void MantelCommand::help(){
try {
+ m->mothurOut("Sokal, R. R., & Rohlf, F. J. (1995). Biometry, 3rd edn. New York: Freeman.\n");
m->mothurOut("The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n");
- m->mothurOut("The mantel command parameters are phylip1, phylip2 and method. The phylip1 and phylip2 parameters are required. Matrices must be the same size and contain the same names.\n");
+ m->mothurOut("The mantel command parameters are phylip1, phylip2, iters and method. The phylip1 and phylip2 parameters are required. Matrices must be the same size and contain the same names.\n");
m->mothurOut("The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n");
+ m->mothurOut("The iters parameter allows you to set number of randomization for the P value. The default is 1000. \n");
m->mothurOut("The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n");
m->mothurOut("The mantel command outputs a .mantel file.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n");
//read phylip2
ReadPhylipVector readMatrix2(phylipfile2);
- vector<seqDist> temp; //seqDist - int, int, float
- vector<string> names2 = readMatrix2.read(temp);
+ vector< vector<double> > matrix2;
+ vector<string> names2 = readMatrix2.read(matrix2);
if (m->control_pressed) { return 0; }
- //fill matrix2 making sure to make sure the distances are in the same order as matrix1
- vector< vector<double> > matrix2;
+ //make sure matrix2 and matrix1 are in the same order
if (names1 == names2) { //then everything is in same order and same size
-
- //initialize space
- matrix2.resize(names2.size());
- for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
-
- //fill matrix2
- for (int i = 0; i < temp.size(); i++) {
- matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
- matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
- }
-
}else if (names1.size() != names2.size()) { //wrong size no need to order, abort
m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
m->control_pressed = true;
}else { //sizes are the same, but either the names are different or they are in different order
-
- //map location of name in names1 to location of name in names2
- map<string, int> names1Map;
- map<string, int>::iterator it;
- for (int i = 0; i < names1.size(); i++) { names1Map[names1[i]] = i; }
-
- map<string, int> names2Map;
- bool nameError = false;
- for (int i = 0; i < names2.size(); i++) {
-
- //if you find one name error stop looking
- if (!nameError) {
- it = names1Map.find(names2[i]);
- if (it == names1Map.end()) { nameError = true; }
- }
-
- //are names different
- names2Map[names2[i]] = i;
- }
-
- //initialize space
- matrix2.resize(names2.size());
- for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
-
- //fill matrix2
- //are we comparing apples to apples?
- if (nameError) {
- m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
-
- for (int i = 0; i < temp.size(); i++) {
- matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
- matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
- }
-
- }else { //no name error just different orders, so reorder
-
- for (int i = 0; i < temp.size(); i++) {
-
- //what's the location of this distance comparison in matrix1
- string matrix2NameI = names2[temp[i].seq1];
- string matrix2NameJ = names2[temp[i].seq2];
- int locationI = names1Map[matrix2NameI];
- int locationJ = names1Map[matrix2NameJ];
-
- matrix2[locationI][locationJ] = temp[i].dist;
- matrix2[locationJ][locationI] = temp[i].dist;
- }
- }
-
- }
-
- //frees up space
- temp.clear();
+ m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
+ }
if (m->control_pressed) { return 0; }