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 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 poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
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, 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";
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"; }
+ temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
perm = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ m->mothurConvert(temp, fontsize);
}
//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);
input = new InputData(inputfile, format);
string lastLabel;