metric = m->isTrue(temp);
label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); }
+ if (label == "not found") { label = ""; labels = globaldata->labels; if(labels.size() == 0) { m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } }
else { m->splitAtDash(label, labels); }
groups = validParameter.validFile(parameters, "groups", false);
//**********************************************************************************************************************
void PCACommand::help(){
try {
- m->mothurOut("The pca command can only be run after a successful read.otu command."); m->mothurOutEndLine();
+ m->mothurOut("The pca command can only be run after a successful read.otu command of a shared or relabund file."); m->mothurOutEndLine();
m->mothurOut("The pca command parameters are label, groups and metric. No parameters are required."); m->mothurOutEndLine();
m->mothurOut("The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multpile labels may be separated by dashes.\n");
m->mothurOut("The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n");