X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapsimcommand.cpp;h=98739b68291fd42d83d1190a46313886126f02bf;hp=5a84391813b768b33ed55f3dbc50d612f01111f2;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6 diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp index 5a84391..98739b6 100644 --- a/heatmapsimcommand.cpp +++ b/heatmapsimcommand.cpp @@ -23,15 +23,17 @@ //********************************************************************************************************************** vector HeatMapSimCommand::setParameters(){ try { - CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared); - CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname); - CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","svg",false,false,true); parameters.push_back(pshared); + CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","svg",false,false); parameters.push_back(pphylip); + CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pcount); + CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName","svg",false,false); parameters.push_back(pcolumn); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "","",true,false); parameters.push_back(pcalc); + CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize); + 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); } @@ -46,22 +48,23 @@ vector HeatMapSimCommand::setParameters(){ string HeatMapSimCommand::getHelpString(){ try { string helpString = ""; - helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc and label. shared or phylip or column and name are required unless valid current files exist.\n"; - helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n"; - helpString += "With the read.otu command you may use the groups, label and calc parameters. \n"; + ValidCalculators validCalculator; + helpString += "The heatmap.sim command parameters are shared, phylip, column, name, count, groups, calc, fontsize and label. shared or phylip or column and name are required unless valid current files exist.\n"; + helpString += "There are two ways to use the heatmap.sim command. The first is with a shared file, and you may use the groups, label and calc parameter. \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 group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is 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.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n"; helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\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 += validCalculator->printCalc("heat"); + helpString += validCalculator.printCalc("heat"); helpString += "The default value for calc is jclass-thetayc.\n"; helpString += "The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n"; helpString += "The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n"; helpString += "Using the command this way, the phylip or column parameter are required, and only one may be used. If you use a column file the name filename is required. \n"; helpString += "The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n"; helpString += "Example heatmap.sim(phylip=amazonGroups.dist).\n"; - helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"; + helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n"; return helpString; } catch(exception& e) { @@ -70,6 +73,21 @@ string HeatMapSimCommand::getHelpString(){ } } //********************************************************************************************************************** +string HeatMapSimCommand::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); + } +} +//********************************************************************************************************************** HeatMapSimCommand::HeatMapSimCommand(){ try { abort = true; calledHelp = true; @@ -90,7 +108,8 @@ HeatMapSimCommand::HeatMapSimCommand(string option) { allLines = 1; //allow user to run help - if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -111,9 +130,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option) { outputTypes["svg"] = tempOutNames; format = ""; - //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 = ""; } - + //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 = ""; } @@ -150,28 +167,43 @@ HeatMapSimCommand::HeatMapSimCommand(string option) { //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("count"); + //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["count"] = inputDir + it->second; } + } } //required parameters phylipfile = validParameter.validFile(parameters, "phylip", true); if (phylipfile == "not open") { abort = true; } else if (phylipfile == "not found") { phylipfile = ""; } - else { format = "phylip"; inputfile = phylipfile; if (outputDir == "") { outputDir += m->hasPath(phylipfile); } } + else { format = "phylip"; inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); } } columnfile = validParameter.validFile(parameters, "column", true); if (columnfile == "not open") { abort = true; } else if (columnfile == "not found") { columnfile = ""; } - else { format = "column"; inputfile = columnfile; if (outputDir == "") { outputDir += m->hasPath(columnfile); } } + else { format = "column"; inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } } sharedfile = validParameter.validFile(parameters, "shared", true); if (sharedfile == "not open") { abort = true; } else if (sharedfile == "not found") { sharedfile = ""; } - else { format = "shared"; inputfile = sharedfile; if (outputDir == "") { outputDir += m->hasPath(sharedfile); } } + else { format = "shared"; inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } } namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not open") { abort = true; } else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { abort = true; countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; } //error checking on files if ((sharedfile == "") && ((phylipfile == "") && (columnfile == ""))) { @@ -199,12 +231,20 @@ HeatMapSimCommand::HeatMapSimCommand(string option) { namefile = m->getNameFile(); if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); } else { - m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); - abort = true; + countfile = m->getCountTableFile(); + if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You need to provide a name or count file if you are going to use the column format."); 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... @@ -221,21 +261,28 @@ HeatMapSimCommand::HeatMapSimCommand(string option) { if (calc == "default") { calc = "jest-thetayc"; } } m->splitAtDash(calc, Estimators); + if (m->inUsersGroups("citation", Estimators)) { + ValidCalculators validCalc; validCalc.printCitations(Estimators); + //remove citation from list of calcs + for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } } + } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); } + string temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; } + m->mothurConvert(temp, fontsize); if (abort == false) { - validCalculator = new ValidCalculators(); + ValidCalculators validCalculator; int i; for (i=0; iisValidCalculator("heat", Estimators[i]) == true) { + if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) { if (Estimators[i] == "jabund") { heatCalculators.push_back(new JAbund()); }else if (Estimators[i] == "sorabund") { @@ -278,16 +325,15 @@ int HeatMapSimCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } - heatmap = new HeatMapSim(outputDir, inputfile); + heatmap = new HeatMapSim(outputDir, inputfile, fontsize); if (format == "shared") { runCommandShared(); }else{ runCommandDist(); } delete heatmap; - delete validCalculator; - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -318,12 +364,12 @@ int HeatMapSimCommand::runCommandShared() { set processedLabels; set userLabels = labels; - if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; } + if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; } //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))) { - if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; } + if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; } if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ @@ -363,7 +409,7 @@ int HeatMapSimCommand::runCommandShared() { } - if (m->control_pressed) { delete input; m->Groups.clear(); return 0; } + if (m->control_pressed) { delete input; m->clearGroups(); return 0; } //output error messages about any remaining user labels set::iterator it; @@ -378,7 +424,7 @@ int HeatMapSimCommand::runCommandShared() { } } - if (m->control_pressed) { delete input; m->Groups.clear(); return 0; } + if (m->control_pressed) { delete input; m->clearGroups(); return 0; } //run last label if you need to if (needToRun == true) { @@ -392,10 +438,10 @@ int HeatMapSimCommand::runCommandShared() { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } - if (m->control_pressed) { delete input; m->Groups.clear(); return 0; } + if (m->control_pressed) { delete input; m->clearGroups(); return 0; } //reset groups parameter - m->Groups.clear(); + m->clearGroups(); delete input; @@ -485,20 +531,28 @@ int HeatMapSimCommand::runCommandDist() { in.close(); }else { //read names file - NameAssignment* nameMap = new NameAssignment(namefile); - nameMap->readMap(); - - //put names in order in vector - for (int i = 0; i < nameMap->size(); i++) { - names.push_back(nameMap->get(i)); - } - - //resize matrix - matrix.resize(nameMap->size()); - for (int i = 0; i < nameMap->size(); i++) { - matrix[i].resize(nameMap->size(), 0.0); - } - + NameAssignment* nameMap; + CountTable ct; + if (namefile != "") { + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + + //put names in order in vector + for (int i = 0; i < nameMap->size(); i++) { + names.push_back(nameMap->get(i)); + } + }else if (countfile != "") { + nameMap = NULL; + ct.readTable(countfile); + names = ct.getNamesOfSeqs(); + } + + //resize matrix + matrix.resize(names.size()); + for (int i = 0; i < names.size(); i++) { + matrix[i].resize(names.size(), 0.0); + } + //read column file string first, second; double dist; @@ -509,19 +563,26 @@ int HeatMapSimCommand::runCommandDist() { if (m->control_pressed) { return 0; } - map::iterator itA = nameMap->find(first); - map::iterator itB = nameMap->find(second); - - if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << first << "' was not found in the names file, please correct\n"; exit(1); } - if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << second << "' was not found in the names file, please correct\n"; exit(1); } - - //save distance - matrix[itA->second][itB->second] = dist; - matrix[itB->second][itA->second] = dist; + if (namefile != "") { + map::iterator itA = nameMap->find(first); + map::iterator itB = nameMap->find(second); + + if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); } + if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); } + + //save distance + matrix[itA->second][itB->second] = dist; + matrix[itB->second][itA->second] = dist; + }else if (countfile != "") { + int itA = ct.get(first); + int itB = ct.get(second); + matrix[itA][itB] = dist; + matrix[itB][itA] = dist; + } } in.close(); - delete nameMap; + if (namefile != "") { delete nameMap; } }