//**********************************************************************************************************************
-HeatMapCommand::HeatMapCommand(){
+HeatMapCommand::HeatMapCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- heatmap = new HeatMap();
- format = globaldata->getFormat();
+ abort = false;
+ allLines = 1;
+ labels.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"groups","label","sorted","scale","fontsize","numotu","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //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 = "";
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) {
+ m->mothurOut("You must read a list, rabund, sabund, or a list and a group, shared, or relabund file before you can use the heatmap.bin command."); m->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") { m->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;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, numOTU);
+
+ temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ convert(temp, fontSize);
+
+ sorted = validParameter.validFile(parameters, "sorted", false);
+ if (sorted == "not found") {
+ //if numOTU is used change default
+ if (numOTU != 0) { sorted = "topotu"; }
+ else { sorted = "shared"; }
+ }
+
+ scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; }
+
+ if ((sorted != "none") && (sorted != "shared") && (sorted != "topotu") && (sorted != "topgroup")) { m->mothurOut(sorted + " is not a valid sorting option. Sorted options are: none, shared, topotu, topgroup"); m->mothurOutEndLine(); abort=true; }
+ }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void HeatMapCommand::help(){
+ try {
+ m->mothurOut("The heatmap.bin command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("The heatmap.bin command parameters are groups, sorted, scale, numotu, fontsize and label. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
+ m->mothurOut("The sorted parameter allows you to order the otus displayed, default=shared, meaning display the shared otus first. Other options for sorted are none, meaning the exact representation of your otus, \n");
+ m->mothurOut("topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n");
+ m->mothurOut("The scale parameter allows you to choose the range of color your bin information will be displayed with.\n");
+ m->mothurOut("The numotu parameter allows you to display only the top N otus, by default all the otus are displayed. You could choose to look at the top 10, by setting numotu=10. The default for sorted is topotu when numotu is used.\n");
+ m->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 are also separated by dashes.\n");
+ m->mothurOut("The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n");
+ m->mothurOut("The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n");
+ m->mothurOut("Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
+ m->mothurOut("The default value for scale is log10; your other options are log2 and linear.\n");
+ m->mothurOut("The heatmap.bin command outputs a .svg file for each label you specify.\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, "HeatMapCommand", "help");
exit(1);
- }
+ }
}
+
//**********************************************************************************************************************
HeatMapCommand::~HeatMapCommand(){
- delete input;
- delete read;
- delete heatmap;
}
//**********************************************************************************************************************
int HeatMapCommand::execute(){
try {
- int count = 1;
- RAbundVector* lastRAbund;
- vector<SharedRAbundVector*> lastLookup;
+ if (abort == true) { return 0; }
+
+ heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir);
+ format = globaldata->getFormat();
+
+ string lastLabel;
+
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+ input = globaldata->ginput;
+
if (format == "sharedfile") {
//you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- lastLookup = lookup;
- }else if (format == "list") {
+ lastLabel = lookup[0]->getLabel();
+
+ }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
//you are using just a list file and have only one group
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
rabund = globaldata->rabund;
- lastRAbund = globaldata->rabund;
- input = globaldata->ginput;
+ lastLabel = rabund->getLabel();
+ }else if (format == "relabund") {
+ //you have groups
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ lastLabel = lookupFloat[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 = globaldata->labels;
- set<int> userLines = globaldata->lines;
+ set<string> userLabels = labels;
- if (format != "list") {
+ if (format == "sharedfile") {
//as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ globaldata->Groups.clear();
+ delete read; delete heatmap; return 0;
+ }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- cout << lookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lookup);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ outputNames.push_back(heatmap->getPic(lookup));
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup);
+ 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();
+
+ outputNames.push_back(heatmap->getPic(lookup));
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
+ lastLabel = lookup[0]->getLabel();
//prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
-
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
+
//get next line to process
lookup = input->getSharedRAbundVectors();
- count++;
}
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ globaldata->Groups.clear();
+ delete read; delete heatmap; 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++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ 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 {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup);
+ 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();
+ outputNames.push_back(heatmap->getPic(lookup));
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
-
//reset groups parameter
globaldata->Groups.clear();
- }else{
-
- while((rabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
+
+ while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ delete rabund; delete read; delete heatmap; return 0;
+ }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){
+ if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
- cout << rabund->getLabel() << '\t' << count << endl;
- heatmap->getPic(rabund);
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+ outputNames.push_back(heatmap->getPic(rabund));
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
-
- cout << lastRAbund->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastRAbund);
+ if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = rabund->getLabel();
+
+ delete rabund;
+ rabund = input->getRAbundVector(lastLabel);
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ outputNames.push_back(heatmap->getPic(rabund));
+
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
- processedLabels.insert(lastRAbund->getLabel());
- userLabels.erase(lastRAbund->getLabel());
+ //restore real lastlabel to save below
+ rabund->setLabel(saveLabel);
}
- if (count != 1) { delete lastRAbund; }
- lastRAbund = rabund;
-
+
+
+ lastLabel = rabund->getLabel();
+ delete rabund;
rabund = input->getRAbundVector();
- count++;
}
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ delete read; delete heatmap; 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();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+
+ if (rabund != NULL) { delete rabund; }
+ rabund = input->getRAbundVector(lastLabel);
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ outputNames.push_back(heatmap->getPic(rabund));
+ delete rabund; globaldata->rabund = NULL;
+ }
+
+ }else {
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ globaldata->Groups.clear();
+ delete read; delete heatmap; return 0;
+ }
+
+ if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
+
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+ outputNames.push_back(heatmap->getPic(lookupFloat));
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookupFloat[0]->getLabel();
+
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+
+ outputNames.push_back(heatmap->getPic(lookupFloat));
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookupFloat[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookupFloat[0]->getLabel();
+ //prevent memory leak
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; }
+
+ //get next line to process
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ }
+
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ globaldata->Groups.clear();
+ delete read; delete heatmap; 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++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastRAbund->getLabel()) != 1) {
- cout << ". I will use " << lastRAbund->getLabel() << "." << endl;
+ 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 {
- cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- cout << lastRAbund->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastRAbund);
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+ outputNames.push_back(heatmap->getPic(lookupFloat));
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
}
- delete lastRAbund;
+ //reset groups parameter
+ globaldata->Groups.clear();
}
- globaldata->setGroups("");
+ globaldata->rabund = NULL;
+ delete input; globaldata->ginput = NULL;
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { remove(outputNames[i].c_str()); } }
+ delete read; delete heatmap; return 0;
+ }
+
+ 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();
+
+ delete read;
+ delete heatmap;
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMapCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff