added distance parameter to unifrac.weighted and unifrac.unweighted commands that allows you to output a distance matrix from the command.
added random parameter to unifrac.weighted and unifrac.unweighted commands that allows you to shut off the comparison to random trees.
}
if (confidence >= confidenceThreshold) {
- confidenceTax = seqTax.name + "(" + toString(confidence) + ");" + confidenceTax;
+ confidenceTax = seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");" + confidenceTax;
simpleTax = seqTax.name + ";" + simpleTax;
}
remove(tempTaxonomyFile.c_str());
taxaBrowser.assignHeirarchyIDs(0);
+ taxaBrowser.binUnclassified();
ofstream outTaxTree;
openOutputFile(taxSummary, outTaxTree);
globaldata = GlobalData::getInstance();
}
//**********************************************************************************************************************
-
void HeatMapSim::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> calcs) {
try {
EstOutput data;
exit(1);
}
}
+//**********************************************************************************************************************
+void HeatMapSim::getPic(vector< vector<double> > dists, vector<string> groups) {
+ try {
+
+ vector<double> sims;
+
+ string filenamesvg = getRootName(globaldata->inputFileName) + "heatmap.sim.svg";
+ openOutputFile(filenamesvg, outsvg);
+
+ //svg image
+ outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString((dists.size() * 150) + 160) + " " + toString((dists.size() * 150) + 160) + "\">\n";
+ outsvg << "<g>\n";
+
+ //white backround
+ outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((dists.size() * 150) + 160) + "\" height=\"" + toString((dists.size() * 150) + 160) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((dists.size() * 75) - 40) + "\" y=\"25\">Heatmap for " + globaldata->inputFileName + "</text>\n";
+
+ //column labels
+ for (int h = 0; h < groups.size(); h++) {
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" y=\"50\">" + groups[h] + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" y=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" x=\"50\">" + groups[h] + "</text>\n";
+ }
+
+ double biggest = -1;
+ float scaler;
+
+ //get sim for each comparison and save them so you can find the relative similairity
+ for(int i = 0; i < (dists.size()-1); i++){
+ for(int j = (i+1); j < dists.size(); j++){
+
+ float sim = 1.0 - dists[i][j];
+ sims.push_back(sim);
+
+ //save biggest similairity to set relative sim
+ if (sim > biggest) { biggest = sim; }
+ }
+ }
+
+ //map biggest similairity found to red
+ scaler = 255.0 / biggest;
+
+ int count = 0;
+ //output similairites to file
+ for(int i = 0; i < (dists.size()-1); i++){
+ for(int j = (i+1); j < dists.size(); j++){
+
+ //find relative color
+ int color = scaler * sims[count];
+ //draw box
+ outsvg << "<rect fill=\"rgb(" + toString(color) + ",0,0)\" stroke=\"rgb(" + toString(color) + ",0,0)\" x=\"" + toString((i*150)+80) + "\" y=\"" + toString((j*150)+75) + "\" width=\"150\" height=\"150\"/>\n";
+ count++;
+ }
+ }
+
+ int y = ((dists.size() * 150) + 120);
+ printLegend(y, biggest);
+
+ outsvg << "</g>\n</svg>\n";
+ outsvg.close();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapSim", "getPic");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
void HeatMapSim::printLegend(int y, float maxSim) {
~HeatMapSim(){};
void getPic(vector<SharedRAbundVector*>, vector<Calculator*>);
+ void getPic(vector< vector<double> >, vector<string>);
private:
void printLegend(int, float);
else {
//valid paramters for this command
- string AlignArray[] = {"groups","label", "calc"};
+ string AlignArray[] = {"groups","label", "calc","phylip","column","name"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //make sure the user has already run the read.otu command
- if (globaldata->getSharedFile() == "") {
- mothurOut("You must read a list and a group, or a shared before you can use the heatmap.sim command."); mothurOutEndLine(); abort = true;
- }
-
- //check for optional parameter and set defaults
- // ...at some point should added some additional type checking...
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
+ format = "";
- //if the user has not specified any labels use the ones from read.otu
- if (label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
+ //required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { format = "phylip"; }
- calc = validParameter.validFile(parameters, "calc", false);
- if (calc == "not found") { calc = "jest-thetayc"; }
- else {
- if (calc == "default") { calc = "jest-thetayc"; }
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { format = "column"; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+
+ //error checking on files
+ if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { mothurOut("You must run the read.otu command or provide a distance file before running the heatmap.sim command."); mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
+
+ if (columnfile != "") {
+ if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
}
- splitAtDash(calc, Estimators);
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ if (format == "") { format = "shared"; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ if (format == "shared") {
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //if the user has not specified any labels use the ones from read.otu
+ if (label == "") {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jest-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jest-thetayc"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
}
if (abort == false) {
validCalculator = new ValidCalculators();
- heatmap = new HeatMapSim();
int i;
for (i=0; i<Estimators.size(); i++) {
void HeatMapSimCommand::help(){
try {
- mothurOut("The heatmap.sim command can only be executed after a successful read.otu command.\n");
- mothurOut("The heatmap.sim command parameters are groups, calc and label. No parameters are required.\n");
+ mothurOut("The heatmap.sim command can only be executed after a successful read.otu command, or by providing a distance file.\n");
+ mothurOut("The heatmap.sim command parameters are phylip, column, name, groups, calc and label. No parameters are required.\n");
+ mothurOut("There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n");
+ mothurOut("With the read.otu command you may use the groups, label and calc parameters. \n");
mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n");
mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n");
validCalculator->printCalc("heat", cout);
mothurOut("The default value for calc is jclass-thetayc.\n");
mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
+ mothurOut("The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n");
+ mothurOut("Using the command this way, the phylip or column parameter are required, and only one may be used. If you use a column file the name filename is required. \n");
+ mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n");
+ mothurOut("Example heatmap.sim(phylip=amazonGroups.dist).\n");
mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
//**********************************************************************************************************************
-HeatMapSimCommand::~HeatMapSimCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete heatmap;
- delete validCalculator;
- }
-}
+HeatMapSimCommand::~HeatMapSimCommand(){}
//**********************************************************************************************************************
if (abort == true) { return 0; }
+ heatmap = new HeatMapSim();
+
+ if (format == "shared") {
+ runCommandShared();
+ }else if (format == "phylip") {
+ globaldata->inputFileName = phylipfile;
+ runCommandDist();
+ }else if (format == "column") {
+ globaldata->inputFileName = columnfile;
+ runCommandDist();
+ }
+
+ delete heatmap;
+ delete validCalculator;
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapSimCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int HeatMapSimCommand::runCommandShared() {
+ try {
//if the users entered no valid calculators don't execute command
if (heatCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
//reset groups parameter
globaldata->Groups.clear();
+ delete input; globaldata->ginput = NULL;
+ delete read;
+
return 0;
}
catch(exception& e) {
- errorOut(e, "HeatMapSimCommand", "execute");
+ errorOut(e, "HeatMapSimCommand", "runCommandShared");
exit(1);
}
}
+//**********************************************************************************************************************
+int HeatMapSimCommand::runCommandDist() {
+ try {
+
+ vector< vector<double> > matrix;
+ vector<string> names;
+ ifstream in;
+
+ //read distance file and create distance vector and names vector
+ if (format == "phylip") {
+ //read phylip file
+ openInputFile(phylipfile, in);
+
+ string name;
+ int numSeqs;
+ in >> numSeqs >> name;
+
+ //save name
+ names.push_back(name);
+
+ //resize the matrix and fill with zeros
+ matrix.resize(numSeqs);
+ for(int i = 0; i < numSeqs; i++) {
+ matrix[i].resize(numSeqs, 0.0);
+ }
+
+ //determine if matrix is square or lower triangle
+ //if it is square read the distances for the first sequence
+ char d;
+ bool square;
+ while((d=in.get()) != EOF){
+
+ //is d a number meaning its square
+ if(isalnum(d)){
+ square = true;
+ in.putback(d);
+
+ for(int i=0;i<numSeqs;i++){
+ in >> matrix[0][i];
+ }
+ break;
+ }
+
+ //is d a line return meaning its lower triangle
+ if(d == '\n'){
+ square = false;
+ break;
+ }
+ }
+
+ //read rest of matrix
+ if (square == true) {
+ for(int i=1;i<numSeqs;i++){
+ in >> name;
+ names.push_back(name);
+
+ for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
+ gobble(in);
+ }
+ }else {
+ double dist;
+ for(int i=1;i<numSeqs;i++){
+ in >> name;
+ names.push_back(name);
+
+ for(int j=0;j<i;j++){
+ in >> dist;
+ matrix[i][j] = dist; matrix[j][i] = dist;
+ }
+ gobble(in);
+ }
+ }
+ in.close();
+ }else {
+ //read names file
+ NameAssignment* nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+
+ //put names in order in vector
+ for (int i = 0; i < nameMap->size(); i++) {
+ names.push_back(nameMap->get(i));
+ }
+
+ //resize matrix
+ matrix.resize(nameMap->size());
+ for (int i = 0; i < nameMap->size(); i++) {
+ matrix[i].resize(nameMap->size(), 0.0);
+ }
+
+ //read column file
+ string first, second;
+ double dist;
+ openInputFile(columnfile, in);
+
+ while (!in.eof()) {
+ in >> first >> second >> dist; gobble(in);
+
+ map<string, int>::iterator itA = nameMap->find(first);
+ map<string, int>::iterator itB = nameMap->find(second);
+
+ if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << first << "' was not found in the names file, please correct\n"; exit(1); }
+ if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << second << "' was not found in the names file, please correct\n"; exit(1); }
+
+ //save distance
+ matrix[itA->second][itB->second] = dist;
+ matrix[itB->second][itA->second] = dist;
+ }
+ in.close();
+
+ delete nameMap;
+ }
+
+ heatmap->getPic(matrix, names); //vector<vector<double>>, vector<string>
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapSimCommand", "runCommandDist");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
+
+
+
+
+
+
map<string, string>::iterator it;
bool abort, allLines;
set<string> labels; //holds labels to be used
- string format, groups, label, calc;
+ string format, groups, label, calc, phylipfile, columnfile, namefile;
vector<string> Estimators, Groups;
+
+ int runCommandShared();
+ int runCommandDist();
};
else {
//valid paramters for this command
- string Array[] = {"phylip","lt"};
+ string Array[] = {"phylip"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
// if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
//}
- string temp = validParameter.validFile(parameters, "lt", false); if (temp == "not found") { temp = "false"; }
- bool lt = isTrue(temp);
+ //string temp = validParameter.validFile(parameters, "lt", false); if (temp == "not found") { temp = "false"; }
+ //bool lt = isTrue(temp);
- if (lt) { matrix = 2; }
- else { matrix = 1; }
+ //if (lt) { matrix = 2; }
+ //else { matrix = 1; }
}
else{
fbase += ".";
}
- read(filename, matrix, names, D);
+ read(filename, names, D);
double offset = 0.0000;
vector<double> d;
vector<double> e;
vector<vector<double> > G = D;
vector<vector<double> > copy_G;
- int rank = D.size();
+ //int rank = D.size();
cout << "\nProcessing...\n";
/*********************************************************************************************************************************/
-void PCACommand::read_mega(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
+void PCACommand::read_mega(istream& f, vector<string>& name_list, vector<vector<double> >& d){
try {
get_comment(f, '#', '\n');
/*********************************************************************************************************************************/
-void PCACommand::read(string fname, int m, vector<string>& names, vector<vector<double> >& D){
+void PCACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
try {
- ifstream f(fname.c_str());
- if(!f) {
- cerr << "Error: Could not open " << fname << endl;
- exit(1);
- }
+ ifstream f;
+ openInputFile(fname, f);
+
char test = f.peek();
if(test == '#'){
- read_mega(f, m, names, D);
+ read_mega(f, names, D);
}
else{
+ //check whether matrix is square
+ char d;
+ int m = 1;
+ int numSeqs;
+ string name;
+
+ f >> numSeqs >> name;
+
+ while((d=f.get()) != EOF){
+
+ //is d a number meaning its square
+ if(isalnum(d)){
+ m = 1;
+ break;
+ }
+
+ //is d a line return meaning its lower triangle
+ if(d == '\n'){
+ m = 2;
+ break;
+ }
+ }
+ f.close();
+
+ //reopen to get back to beginning
+ openInputFile(fname, f);
read_phylip(f, m, names, D);
}
- int rank = D.size();
+ //int rank = D.size();
}
catch(exception& e) {
errorOut(e, "PCACommand", "read");
bool abort;
string phylipfile, columnfile, namefile, format, filename, fbase;
float cutoff, precision;
- int matrix;
void get_comment(istream&, char, char);
- void read_mega(istream&, int, vector<string>&, vector<vector<double> >&);
+ void read_mega(istream&, vector<string>&, vector<vector<double> >&);
void read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
- void read(string, int, vector<string>&, vector<vector<double> >&);
+ void read(string, vector<string>&, vector<vector<double> >&);
double pythag(double, double);
void matrix_mult(vector<vector<double> >, vector<vector<double> >, vector<vector<double> >&);
void recenter(double, vector<vector<double> >, vector<vector<double> >&);
numSeqs = 0;
tree.push_back(TaxNode("Root"));
tree[0].heirarchyID = "0";
+ maxLevel = 0;
ifstream in;
openInputFile(tfile, in);
tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
counter++;
tree[it->second].level = tree[index].level + 1;
+
+ //save maxLevel for binning the unclassified seqs
+ if (tree[it->second].level > maxLevel) { maxLevel = tree[it->second].level; }
+
assignHeirarchyIDs(it->second);
}
}
exit(1);
}
}
-
+/**************************************************************************************************/
+void PhyloTree::binUnclassified(){
+ try {
+ map<string, int>::iterator itBin;
+ map<string, int>::iterator childPointer;
+
+ //go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
+ for (itBin = name2Taxonomy.begin(); itBin != name2Taxonomy.end(); itBin++) {
+
+ int level = tree[itBin->second].level;
+ int currentNode = itBin->second;
+
+ //this sequence is unclassified at some levels
+ while(level != maxLevel){
+
+ level++;
+
+ string taxon = "unclassified";
+
+ //does the parent have a child names 'unclassified'?
+ childPointer = tree[currentNode].children.find(taxon);
+
+ if(childPointer != tree[currentNode].children.end()){ //if the node already exists, move on
+ currentNode = childPointer->second; //currentNode becomes 'unclassified'
+ tree[currentNode].accessions.push_back(itBin->first); //add this seq
+ name2Taxonomy[itBin->first] = currentNode;
+ }
+ else{ //otherwise, create it
+ tree.push_back(TaxNode(taxon));
+ numNodes++;
+ tree[currentNode].children[taxon] = numNodes-1;
+ tree[numNodes-1].parent = currentNode;
+
+ currentNode = tree[currentNode].children[taxon];
+ tree[currentNode].accessions.push_back(itBin->first);
+ name2Taxonomy[itBin->first] = currentNode;
+ }
+
+ if (level == maxLevel) { uniqueTaxonomies[currentNode] = currentNode; }
+ }
+ }
+
+ //clear HeirarchyIDs and reset them
+ for (int i = 1; i < tree.size(); i++) {
+ tree[i].heirarchyID = "";
+ }
+ assignHeirarchyIDs(0);
+
+ }
+ catch(exception& e) {
+ errorOut(e, "PhyloTree", "binUnclassified");
+ exit(1);
+ }
+}
/**************************************************************************************************/
void PhyloTree::print(ofstream& out){
out <<tree[it->second].level << '\t' << tree[it->second].heirarchyID << '\t' << tree[it->second].name << '\t' << tree[it->second].children.size() << '\t' << tree[it->second].accessions.size() << endl;
print(it->second, out);
}
+
+
}
catch(exception& e) {
errorOut(e, "PhyloTree", "print");
void addSeqToTree(string, string);
void assignHeirarchyIDs(int);
void print(ofstream&);
- vector<int> getGenusNodes();
+ vector<int> getGenusNodes();
+ void binUnclassified();
+
TaxNode get(int i) { return tree[i]; }
TaxNode get(string seqName) { return tree[name2Taxonomy[seqName]]; }
int getIndex(string seqName) { return name2Taxonomy[seqName]; }
void print(int, ofstream&);
int numNodes;
int numSeqs;
+ int maxLevel;
};
/**************************************************************************************************/
else {
//valid paramters for this command
- string Array[] = {"groups","iters"};
+ string Array[] = {"groups","iters","distance","random"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
globaldata->Groups = Groups;
}
- itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
+ itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
convert(itersString, iters);
+ string temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
+ phylip = isTrue(temp);
+ temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "true"; }
+ random = isTrue(temp);
+
+ if (!random) { iters = 0; } //turn off random calcs
+
+ //if user selects distance = true and no groups it won't calc the pairwise
+ if ((phylip) && (Groups.size() == 0)) {
+ groups = "all";
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
if (abort == false) {
T = globaldata->gTree;
tmap = globaldata->gTreemap;
void UnifracUnweightedCommand::help(){
try {
mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n");
- mothurOut("The unifrac.unweighted command parameters are groups and iters. No parameters are required.\n");
+ mothurOut("The unifrac.unweighted command parameters are groups, iters, distance and random. 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 1 valid group.\n");
mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
+ mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
+ mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
for (int i = 0; i < T.size(); i++) {
counter = 0;
- output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".unweighted", itersString);
+ if (random) { output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".unweighted", itersString); }
//get unweighted for users tree
rscoreFreq.resize(numComp);
for(int k = 0; k < numComp; k++) {
//saves users score
utreeScores[k].push_back(userData[k]);
-
+
+ //add users score to validscores
+ validScores[userData[k]] = userData[k];
}
//get unweighted scores for random trees
if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
}
- UWScoreSig[a].push_back(rCumul[a][userData[a]]);
+
+ if (random) { UWScoreSig[a].push_back(rCumul[a][userData[a]]); }
+ else { UWScoreSig[a].push_back(0.0); }
}
-
-
- printUnweightedFile();
+ //print output files
printUWSummaryFile(i);
+ if (random) { printUnweightedFile(); delete output; }
+ if (phylip) { createPhylipFile(i); }
- delete output;
rscoreFreq.clear();
rCumul.clear();
validScores.clear();
try {
vector<double> data;
vector<string> tags;
- tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
+ tags.push_back("Score");
+ tags.push_back("RandFreq"); tags.push_back("RandCumul");
+
for(int a = 0; a < numComp; a++) {
output->initFile(groupComb[a], tags);
//print each line
for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
- data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
+ data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
output->output(data);
data.clear();
}
outSum << i+1 << '\t';
mothurOut(toString(i+1) + "\t");
- if (UWScoreSig[a][0] > (1/(float)iters)) {
- outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
- cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
- mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); mothurOutEndLine();
- }else {
- outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
- cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
- mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); mothurOutEndLine();
+ if (random) {
+ if (UWScoreSig[a][0] > (1/(float)iters)) {
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
+ mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); mothurOutEndLine();
+ }else {
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); mothurOutEndLine();
+ }
+ }else{
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
+ mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00"); mothurOutEndLine();
}
}
exit(1);
}
}
-
/***********************************************************/
+void UnifracUnweightedCommand::createPhylipFile(int i) {
+ try {
+ string phylipFileName = globaldata->getTreeFile() + toString(i+1) + ".unweighted.dist";
+ ofstream out;
+ openOutputFile(phylipFileName, out);
+
+ //output numSeqs
+ out << globaldata->Groups.size() << endl;
+
+ //make matrix with scores in it
+ vector< vector<float> > dists; dists.resize(globaldata->Groups.size());
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ dists[i].resize(globaldata->Groups.size(), 0.0);
+ }
+
+ //flip it so you can print it
+ int count = 0;
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ for (int l = r+1; l < globaldata->Groups.size(); l++) {
+ dists[r][l] = (1.0 - utreeScores[count][0]);
+ dists[l][r] = (1.0 - utreeScores[count][0]);
+ count++;
+ }
+ }
+
+ //output to file
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ //output name
+ out << globaldata->Groups[r] << '\t';
+
+ //output distances
+ for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; }
+ out << endl;
+ }
+ out.close();
+ }
+ catch(exception& e) {
+ errorOut(e, "UnifracUnweightedCommand", "createPhylipFile");
+ exit(1);
+ }
+}
+/***********************************************************/
+
vector< map<float, float> > rscoreFreq; //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
vector< map<float, float> > rCumul; //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
- bool abort;
+ bool abort, phylip, random;
string groups, itersString;
vector<string> Groups; //holds groups to be used
void printUWSummaryFile(int);
void printUnweightedFile();
+ void createPhylipFile(int);
};
else {
//valid paramters for this command
- string Array[] = {"groups","iters"};
+ string Array[] = {"groups","iters","distance","random"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
convert(itersString, iters);
+
+ string temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
+ phylip = isTrue(temp);
+ temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "true"; }
+ random = isTrue(temp);
+
+ if (!random) { iters = 0; } //turn off random calcs
+
if (abort == false) {
T = globaldata->gTree;
void UnifracWeightedCommand::help(){
try {
mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n");
- mothurOut("The unifrac.weighted command parameters are groups and iters. No parameters are required.\n");
+ mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random. 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 trees you would like compared to your tree.\n");
+ mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
+ mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n");
mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n");
mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
if (abort == true) { return 0; }
Progress* reading;
- reading = new Progress("Comparing to random:", iters);
+ if (random) { reading = new Progress("Comparing to random:", iters); }
//get weighted for users tree
userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
- output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted", itersString);
+ if (random) { output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted", itersString); }
userData = weighted->getValues(T[i]); //userData[0] = weightedscore
//removeValidScoresDuplicates();
//find the signifigance of the score for summary file
- for (int f = 0; f < numComp; f++) {
- //sort random scores
- sort(rScores[f].begin(), rScores[f].end());
+ if (random) {
+ for (int f = 0; f < numComp; f++) {
+ //sort random scores
+ sort(rScores[f].begin(), rScores[f].end());
+
+ //the index of the score higher than yours is returned
+ //so if you have 1000 random trees the index returned is 100
+ //then there are 900 trees with a score greater then you.
+ //giving you a signifigance of 0.900
+ int index = findIndex(userData[f], f); if (index == -1) { mothurOut("error in UnifracWeightedCommand"); mothurOutEndLine(); exit(1); } //error code
+
+ //the signifigance is the number of trees with the users score or higher
+ WScoreSig.push_back((iters-index)/(float)iters);
+ }
- //the index of the score higher than yours is returned
- //so if you have 1000 random trees the index returned is 100
- //then there are 900 trees with a score greater then you.
- //giving you a signifigance of 0.900
- int index = findIndex(userData[f], f); if (index == -1) { mothurOut("error in UnifracWeightedCommand"); mothurOutEndLine(); exit(1); } //error code
-
- //the signifigance is the number of trees with the users score or higher
- WScoreSig.push_back((iters-index)/(float)iters);
+ //out << "Tree# " << i << endl;
+ calculateFreqsCumuls();
+ printWeightedFile();
+
+ delete output;
}
- //out << "Tree# " << i << endl;
- calculateFreqsCumuls();
- printWeightedFile();
-
- delete output;
-
//clear data
rScores.clear();
uScores.clear();
}
//finish progress bar
- reading->finish();
- delete reading;
+ if (random) { reading->finish(); delete reading; }
printWSummaryFile();
+ if (phylip) { createPhylipFile(); }
+
//clear out users groups
globaldata->Groups.clear();
int count = 0;
for (int i = 0; i < T.size(); i++) {
for (int j = 0; j < numComp; j++) {
- if (WScoreSig[count] > (1/(float)iters)) {
- outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
- mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); mothurOutEndLine();
+ if (random) {
+ if (WScoreSig[count] > (1/(float)iters)) {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
+ mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); mothurOutEndLine();
+ }else{
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); mothurOutEndLine();
+ }
}else{
- outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
- mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); mothurOutEndLine();
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
+ mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); mothurOutEndLine();
}
count++;
}
exit(1);
}
}
+/***********************************************************/
+void UnifracWeightedCommand::createPhylipFile() {
+ try {
+ int count = 0;
+ //for each tree
+ for (int i = 0; i < T.size(); i++) {
+
+ string phylipFileName = globaldata->getTreeFile() + toString(i+1) + ".weighted.dist";
+ ofstream out;
+ openOutputFile(phylipFileName, out);
+
+ //output numSeqs
+ out << globaldata->Groups.size() << endl;
+
+ //make matrix with scores in it
+ vector< vector<float> > dists; dists.resize(globaldata->Groups.size());
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ dists[i].resize(globaldata->Groups.size(), 0.0);
+ }
+
+ //flip it so you can print it
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ for (int l = r+1; l < globaldata->Groups.size(); l++) {
+ dists[r][l] = (1.0 - utreeScores[count]);
+ dists[l][r] = (1.0 - utreeScores[count]);
+ count++;
+ }
+ }
+ //output to file
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ //output name
+ out << globaldata->Groups[r] << '\t';
+
+ //output distances
+ for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; }
+ out << endl;
+ }
+ out.close();
+ }
+ }
+ catch(exception& e) {
+ errorOut(e, "UnifracWeightedCommand", "createPhylipFile");
+ exit(1);
+ }
+}
/***********************************************************/
int UnifracWeightedCommand::findIndex(float score, int index) {
try{
vector< map<float, float> > rCumul; //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c
map<float, float> validScores; //map contains scores from random
- bool abort;
+ bool abort, phylip, random;
string groups, itersString;
vector<string> Groups; //holds groups to be used
void printWSummaryFile();
void printWeightedFile();
+ void createPhylipFile();
//void removeValidScoresDuplicates();
int findIndex(float, int);
void calculateFreqsCumuls();
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