X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.cpp;h=d4e893b27edbda150ea961ddc3e6484d268a78c8;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=5da80d8179f4cb29f3c005490526ef6e8c5a93ab;hpb=485c02be0cdcd06ce08dd58d551a525b6a1b47c5;p=mothur.git diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp index 5da80d8..d4e893b 100644 --- a/heatmapcommand.cpp +++ b/heatmapcommand.cpp @@ -12,10 +12,79 @@ //********************************************************************************************************************** -HeatMapCommand::HeatMapCommand(){ +HeatMapCommand::HeatMapCommand(string option){ try { globaldata = GlobalData::getInstance(); - format = globaldata->getFormat(); + abort = false; + allLines = 1; + lines.clear(); + labels.clear(); + + //allow user to run help + if(option == "help") { help(); abort = true; } + + else { + //valid paramters for this command + string AlignArray[] = {"groups","line","label","sorted","scale"}; + 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; } + } + + //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; + } + + //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; } + 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 == "")) { + allLines = globaldata->allLines; + labels = globaldata->labels; + lines = globaldata->lines; + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } + + sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found") { sorted = "T"; } + + scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; } + + if (abort == false) { + heatmap = new HeatMap(sorted, scale); + format = globaldata->getFormat(); + } + } + } 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"; @@ -26,84 +95,188 @@ HeatMapCommand::HeatMapCommand(){ 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"; + + } + 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"; + 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(){ - delete input; + delete read; + delete heatmap; } //********************************************************************************************************************** int HeatMapCommand::execute(){ try { + + if (abort == true) { return 0; } + int count = 1; - + RAbundVector* lastRAbund; + vector lastLookup; + if (format == "sharedfile") { //you have groups - read = new ReadPhilFile(globaldata->inputFileName); + read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); input = globaldata->ginput; - order = input->getSharedOrderVector(); - }else if (format == "shared") { - //you are using a list and a groupfile - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); + lookup = input->getSharedRAbundVectors(); + lastLookup = lookup; }else if (format == "list") { //you are using just a list file and have only one group - read = new ReadPhilFile(globaldata->inputFileName); + read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); - - ordersingle = globaldata->gorder; - input = globaldata->ginput; + + rabund = globaldata->rabund; + lastRAbund = globaldata->rabund; + input = globaldata->ginput; } + //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") { - while(order != NULL){ - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + //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))) { + + if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ - cout << order->getLabel() << '\t' << count << endl; -//call heatmap class to make file + cout << lookup[0]->getLabel() << '\t' << count << endl; + 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); + + processedLabels.insert(lastLookup[0]->getLabel()); + userLabels.erase(lastLookup[0]->getLabel()); } - + + //prevent memory leak + if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } } + lastLookup = lookup; + //get next line to process - if (format == "sharedfile") { - order = input->getSharedOrderVector(); + lookup = input->getSharedRAbundVectors(); + count++; + } + + //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; + needToRun = true; }else { - //you are using a list and a groupfile - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - }else { - break; - } + cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl; } - count++; } + + //run last line if you need to + if (needToRun == true) { + cout << lastLookup[0]->getLabel() << '\t' << count << endl; + heatmap->getPic(lastLookup); + } + + for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + globaldata->Groups.clear(); }else{ - while(ordersingle != NULL){ - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + + if(allLines == 1 || lines.count(count) == 1 || labels.count(rabund->getLabel()) == 1){ - cout << order->getLabel() << '\t' << count << endl; -//call heatmap class to make file + cout << rabund->getLabel() << '\t' << count << endl; + heatmap->getPic(rabund); + + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); + userLines.erase(count); } - ordersingle = (input->getOrderVector()); + if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) { + + cout << lastRAbund->getLabel() << '\t' << count << endl; + heatmap->getPic(lastRAbund); + + processedLabels.insert(lastRAbund->getLabel()); + userLabels.erase(lastRAbund->getLabel()); + } + + if (count != 1) { delete lastRAbund; } + lastRAbund = rabund; + + rabund = input->getRAbundVector(); count++; } + + //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; + needToRun = true; + }else { + cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl; + } + } + + //run last line if you need to + if (needToRun == true) { + cout << lastRAbund->getLabel() << '\t' << count << endl; + heatmap->getPic(lastRAbund); + } + + delete lastRAbund; + } + delete input; return 0; } catch(exception& e) { @@ -118,3 +291,4 @@ int HeatMapCommand::execute(){ //********************************************************************************************************************** +