X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=heatmapcommand.cpp;h=19a320afa409e9e7be546b69c85f8c3c99e05fa6;hb=095a4c7aed0cf5ef79eaf28f0d79d3aa51c2811e;hp=413889ea1f1a1028420f4181cf17485266cb73b7;hpb=016a30dacbe75869aef5fdb58d2d1bf9eb8f9b33;p=mothur.git diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp index 413889e..19a320a 100644 --- a/heatmapcommand.cpp +++ b/heatmapcommand.cpp @@ -9,23 +9,68 @@ #include "heatmapcommand.h" - +//********************************************************************************************************************** +vector HeatMapCommand::getValidParameters(){ + try { + string Array[] = {"groups","label","sorted","scale","fontsize","numotu","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "HeatMapCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +HeatMapCommand::HeatMapCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["svg"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "HeatMapCommand", "HeatMapCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector HeatMapCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "HeatMapCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector HeatMapCommand::getRequiredFiles(){ + try { + string Array[] = {"list","sabund","rabund","shared","relabund","or"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "HeatMapCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** -HeatMapCommand::HeatMapCommand(string option){ +HeatMapCommand::HeatMapCommand(string option) { try { globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - lines.clear(); labels.clear(); //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command - string AlignArray[] = {"groups","line","label","sorted","scale"}; + string AlignArray[] = {"groups","label","sorted","scale","fontsize","numotu","outputdir","inputdir"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); OptionParser parser(option); @@ -38,100 +83,98 @@ HeatMapCommand::HeatMapCommand(string option){ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["svg"] = tempOutNames; + + //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->getSharedFile() == "")) { - cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap.bin command." << endl; abort = true; + 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... - line = validParameter.validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } - } - label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - //make sure user did not use both the line and label parameters - if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; } - //if the user has not specified any line or labels use the ones from read.otu - else if ((line == "") && (label == "")) { + //if the user has not specified any labels use the ones from read.otu + if (label == "") { allLines = globaldata->allLines; labels = globaldata->labels; - lines = globaldata->lines; } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } - sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found") { sorted = "T"; } + 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 (abort == false) { - heatmap = new HeatMap(sorted, scale); - format = globaldata->getFormat(); - } + 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"; - exit(1); - } } //********************************************************************************************************************** void HeatMapCommand::help(){ try { - cout << "The heatmap.bin command can only be executed after a successful read.otu command." << "\n"; - cout << "The heatmap.bin command parameters are groups, sorted, scale, line and label. No parameters are required, but you may not use line and label at the same time." << "\n"; - cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n"; - cout << "The sorted parameter allows you to choose to see the file with the shared otus at the top or the otus in the order they appear in your input file. " << "\n"; - cout << "The scale parameter allows you to choose the range of color your bin information will be displayed with." << "\n"; - cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n"; - cout << "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n"; - cout << "Example heatmap.bin(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n"; - cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n"; - cout << "The default value for sorted is T meaning you want the shared otus on top, you may change it to F meaning the exact representation of your input file." << "\n"; - cout << "The default value for scale is log10; your other options are log2 and linear." << "\n"; - cout << "The heatmap.bin command outputs a .svg file for each line or label you specify." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n"; + 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) { - cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "HeatMapCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** HeatMapCommand::~HeatMapCommand(){ - if (abort == false) { - delete read; - delete heatmap; - } } //********************************************************************************************************************** @@ -139,121 +182,150 @@ HeatMapCommand::~HeatMapCommand(){ int HeatMapCommand::execute(){ try { - if (abort == true) { return 0; } - - int count = 1; + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + 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(); lastLabel = lookup[0]->getLabel(); - }else if (format == "list") { + + }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; lastLabel = rabund->getLabel(); - input = globaldata->ginput; + }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 = labels; - set userLines = lines; - 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) && ((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()); } } outputTypes.clear(); + globaldata->Groups.clear(); + delete read; delete heatmap; return 0; + } - if(allLines == 1 || lines.count(count) == 1 || 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(); + string outputFileName = heatmap->getPic(lookup); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - cout << lastLabel << '\t' << count << endl; + 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(); - heatmap->getPic(lookup); + string outputFileName = heatmap->getPic(lookup); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } lastLabel = lookup[0]->getLabel(); //prevent memory leak - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + 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()); } } outputTypes.clear(); + 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; + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - cout << ". I will use " << lastLabel << "." << endl; + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLabel << "." << 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 << lastLabel << '\t' << count << endl; - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } lookup = input->getSharedRAbundVectors(lastLabel); - - heatmap->getPic(lookup); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + string outputFileName = heatmap->getPic(lookup); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } - - //reset groups parameter globaldata->Groups.clear(); - }else{ - - while((rabund != NULL) && ((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()); } } outputTypes.clear(); + delete rabund; delete read; delete heatmap; return 0; + } - if(allLines == 1 || lines.count(count) == 1 || 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(); + string outputFileName = heatmap->getPic(rabund); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); processedLabels.insert(rabund->getLabel()); userLabels.erase(rabund->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - - cout << lastLabel << '\t' << count << endl; + 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(); - heatmap->getPic(rabund); + string outputFileName = heatmap->getPic(rabund); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); processedLabels.insert(rabund->getLabel()); userLabels.erase(rabund->getLabel()); + + //restore real lastlabel to save below + rabund->setLabel(saveLabel); } @@ -261,45 +333,142 @@ int HeatMapCommand::execute(){ 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()); } } outputTypes.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; + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - cout << ". I will use " << lastLabel << "." << endl; + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLabel << "." << 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 << lastLabel << '\t' << count << endl; - delete rabund; + + if (rabund != NULL) { delete rabund; } rabund = input->getRAbundVector(lastLabel); + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); - heatmap->getPic(rabund); + string outputFileName = heatmap->getPic(rabund); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); 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()); } } outputTypes.clear(); + 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(); + string outputFileName = heatmap->getPic(lookupFloat); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + + 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(); + + string outputFileName = heatmap->getPic(lookupFloat); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + + 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()); } } outputTypes.clear(); + 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++) { + 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) { + 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(); + string outputFileName = heatmap->getPic(lookupFloat); + outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); + for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } + } + + //reset groups parameter + globaldata->Groups.clear(); + } + 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()); } } outputTypes.clear(); + 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); - } } //**********************************************************************************************************************