+++ /dev/null
-/*
- * heatmapcommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 3/25/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "heatmapcommand.h"
-
-//**********************************************************************************************************************
-vector<string> HeatMapCommand::setParameters(){
- try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",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<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string HeatMapCommand::getHelpString(){
- try {
- 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", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-HeatMapCommand::HeatMapCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["svg"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-HeatMapCommand::HeatMapCommand(string option) {
- try {
- abort = false; calledHelp = false;
- allLines = 1;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
- map<string,string>::iterator it;
-
- ValidParameters validParameter;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["svg"] = tempOutNames;
-
- //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; }
- }
- }
-
- //check for required parameters
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { listfile = ""; 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") { sabundfile = ""; 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") { rabundfile = ""; 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") { sharedfile = ""; 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") { relabundfile = ""; 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);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- m->splitAtDash(groups, Groups);
- m->setGroups(Groups);
- }
-
- string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; }
- m->mothurConvert(temp, numOTU);
-
- temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
- m->mothurConvert(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) {
- m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int HeatMapCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
-
- string lastLabel;
- input = new InputData(inputfile, format);
-
- if (format == "sharedfile") {
- //you have groups
- lookup = input->getSharedRAbundVectors();
- lastLabel = lookup[0]->getLabel();
-
- }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
- //you are using just a list file and have only one group
- rabund = input->getRAbundVector();
- 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<string> processedLabels;
- set<string> userLabels = labels;
-
- 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))) {
- 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") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
- m->clearGroups();
- delete input; delete heatmap; return 0;
- }
-
- if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
- 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());
- }
-
- 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();
-
- 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]; lookup[i] = NULL; }
-
- //get next line to process
- lookup = input->getSharedRAbundVectors();
- }
-
-
- if (m->control_pressed) {
- 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
- set<string>::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 < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
- lookup = input->getSharedRAbundVectors(lastLabel);
-
- 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
- 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") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
- delete rabund; delete input; delete heatmap; return 0;
- }
-
- if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
-
- 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());
- }
-
- 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();
-
- 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);
- }
-
-
-
- lastLabel = rabund->getLabel();
- delete rabund;
- rabund = input->getRAbundVector();
- }
-
- if (m->control_pressed) {
- 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
- set<string>::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();
-
- string outputFileName = heatmap->getPic(rabund);
- outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
- delete rabund;
- }
-
- }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") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
- m->clearGroups();
- delete input; 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") { m->mothurRemove(outputNames[i]); } } outputTypes.clear();
- m->clearGroups();
- delete input; delete heatmap; return 0;
- }
-
- //output error messages about any remaining user labels
- set<string>::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
- m->clearGroups();
-
- }
-
- delete input;
- delete heatmap;
-
- if (m->control_pressed) {
- 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();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-
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