//**********************************************************************************************************************
vector<string> VennCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "String", "", "", "", "", "",false,false); parameters.push_back(pcalc);
- CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnseqs);
- CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppermute);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "String", "", "", "", "", "","",false,false); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnseqs);
+ CommandParameter psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
+ CommandParameter ppermute("permute", "Multiple", "1-2-3-4", "4", "", "", "","",false,false); parameters.push_back(ppermute); 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); }
string VennCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
+ helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, sharedotus, 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 venn diagram, you may only use a maximum of 4 groups.\n";
helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram 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 venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n";
helpString += "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n";
helpString += "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a shared file.\n";
helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
- helpString += "If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n";
+ helpString += "If you have more than 4 groups, you can use the permute parameter to set the number of groups you would like mothur to divide the samples into to draw the venn diagrams for all possible combos. Default=4.\n";
helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
+ helpString += "The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t.\n";
helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\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) {
exit(1);
}
}
+//**********************************************************************************************************************
+string VennCommand::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, "VennCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
VennCommand::VennCommand(){
//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();
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
- else { format = "sharedfile"; inputfile = sharedfile; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
if ((sharedfile == "") && (listfile == "")) {
//is there are current file available for any of these?
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
calc = validParameter.validFile(parameters, "calc", false);
}
}
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; } }
+ }
string temp;
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
- convert(temp, abund);
+ m->mothurConvert(temp, abund);
temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; }
nseqs = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
- perm = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "4"; }
+ m->mothurConvert(temp, perm);
+ if ((perm == 1) || (perm == 2) || (perm == 3) || (perm == 4)) { }
+ else { m->mothurOut("[ERROR]: Not a valid permute value. Valid values are 1, 2, 3, and 4."); m->mothurOutEndLine(); abort = true; }
+
+ temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; }
+ sharedOtus = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ m->mothurConvert(temp, fontsize);
}
}else if (Estimators[i] == "chao") {
vennCalculators.push_back(new Chao1());
}else if (Estimators[i] == "ace") {
- if(abund < 5)
- abund = 10;
+ if(abund < 5) { abund = 10; }
vennCalculators.push_back(new Ace(abund));
}
}
//if the users entered no valid calculators don't execute command
if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; }
- venn = new Venn(outputDir, nseqs, inputfile);
+ venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus);
input = new InputData(inputfile, format);
string lastLabel;
lookup = input->getSharedRAbundVectors();
lastLabel = lookup[0]->getLabel();
- if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
+ if ((lookup.size() > 4)) { combos = findCombinations(lookup.size()); }
}else if (format == "list") {
sabund = input->getSAbundVector();
lastLabel = sabund->getLabel();
if (m->control_pressed) {
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- m->Groups.clear(); delete venn; delete input;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ m->clearGroups(); delete venn; delete input;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if ((lookup.size() > 4) && (!perm)){
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
- for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
- }else if ((lookup.size() > 4) && (perm)) {
+ if (lookup.size() > 4) {
set< set<int> >::iterator it3;
set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+ for (it3 = combos.begin(); it3 != combos.end(); it3++) {
set<int> poss = *it3;
vector<SharedRAbundVector*> subset;
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if ((lookup.size() > 4) && (!perm)){
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
- for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
-
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
-
- }else if ((lookup.size() > 4) && (perm)) {
+ if (lookup.size() > 4) {
set< set<int> >::iterator it3;
set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+ for (it3 = combos.begin(); it3 != combos.end(); it3++) {
set<int> poss = *it3;
vector<SharedRAbundVector*> subset;
if (m->control_pressed) {
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- m->Groups.clear(); delete venn; delete input;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ m->clearGroups(); delete venn; delete input;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if ((lookup.size() > 4) && (!perm)){
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
- for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
-
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
-
- }else if ((lookup.size() > 4) && (perm)) {
+ if (lookup.size() > 4) {
set< set<int> >::iterator it3;
set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+ for (it3 = combos.begin(); it3 != combos.end(); it3++) {
set<int> poss = *it3;
vector<SharedRAbundVector*> subset;
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
if (m->control_pressed) {
- m->Groups.clear(); delete venn; delete input;
+ m->clearGroups(); delete venn; delete input;
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
if (m->control_pressed) {
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
delete sabund; delete venn; delete input;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
if (m->control_pressed) {
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
delete venn; delete input;
return 0;
}
if (m->control_pressed) {
delete venn; delete input;
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
}
}
}
//**********************************************************************************************************************
-//returns a vector of sets containing the 4 group combinations
+//returns a vector of sets containing the group combinations
set< set<int> > VennCommand::findCombinations(int lookupSize){
try {
set< set<int> > combos;
for (int i = 0; i < lookupSize; i++) { possibles.insert(i); }
getCombos(possibles, combos);
-
+
return combos;
}
}
}
//**********************************************************************************************************************
-//recusively finds combos of 4
+//recusively finds combos of length perm
int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
try {
- if (possibles.size() == 4) { //done
+ if (possibles.size() == perm) { //done
if (combos.count(possibles) == 0) { //no dups
combos.insert(possibles);
}
projects / mothur.git / blobdiff