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", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ 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;
string VennCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, fontsize 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 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";
return helpString;
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);
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();
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;
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;
}
}
//**********************************************************************************************************************
-//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