//**********************************************************************************************************************
-HeatMapCommand::HeatMapCommand(string option){
+HeatMapCommand::HeatMapCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
//allow user to run help
else {
//valid paramters for this command
- string AlignArray[] = {"groups","line","label","sorted","scale"};
+ string AlignArray[] = {"groups","label","sorted","scale","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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 = "";
+ outputDir += 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() == "")) {
+ m->mothurOut("You must read a list, rabund, sabund, or a list and a group, or a shared 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 {
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);
scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "log10"; }
if (abort == false) {
- heatmap = new HeatMap(sorted, scale);
+ heatmap = new HeatMap(sorted, scale, outputDir);
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";
+ 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 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 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");
+ m->mothurOut("The scale parameter allows you to choose the range of color your bin information will be displayed with.\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 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=F, 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 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");
+ 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);
- }
}
//**********************************************************************************************************************
try {
if (abort == true) { return 0; }
-
- int count = 1;
- RAbundVector* lastRAbund;
- vector<SharedRAbundVector*> lastLookup;
+
+ string lastLabel;
if (format == "sharedfile") {
//you have groups
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- lastLookup = lookup;
- }else if (format == "list") {
+ lastLabel = lookup[0]->getLabel();
+
+ }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;
- lastRAbund = globaldata->rabund;
- input = globaldata->ginput;
+ lastLabel = rabund->getLabel();
+ 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<string> processedLabels;
set<string> userLabels = labels;
- set<int> userLines = lines;
- if (format != "list") {
+ if ((format != "list") && (format != "rabund") && (format != "sabund")) {
//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(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();
+ outputNames.push_back(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);
+ if ((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();
+
+ outputNames.push_back(heatmap->getPic(lookup));
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
+ lastLabel = lookup[0]->getLabel();
//prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
-
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
//get next line to process
lookup = input->getSharedRAbundVectors();
- count++;
}
//output error messages about any remaining user labels
set<string>::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;
+ 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 {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << 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 << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup);
+ 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();
+ outputNames.push_back(heatmap->getPic(lookup));
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+
//reset groups parameter
globaldata->Groups.clear();
}else{
-
- while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
+ while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 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();
+ outputNames.push_back(heatmap->getPic(rabund));
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
-
- cout << lastRAbund->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastRAbund);
+ if ((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();
+
+ outputNames.push_back(heatmap->getPic(rabund));
+
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
- processedLabels.insert(lastRAbund->getLabel());
- userLabels.erase(lastRAbund->getLabel());
+ //restore real lastlabel to save below
+ rabund->setLabel(saveLabel);
}
- if (count != 1) { delete lastRAbund; }
- lastRAbund = rabund;
-
+
+
+ lastLabel = rabund->getLabel();
+ delete rabund;
rabund = input->getRAbundVector();
- count++;
}
//output error messages about any remaining user labels
set<string>::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;
+ 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 {
- cout << ". Please refer to " << lastRAbund->getLabel() << "." << 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 << lastRAbund->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastRAbund);
+
+ if (rabund != NULL) { delete rabund; }
+ rabund = input->getRAbundVector(lastLabel);
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ outputNames.push_back(heatmap->getPic(rabund));
+ delete rabund; globaldata->rabund = NULL;
}
- delete lastRAbund; globaldata->rabund = NULL;
-
}
+ globaldata->rabund = NULL;
delete input; globaldata->ginput = NULL;
+
+ 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) {
- 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);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff