else {
//valid paramters for this command
- string AlignArray[] = {"groups","label", "calc"};
+ string AlignArray[] = {"groups","label", "calc","phylip","column","name"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //make sure the user has already run the read.otu command
- if (globaldata->getSharedFile() == "") {
- mothurOut("You must read a list and a group, or a shared before you can use the heatmap.sim command."); mothurOutEndLine(); abort = true;
- }
-
- //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") { splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
+ format = "";
- //if the user has not specified any labels use the ones from read.otu
- if (label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
+ //required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { format = "phylip"; }
- calc = validParameter.validFile(parameters, "calc", false);
- if (calc == "not found") { calc = "jest-thetayc"; }
- else {
- if (calc == "default") { calc = "jest-thetayc"; }
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { format = "column"; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+
+ //error checking on files
+ if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { mothurOut("You must run the read.otu command or provide a distance file before running the heatmap.sim command."); mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
+
+ if (columnfile != "") {
+ if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
}
- splitAtDash(calc, Estimators);
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ if (format == "") { format = "shared"; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ if (format == "shared") {
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ 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;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jest-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jest-thetayc"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
}
if (abort == false) {
validCalculator = new ValidCalculators();
- heatmap = new HeatMapSim();
int i;
for (i=0; i<Estimators.size(); i++) {
void HeatMapSimCommand::help(){
try {
- mothurOut("The heatmap.sim command can only be executed after a successful read.otu command.\n");
- mothurOut("The heatmap.sim command parameters are groups, calc and label. No parameters are required.\n");
+ mothurOut("The heatmap.sim command can only be executed after a successful read.otu command, or by providing a distance file.\n");
+ mothurOut("The heatmap.sim command parameters are phylip, column, name, groups, calc and label. No parameters are required.\n");
+ mothurOut("There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n");
+ mothurOut("With the read.otu command you may use the groups, label and calc parameters. \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 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");
mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n");
validCalculator->printCalc("heat", cout);
mothurOut("The default value for calc is jclass-thetayc.\n");
mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
+ mothurOut("The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n");
+ mothurOut("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");
+ mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n");
+ mothurOut("Example heatmap.sim(phylip=amazonGroups.dist).\n");
mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
//**********************************************************************************************************************
-HeatMapSimCommand::~HeatMapSimCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete heatmap;
- delete validCalculator;
- }
-}
+HeatMapSimCommand::~HeatMapSimCommand(){}
//**********************************************************************************************************************
if (abort == true) { return 0; }
+ heatmap = new HeatMapSim();
+
+ if (format == "shared") {
+ runCommandShared();
+ }else if (format == "phylip") {
+ globaldata->inputFileName = phylipfile;
+ runCommandDist();
+ }else if (format == "column") {
+ globaldata->inputFileName = columnfile;
+ runCommandDist();
+ }
+
+ delete heatmap;
+ delete validCalculator;
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapSimCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int HeatMapSimCommand::runCommandShared() {
+ try {
//if the users entered no valid calculators don't execute command
if (heatCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
//reset groups parameter
globaldata->Groups.clear();
+ delete input; globaldata->ginput = NULL;
+ delete read;
+
return 0;
}
catch(exception& e) {
- errorOut(e, "HeatMapSimCommand", "execute");
+ errorOut(e, "HeatMapSimCommand", "runCommandShared");
exit(1);
}
}
+//**********************************************************************************************************************
+int HeatMapSimCommand::runCommandDist() {
+ try {
+
+ vector< vector<double> > matrix;
+ vector<string> names;
+ ifstream in;
+
+ //read distance file and create distance vector and names vector
+ if (format == "phylip") {
+ //read phylip file
+ openInputFile(phylipfile, in);
+
+ string name;
+ int numSeqs;
+ in >> numSeqs >> name;
+
+ //save name
+ names.push_back(name);
+
+ //resize the matrix and fill with zeros
+ matrix.resize(numSeqs);
+ for(int i = 0; i < numSeqs; i++) {
+ matrix[i].resize(numSeqs, 0.0);
+ }
+
+ //determine if matrix is square or lower triangle
+ //if it is square read the distances for the first sequence
+ char d;
+ bool square;
+ while((d=in.get()) != EOF){
+
+ //is d a number meaning its square
+ if(isalnum(d)){
+ square = true;
+ in.putback(d);
+
+ for(int i=0;i<numSeqs;i++){
+ in >> matrix[0][i];
+ }
+ break;
+ }
+
+ //is d a line return meaning its lower triangle
+ if(d == '\n'){
+ square = false;
+ break;
+ }
+ }
+
+ //read rest of matrix
+ if (square == true) {
+ for(int i=1;i<numSeqs;i++){
+ in >> name;
+ names.push_back(name);
+
+ for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
+ gobble(in);
+ }
+ }else {
+ double dist;
+ for(int i=1;i<numSeqs;i++){
+ in >> name;
+ names.push_back(name);
+
+ for(int j=0;j<i;j++){
+ in >> dist;
+ matrix[i][j] = dist; matrix[j][i] = dist;
+ }
+ gobble(in);
+ }
+ }
+ 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);
+ }
+
+ //read column file
+ string first, second;
+ double dist;
+ openInputFile(columnfile, in);
+
+ while (!in.eof()) {
+ in >> first >> second >> dist; gobble(in);
+
+ map<string, int>::iterator itA = nameMap->find(first);
+ map<string, int>::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;
+ }
+ in.close();
+
+ delete nameMap;
+ }
+
+ heatmap->getPic(matrix, names); //vector<vector<double>>, vector<string>
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "HeatMapSimCommand", "runCommandDist");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
+
+
+
+
+
+
projects / mothur.git / blobdiff