#include "heatmapcommand.h"
-
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","label","sorted","scale","fontsize","numotu","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+HeatMapCommand::HeatMapCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["svg"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"list","sabund","rabund","shared","relabund","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-HeatMapCommand::HeatMapCommand(string option){
+HeatMapCommand::HeatMapCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- lines.clear();
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string AlignArray[] = {"groups","line","label","sorted","scale"};
+ string AlignArray[] = {"groups","label","sorted","scale","fontsize","numotu","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; }
}
+ //initialize outputTypes
+ vector<string> 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
+ }
+
//make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "")) {
- 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."); mothurOutEndLine(); abort = true;
+ 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 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; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); 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);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
- sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found") { sorted = "T"; }
+ string temp = validParameter.validFile(parameters, "numotu", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, numOTU);
+
+ temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ convert(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 (abort == false) {
- heatmap = new HeatMap(sorted, scale);
- format = globaldata->getFormat();
- }
+ 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) {
- errorOut(e, "HeatMapCommand", "HeatMapCommand");
+ m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
exit(1);
}
}
void HeatMapCommand::help(){
try {
- mothurOut("The heatmap.bin command can only be executed after a successful read.otu command.\n");
- mothurOut("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");
- mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
- 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");
- mothurOut("The scale parameter allows you to choose the range of color your bin information will be displayed with.\n");
- mothurOut("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");
- mothurOut("The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels).\n");
- mothurOut("Example heatmap.bin(groups=A-B-C, line=1-3-5, sorted=F, scale=log10).\n");
- mothurOut("The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used.\n");
- 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");
- mothurOut("The default value for scale is log10; your other options are log2 and linear.\n");
- mothurOut("The heatmap.bin command outputs a .svg file for each line or label you specify.\n");
- mothurOut("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, 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) {
- errorOut(e, "HeatMapCommand", "help");
+ m->errorOut(e, "HeatMapCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
HeatMapCommand::~HeatMapCommand(){
- if (abort == false) {
- delete read;
- delete heatmap;
- }
}
//**********************************************************************************************************************
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();
- int count = 1;
string lastLabel;
-
+
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+ input = globaldata->ginput;
+
if (format == "sharedfile") {
//you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
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
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
rabund = globaldata->rabund;
lastLabel = rabund->getLabel();
- input = globaldata->ginput;
-
+ }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;
- set<int> userLines = lines;
- if ((format != "list") && (format != "rabund") && (format != "sabund")) {
+ 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) || (userLines.size() != 0))) {
+ 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;
+ }
- if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- heatmap->getPic(lookup);
+ 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());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- heatmap->getPic(lookup);
+ 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]; }
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
//get next line to process
lookup = input->getSharedRAbundVectors();
- count++;
}
+
+ 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;
+ }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ 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) {
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- heatmap->getPic(lookup);
+ 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
globaldata->Groups.clear();
- }else{
+ }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
- while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ 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;
+ }
- if(allLines == 1 || lines.count(count) == 1 || labels.count(rabund->getLabel()) == 1){
+ if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
- mothurOut(rabund->getLabel()); mothurOutEndLine();
- heatmap->getPic(rabund);
+ 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());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
-
+ if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = rabund->getLabel();
+
delete rabund;
rabund = input->getRAbundVector(lastLabel);
- mothurOut(rabund->getLabel()); mothurOutEndLine();
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- heatmap->getPic(rabund);
+ 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();
- count++;
}
+ 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;
+ }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ 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) {
if (rabund != NULL) { delete rabund; }
rabund = input->getRAbundVector(lastLabel);
- mothurOut(rabund->getLabel()); mothurOutEndLine();
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- heatmap->getPic(rabund);
+ string outputFileName = heatmap->getPic(rabund);
+ outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
delete rabund; globaldata->rabund = NULL;
}
+ }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") { remove(outputNames[i].c_str()); } } outputTypes.clear();
+ globaldata->Groups.clear();
+ delete read; 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") { remove(outputNames[i].c_str()); } } outputTypes.clear();
+ globaldata->Groups.clear();
+ delete read; 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
+ globaldata->Groups.clear();
+
}
globaldata->rabund = NULL;
delete input; globaldata->ginput = NULL;
+
+ 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;
+ }
+
+ 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;
}
catch(exception& e) {
- errorOut(e, "HeatMapCommand", "execute");
+ m->errorOut(e, "HeatMapCommand", "execute");
exit(1);
}
}
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