*/
#include "corraxescommand.h"
+#include "sharedutilities.h"
//********************************************************************************************************************
//sorts highes to lowest
metadatafile = validParameter.validFile(parameters, "metadata", true);
if (metadatafile == "not open") { abort = true; }
else if (metadatafile == "not found") { metadatafile = ""; }
+ else { inputFileName = metadatafile; }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; pickedGroups = false; }
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
- if ((relabundfile == "") && (sharedfile == "")) { m->mothurOut("You must provide either a shared or relabund file."); m->mothurOutEndLine(); abort = true; }
-
- if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true; }
+ if ((relabundfile == "") && (sharedfile == "") && (metadatafile == "")) { m->mothurOut("You must provide either a shared, relabund, or metadata file."); m->mothurOutEndLine(); abort = true; }
+ if (metadatafile != "") {
+ if ((relabundfile != "") || (sharedfile != "")) { m->mothurOut("You may only use one of the following : shared, relabund or metadata file."); m->mothurOutEndLine(); abort = true; }
+ }else {
+ if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may only use one of the following : shared, relabund or metadata file."); m->mothurOutEndLine(); abort = true; }
+ }
string temp;
temp = validParameter.validFile(parameters, "numaxes", false); if (temp == "not found"){ temp = "3"; }
convert(temp, numaxes);
void CorrAxesCommand::help(){
try {
-
+ m->mothurOut("The corr.axes command reads a shared, relabund or metadata file as well as an axes file and calculates the correlation coefficient.\n");
+ m->mothurOut("The corr.axes command parameters are shared, relabund, axes, metadata, groups, method, numaxes and label. The shared, relabund or metadata and axes parameters are required. If shared is given the relative abundance is calculated.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n");
+ m->mothurOut("The label parameter allows you to select what distance level you would like used, if none is given the first distance is used.\n");
+ m->mothurOut("The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n");
+ m->mothurOut("The numaxes parameter allows you to select the number of axes you would like to use. Default=3.\n");
+ m->mothurOut("The corr.axes command should be in the following format: corr.axes(axes=yourPcoaFile, shared=yourSharedFile, method=yourMethod).\n");
+ m->mothurOut("Example corr.axes(axes=genus.pool.thetayc.genus.lt.pcoa, shared=genus.pool.shared, method=kendall).\n");
+ m->mothurOut("The corr.axes command outputs a .corr.axes file.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
catch(exception& e) {
m->errorOut(e, "CorrAxesCommand", "help");
// use smart distancing to get right sharedRabund and convert to relabund if needed //
/************************************************************************************/
if (sharedfile != "") {
- getShared();
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
- if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
+ InputData* input = new InputData(sharedfile, "sharedfile");
+ getSharedFloat(input);
+ delete input;
- //fills lookupFloat with relative abundance values from lookup
- convertToRelabund();
+ if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+ if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
+
+ }else if (relabundfile != "") {
+ InputData* input = new InputData(relabundfile, "relabund");
+ getSharedFloat(input);
+ delete input;
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- }else {
- getSharedFloat();
if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
+ }else if (metadatafile != "") {
+ getMetadata(); //reads metadata file and store in lookupFloat, saves column headings in metadataLabels for later
+ if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+ if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading metadata file."); m->mothurOutEndLine(); return 0; }
+
if (pickedGroups) { eliminateZeroOTUS(lookupFloat); }
- }
+
+ }else { m->mothurOut("[ERROR]: no file given."); m->mothurOutEndLine(); return 0; }
if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
// calc the r values //
/************************************************************************************/
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + "corr.axes";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + ".corr.axes";
outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
//output headings
- out << "OTU\t";
- for (int i = 0; i < numaxes; i++) { out << "axis" << (i+1) << '\t'; }
- out << endl;
+ if (metadatafile == "") { out << "OTU"; }
+ else { out << "Feature"; }
+
+ for (int i = 0; i < numaxes; i++) { out << '\t' << "axis" << (i+1); }
+ out << "\tlength" << endl;
if (method == "pearson") { calcPearson(axes, out); }
else if (method == "spearman") { calcSpearman(axes, out); }
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
- out << i+1 << '\t';
-
+ if (metadatafile == "") { out << i+1; }
+ else { out << metadataLabels[i]; }
+
//find the averages this otu - Y
float sumOtu = 0.0;
for (int j = 0; j < lookupFloat.size(); j++) {
}
float Ybar = sumOtu / (float) lookupFloat.size();
+ vector<float> rValues(averageAxes.size());
+
//find r value for each axis
for (int k = 0; k < averageAxes.size(); k++) {
double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
r = numerator / denom;
-
- out << r << '\t';
+ rValues[k] = r;
+ out << '\t' << r;
}
- out << endl;
+ double sum = 0;
+ for(int k=0;k<rValues.size();k++){
+ sum += rValues[k] * rValues[k];
+ }
+ out << '\t' << sqrt(sum) << endl;
}
return 0;
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
- out << i+1 << '\t';
+ if (metadatafile == "") { out << i+1; }
+ else { out << metadataLabels[i]; }
//find the ranks of this otu - Y
vector<spearmanRank> otuScores;
}
}
+ vector<double> pValues(numaxes);
//calc spearman ranks for each axis for this otu
for (int j = 0; j < numaxes; j++) {
int n = lookupFloat.size();
double p = 1.0 - ((6 * di) / (float) (n * ((n*n) - 1)));
- out << p << '\t';
+ out << '\t' << p;
+ pValues[j] = p;
+
}
-
-
- out << endl;
+
+ double sum = 0;
+ for(int k=0;k<numaxes;k++){
+ sum += pValues[k] * pValues[k];
+ }
+ out << '\t' << sqrt(sum) << endl;
}
return 0;
//sort each axis
for (int i = 0; i < numaxes; i++) { sort(scores[i].begin(), scores[i].end(), compareSpearman); }
- //find ranks of xi in each axis
- map<string, vector<float> > rankAxes;
+ //convert scores to ranks of xi in each axis
for (int i = 0; i < numaxes; i++) {
- vector<spearmanRank> ties;
+ vector<spearmanRank*> ties;
int rankTotal = 0;
for (int j = 0; j < scores[i].size(); j++) {
rankTotal += j;
- ties.push_back(scores[i][j]);
+ ties.push_back(&(scores[i][j]));
if (j != scores.size()-1) { // you are not the last so you can look ahead
if (scores[i][j].score != scores[i][j+1].score) { // you are done with ties, rank them and continue
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
- rankAxes[ties[k].name].push_back(thisrank);
+ (*ties[k]).score = thisrank;
}
ties.clear();
rankTotal = 0;
}else { // you are the last one
for (int k = 0; k < ties.size(); k++) {
float thisrank = rankTotal / (float) ties.size();
- rankAxes[ties[k].name].push_back(thisrank);
+ (*ties[k]).score = thisrank;
}
}
}
}
-
-
//for each otu
for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
-
- out << i+1 << '\t';
+
+ if (metadatafile == "") { out << i+1; }
+ else { out << metadataLabels[i]; }
//find the ranks of this otu - Y
vector<spearmanRank> otuScores;
spearmanRank member(lookupFloat[j]->getGroup(), lookupFloat[j]->getAbundance(i));
otuScores.push_back(member);
}
-
+
sort(otuScores.begin(), otuScores.end(), compareSpearman);
map<string, float> rankOtus;
}
}
}
+ vector<double> pValues(numaxes);
- //calc kendall coeffient for each axis for this otu
+ //calc spearman ranks for each axis for this otu
for (int j = 0; j < numaxes; j++) {
+
+ int P = 0;
+ //assemble otus ranks in same order as axis ranks
+ vector<spearmanRank> otus;
+ for (int l = 0; l < scores[j].size(); l++) {
+ spearmanRank member(scores[j][l].name, rankOtus[scores[j][l].name]);
+ otus.push_back(member);
+ }
- int numConcordant = 0;
- int numDiscordant = 0;
-
- for (int f = 0; f < j; f++) {
+ for (int l = 0; l < scores[j].size(); l++) {
- for (int k = 0; k < lookupFloat.size(); k++) {
-
- float xi = rankAxes[lookupFloat[k]->getGroup()][j];
- float yi = rankOtus[lookupFloat[k]->getGroup()];
-
- for (int h = 0; h < k; h++) {
-
- float xj = rankAxes[lookupFloat[k]->getGroup()][f];
- float yj = rankOtus[lookupFloat[h]->getGroup()];
-
- if ( ((xi > xj) && (yi < yj)) || ((xi < xj) && (yi > yj)) ){ numDiscordant++; }
- if ( ((xi > xj) && (yi > yj)) || ((xi < xj) && (yi < yj)) ){ numConcordant++; }
- }
+ int numWithHigherRank = 0;
+ float thisrank = otus[l].score;
+
+ for (int u = l; u < scores[j].size(); u++) {
+ if (otus[u].score > thisrank) { numWithHigherRank++; }
}
+
+ P += numWithHigherRank;
}
int n = lookupFloat.size();
- double p = (numConcordant - numDiscordant) / (float) (0.5 * n * (n - 1));
-
- out << p << '\t';
- }
-
-
- out << endl;
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "CorrAxesCommand", "calcKendall");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int CorrAxesCommand::getShared(){
- try {
- InputData* input = new InputData(sharedfile, "sharedfile");
- lookup = input->getSharedRAbundVectors();
- string lastLabel = lookup[0]->getLabel();
-
- if (label == "") { label = lastLabel; delete input; return 0; }
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> labels; labels.insert(label);
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && (userLabels.size() != 0)) {
- if (m->control_pressed) { delete input; return 0; }
-
- if(labels.count(lookup[0]->getLabel()) == 1){
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
- break;
- }
-
- 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);
+ double p = ( (4 * P) / (float) (n * (n - 1)) ) - 1.0;
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- break;
+ out << '\t' << p;
+ pValues[j] = p;
+
}
- lastLabel = lookup[0]->getLabel();
-
- //get next line to process
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input->getSharedRAbundVectors();
- }
-
-
- if (m->control_pressed) { delete input; return 0; }
-
- //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();
+ double sum = 0;
+ for(int k=0;k<numaxes;k++){
+ sum += pValues[k] * pValues[k];
}
+ out << '\t' << sqrt(sum) << endl;
}
- //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);
- }
-
- delete input;
return 0;
}
catch(exception& e) {
- m->errorOut(e, "CorrAxesCommand", "getShared");
+ m->errorOut(e, "CorrAxesCommand", "calcKendall");
exit(1);
}
}
//**********************************************************************************************************************
-int CorrAxesCommand::getSharedFloat(){
+int CorrAxesCommand::getSharedFloat(InputData* input){
try {
- InputData* input = new InputData(relabundfile, "relabund");
lookupFloat = input->getSharedRAbundFloatVectors();
string lastLabel = lookupFloat[0]->getLabel();
- if (label == "") { label = lastLabel; delete input; return 0; }
+ if (label == "") { label = lastLabel; return 0; }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> labels; labels.insert(label);
//as long as you are not at the end of the file or done wih the lines you want
while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
- if (m->control_pressed) { delete input; return 0; }
+ if (m->control_pressed) { return 0; }
if(labels.count(lookupFloat[0]->getLabel()) == 1){
processedLabels.insert(lookupFloat[0]->getLabel());
}
- if (m->control_pressed) { delete input; return 0; }
+ if (m->control_pressed) { return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
}
- delete input;
return 0;
}
catch(exception& e) {
exit(1);
}
}
-/*****************************************************************/
-int CorrAxesCommand::convertToRelabund(){
- try {
-
- vector<SharedRAbundFloatVector*> newLookup;
- for (int i = 0; i < lookup.size(); i++) {
- SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
- temp->setLabel(lookup[i]->getLabel());
- temp->setGroup(lookup[i]->getGroup());
- newLookup.push_back(temp);
- }
-
- for (int i = 0; i < lookup.size(); i++) {
-
- for (int j = 0; j < lookup[i]->getNumBins(); j++) {
-
- if (m->control_pressed) { return 0; }
-
- int abund = lookup[i]->getAbundance(j);
-
- float relabund = abund / (float) lookup[i]->getNumSeqs();
-
- newLookup[i]->push_back(relabund, lookup[i]->getGroup());
- }
- }
-
- if (pickedGroups) { eliminateZeroOTUS(newLookup); }
-
- lookupFloat = newLookup;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "CorrAxesCommand", "convertToRelabund");
- exit(1);
- }
-}
//**********************************************************************************************************************
int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
try {
}else { done = true; }
}
+ if (numaxes > count) { m->mothurOut("You requested " + toString(numaxes) + " axes, but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine(); numaxes = count; }
+
while (!in.eof()) {
if (m->control_pressed) { in.close(); return axes; }
return axes;
}
catch(exception& e) {
- m->errorOut(e, "CorrAxesCommand", "convertToRelabund");
+ m->errorOut(e, "CorrAxesCommand", "readAxes");
+ exit(1);
+ }
+}
+/*****************************************************************/
+int CorrAxesCommand::getMetadata(){
+ try {
+ vector<string> groupNames;
+
+ ifstream in;
+ m->openInputFile(axesfile, in);
+
+ string headerLine = m->getline(in); m->gobble(in);
+ istringstream iss (headerLine,istringstream::in);
+
+ //read the first label, because it refers to the groups
+ string columnLabel;
+ iss >> columnLabel; m->gobble(iss);
+
+ //save names of columns you are reading
+ while (!iss.eof()) {
+ iss >> columnLabel; m->gobble(iss);
+ metadataLabels.push_back(columnLabel);
+ }
+ int count = metadataLabels.size();
+
+ //read rest of file
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ string group = "";
+ in >> group; m->gobble(in);
+ groupNames.push_back(group);
+
+ SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
+ tempLookup->setGroup(group);
+ tempLookup->setLabel("1");
+
+ for (int i = 0; i < count; i++) {
+ float temp = 0.0;
+ in >> temp;
+
+ tempLookup->push_back(temp, group);
+ }
+
+ lookupFloat.push_back(tempLookup);
+
+ m->gobble(in);
+ }
+ in.close();
+
+ //remove any groups the user does not want, and set globaldata->groups with only valid groups
+ SharedUtil* util;
+ util = new SharedUtil();
+
+ util->setGroups(globaldata->Groups, groupNames);
+
+ for (int i = 0; i < lookupFloat.size(); i++) {
+ //if this sharedrabund is not from a group the user wants then delete it.
+ if (util->isValidGroup(lookupFloat[i]->getGroup(), globaldata->Groups) == false) {
+ delete lookupFloat[i]; lookupFloat[i] = NULL;
+ lookupFloat.erase(lookupFloat.begin()+i);
+ i--;
+ }
+ }
+
+ delete util;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "getMetadata");
exit(1);
}
}
projects / mothur.git / blobdiff