X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.cpp;h=bb82702e9089b04f73571be314956567fb88f40e;hb=2bf3df7736ef2a17286d99394e211f51751d6829;hp=e99537dcd50f5987a8104be73fc1f3b36e74dc85;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp index e99537d..bb82702 100644 --- a/heatmapcommand.cpp +++ b/heatmapcommand.cpp @@ -12,180 +12,404 @@ //********************************************************************************************************************** -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 myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::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 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 processedLabels; - set userLabels = globaldata->labels; - set userLines = globaldata->lines; + set 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::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::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::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); - } } //**********************************************************************************************************************