X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapcommand.cpp;h=e07ae220eba02c86117feaa656e2b07015a4b94b;hp=dc4fec28a2c6edeb799dac61a90c5ecbff247a51;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281 diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp index dc4fec2..e07ae22 100644 --- a/heatmapcommand.cpp +++ b/heatmapcommand.cpp @@ -10,49 +10,83 @@ #include "heatmapcommand.h" //********************************************************************************************************************** -vector HeatMapCommand::getValidParameters(){ +vector HeatMapCommand::setParameters(){ try { - string Array[] = {"groups","label","sorted","scale","fontsize","numotu","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist); + CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund); + CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prelabund); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "","",false,false); parameters.push_back(pscale); + CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "","",false,false); parameters.push_back(psorted); + CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnumotu); + CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "HeatMapCommand", "getValidParameters"); + m->errorOut(e, "HeatMapCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -HeatMapCommand::HeatMapCommand(){ +string HeatMapCommand::getHelpString(){ try { - //initialize outputTypes - vector tempOutNames; - outputTypes["svg"] = tempOutNames; + string helpString = ""; + helpString += "The heatmap.bin command parameters are shared, relabund, list, rabund, sabund, groups, sorted, scale, numotu, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n"; + helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n"; + helpString += "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"; + helpString += "topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n"; + helpString += "The scale parameter allows you to choose the range of color your bin information will be displayed with.\n"; + helpString += "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"; + helpString += "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"; + helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n"; + helpString += "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n"; + helpString += "Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n"; + helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n"; + helpString += "The default value for scale is log10; your other options are log2 and linear.\n"; + helpString += "The heatmap.bin command outputs a .svg file for each label you specify.\n"; + helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "HeatMapCommand", "HeatMapCommand"); + m->errorOut(e, "HeatMapCommand", "getHelpString"); exit(1); } } + //********************************************************************************************************************** -vector HeatMapCommand::getRequiredParameters(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "HeatMapCommand", "getRequiredParameters"); - exit(1); - } +string HeatMapCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "svg") { pattern = "[filename],svg"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "HeatMapCommand", "getOutputPattern"); + exit(1); + } } + //********************************************************************************************************************** -vector HeatMapCommand::getRequiredFiles(){ +HeatMapCommand::HeatMapCommand(){ try { - string Array[] = {"list","sabund","rabund","shared","relabund","or"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["svg"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "HeatMapCommand", "getRequiredFiles"); + m->errorOut(e, "HeatMapCommand", "HeatMapCommand"); exit(1); } } @@ -60,26 +94,24 @@ vector HeatMapCommand::getRequiredFiles(){ HeatMapCommand::HeatMapCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - labels.clear(); //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = 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))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } @@ -87,17 +119,111 @@ HeatMapCommand::HeatMapCommand(string option) { 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 + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("shared"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["shared"] = inputDir + it->second; } + } + + it = parameters.find("rabund"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["rabund"] = inputDir + it->second; } + } + + it = parameters.find("sabund"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["sabund"] = inputDir + it->second; } + } + + it = parameters.find("list"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["list"] = inputDir + it->second; } + } + + it = parameters.find("relabund"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["relabund"] = inputDir + it->second; } + } } - //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 required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; inputfile = listfile; m->setListFile(listfile); } + + sabundfile = validParameter.validFile(parameters, "sabund", true); + if (sabundfile == "not open") { abort = true; } + else if (sabundfile == "not found") { sabundfile = ""; } + else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); } + + rabundfile = validParameter.validFile(parameters, "rabund", true); + if (rabundfile == "not open") { abort = true; } + else if (rabundfile == "not found") { rabundfile = ""; } + else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); } + + relabundfile = validParameter.validFile(parameters, "relabund", true); + if (relabundfile == "not open") { abort = true; } + else if (relabundfile == "not found") { relabundfile = ""; } + else { format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); } + + + if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) { + //is there are current file available for any of these? + //give priority to shared, then list, then rabund, then sabund + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + rabundfile = m->getRabundFile(); + if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); } + else { + sabundfile = m->getSabundFile(); + if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); } + else { + relabundfile = m->getRelAbundFile(); + if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine(); + 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 = m->hasPath(inputfile); } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... label = validParameter.validFile(parameters, "label", false); @@ -107,24 +233,19 @@ HeatMapCommand::HeatMapCommand(string option) { 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; + m->setGroups(Groups); } string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; } - convert(temp, numOTU); + m->mothurConvert(temp, numOTU); temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; } - convert(temp, fontSize); + m->mothurConvert(temp, fontSize); sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found") { @@ -144,54 +265,17 @@ HeatMapCommand::HeatMapCommand(string option) { exit(1); } } - -//********************************************************************************************************************** - -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(){ -} - //********************************************************************************************************************** int HeatMapCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } - heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir); - format = globaldata->getFormat(); + heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile); string lastLabel; - - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - input = globaldata->ginput; + input = new InputData(inputfile, format); if (format == "sharedfile") { //you have groups @@ -200,7 +284,7 @@ int HeatMapCommand::execute(){ }else if ((format == "list") || (format == "rabund") || (format == "sabund")) { //you are using just a list file and have only one group - rabund = globaldata->rabund; + rabund = input->getRAbundVector(); lastLabel = rabund->getLabel(); }else if (format == "relabund") { //you have groups @@ -218,9 +302,9 @@ int HeatMapCommand::execute(){ 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; + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + m->clearGroups(); + delete input; delete heatmap; return 0; } if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ @@ -261,9 +345,9 @@ int HeatMapCommand::execute(){ 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; + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + m->clearGroups(); + delete input; delete heatmap; return 0; } //output error messages about any remaining user labels @@ -291,14 +375,14 @@ int HeatMapCommand::execute(){ } //reset groups parameter - globaldata->Groups.clear(); + m->clearGroups(); }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; + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + delete rabund; delete input; delete heatmap; return 0; } if(allLines == 1 || labels.count(rabund->getLabel()) == 1){ @@ -336,8 +420,8 @@ int HeatMapCommand::execute(){ } 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; + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + delete input; delete heatmap; return 0; } //output error messages about any remaining user labels @@ -362,7 +446,7 @@ int HeatMapCommand::execute(){ string outputFileName = heatmap->getPic(rabund); outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName); - delete rabund; globaldata->rabund = NULL; + delete rabund; } }else { @@ -371,9 +455,9 @@ int HeatMapCommand::execute(){ 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; + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + m->clearGroups(); + delete input; delete heatmap; return 0; } if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){ @@ -413,9 +497,9 @@ int HeatMapCommand::execute(){ 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; + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); + m->clearGroups(); + delete input; delete heatmap; return 0; } //output error messages about any remaining user labels @@ -443,25 +527,21 @@ int HeatMapCommand::execute(){ } //reset groups parameter - globaldata->Groups.clear(); + m->clearGroups(); } - globaldata->rabund = NULL; - delete input; globaldata->ginput = NULL; + delete input; + delete heatmap; 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; + for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { m->mothurRemove(outputNames[i]); } } outputTypes.clear(); 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; }