1));
-
- //ss = tmp - pow(accumulate(rankSums.begin(), rankSums.end(), 0), 2);
+ if (m->control_pressed) { return 0; }
- //H = ss / ( (N * (N + 1))/12 );
-
- //correction for ties?
+ //output error messages about any remaining user labels
+ set<string>::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<groupRank> &vec) {
- try {
- double rank = 1;
- double numRanks, avgRank, j;
- vector<groupRank>::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<SharedRAbundVector*>& lookup, DesignMap& designMap) {
+ try {
+ map<string, string> 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<string> 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<spearmanRank> 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<groupRank> &vec) {
-
}
//**********************************************************************************************************************
-//**********************************************************************************************************************
-//**********************************************************************************************************************
+
projects / mothur.git / blobdiff