forked from mothur/mothur
-
Notifications
You must be signed in to change notification settings - Fork 1
/
amovacommand.cpp
468 lines (378 loc) · 17.3 KB
/
amovacommand.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
/*
* amovacommand.cpp
* mothur
*
* Created by westcott on 2/7/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "amovacommand.h"
#include "readphylipvector.h"
#include "groupmap.h"
#include "sharedutilities.h"
//**********************************************************************************************************************
vector<string> AmovaCommand::setParameters(){
try {
CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","amova",false,true,true); parameters.push_back(pdesign);
CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","amova",false,true,true); parameters.push_back(pphylip);
CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
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); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string AmovaCommand::getHelpString(){
try {
string helpString = "";
helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.";
helpString += "The amova command outputs a .amova file.";
helpString += "The amova command parameters are phylip, iters, sets and alpha. The phylip and design parameters are required, unless you have valid current files.";
helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required.";
helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.";
helpString += "The sets parameter allows you to specify which of the sets in your designfile you would like to analyze. The set names are separated by dashes. THe default is all sets in the designfile.\n";
helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000.";
helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design).";
helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string AmovaCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "amova") { pattern = "[filename],amova"; } //makes file like: amazon.align
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
AmovaCommand::AmovaCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["amova"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "AmovaCommand");
exit(1);
}
}
//**********************************************************************************************************************
AmovaCommand::AmovaCommand(string option) {
try {
abort = false; calledHelp = false;
//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();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
//check to make sure all parameters are valid for command
map<string,string>::iterator it;
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["amova"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("design");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["design"] = inputDir + it->second; }
}
it = parameters.find("phylip");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["phylip"] = inputDir + it->second; }
}
}
phylipFileName = validParameter.validFile(parameters, "phylip", true);
if (phylipFileName == "not open") { phylipFileName = ""; abort = true; }
else if (phylipFileName == "not found") {
//if there is a current phylip file, use it
phylipFileName = m->getPhylipFile();
if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
}else { m->setPhylipFile(phylipFileName); }
//check for required parameters
designFileName = validParameter.validFile(parameters, "design", true);
if (designFileName == "not open") { designFileName = ""; abort = true; }
else if (designFileName == "not found") {
//if there is a current design file, use it
designFileName = m->getDesignFile();
if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
}else { m->setDesignFile(designFileName); }
string temp = validParameter.validFile(parameters, "iters", false);
if (temp == "not found") { temp = "1000"; }
m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "alpha", false);
if (temp == "not found") { temp = "0.05"; }
m->mothurConvert(temp, experimentwiseAlpha);
string sets = validParameter.validFile(parameters, "sets", false);
if (sets == "not found") { sets = ""; }
else {
m->splitAtDash(sets, Sets);
}
}
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "AmovaCommand");
exit(1);
}
}
//**********************************************************************************************************************
int AmovaCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read design file
designMap = new GroupMap(designFileName);
designMap->readDesignMap();
if (outputDir == "") { outputDir = m->hasPath(phylipFileName); }
//read in distance matrix and square it
ReadPhylipVector readMatrix(phylipFileName);
vector<string> sampleNames = readMatrix.read(distanceMatrix);
if (Sets.size() != 0) { //user selected sets, so we want to remove the samples not in those sets
SharedUtil util;
vector<string> dGroups = designMap->getNamesOfGroups();
util.setGroups(Sets, dGroups);
for(int i=0;i<distanceMatrix.size();i++){
if (m->control_pressed) { delete designMap; return 0; }
string group = designMap->getGroup(sampleNames[i]);
if (group == "not found") {
m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
}else if (!m->inUsersGroups(group, Sets)){ //not in set we want remove it
//remove from all other rows
for(int j=0;j<distanceMatrix.size();j++){
distanceMatrix[j].erase(distanceMatrix[j].begin()+i);
}
distanceMatrix.erase(distanceMatrix.begin()+i);
sampleNames.erase(sampleNames.begin()+i);
i--;
}
}
}
for(int i=0;i<distanceMatrix.size();i++){
for(int j=0;j<i;j++){
distanceMatrix[i][j] *= distanceMatrix[i][j];
}
}
//link designMap to rows/columns in distance matrix
map<string, vector<int> > origGroupSampleMap;
for(int i=0;i<sampleNames.size();i++){
string group = designMap->getGroup(sampleNames[i]);
if (group == "not found") {
m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
}else { origGroupSampleMap[group].push_back(i); }
}
int numGroups = origGroupSampleMap.size();
if (m->control_pressed) { delete designMap; return 0; }
//create a new filename
ofstream AMOVAFile;
map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
string AMOVAFileName = getOutputFileName("amova", variables);
m->openOutputFile(AMOVAFileName, AMOVAFile);
outputNames.push_back(AMOVAFileName); outputTypes["amova"].push_back(AMOVAFileName);
double fullANOVAPValue = runAMOVA(AMOVAFile, origGroupSampleMap, experimentwiseAlpha);
if(fullANOVAPValue <= experimentwiseAlpha && numGroups > 2){
int numCombos = numGroups * (numGroups-1) / 2;
double pairwiseAlpha = experimentwiseAlpha / (double) numCombos;
map<string, vector<int> >::iterator itA;
map<string, vector<int> >::iterator itB;
for(itA=origGroupSampleMap.begin();itA!=origGroupSampleMap.end();itA++){
itB = itA;itB++;
for(itB;itB!=origGroupSampleMap.end();itB++){
map<string, vector<int> > pairwiseGroupSampleMap;
pairwiseGroupSampleMap[itA->first] = itA->second;
pairwiseGroupSampleMap[itB->first] = itB->second;
runAMOVA(AMOVAFile, pairwiseGroupSampleMap, pairwiseAlpha);
}
}
m->mothurOut("Experiment-wise error rate: " + toString(experimentwiseAlpha) + '\n');
m->mothurOut("Pair-wise error rate (Bonferroni): " + toString(pairwiseAlpha) + '\n');
}
else{
m->mothurOut("Experiment-wise error rate: " + toString(experimentwiseAlpha) + '\n');
}
m->mothurOut("If you have borderline P-values, you should try increasing the number of iterations\n");
AMOVAFile.close();
delete designMap;
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
double AmovaCommand::runAMOVA(ofstream& AMOVAFile, map<string, vector<int> > groupSampleMap, double alpha) {
try {
map<string, vector<int> >::iterator it;
int numGroups = groupSampleMap.size();
int totalNumSamples = 0;
for(it = groupSampleMap.begin();it!=groupSampleMap.end();it++){
totalNumSamples += it->second.size();
}
double ssTotalOrig = calcSSTotal(groupSampleMap);
double ssWithinOrig = calcSSWithin(groupSampleMap);
double ssAmongOrig = ssTotalOrig - ssWithinOrig;
double counter = 0;
for(int i=0;i<iters;i++){
map<string, vector<int> > randomizedGroup = getRandomizedGroups(groupSampleMap);
double ssWithinRand = calcSSWithin(randomizedGroup);
if(ssWithinRand <= ssWithinOrig){ counter++; }
}
double pValue = (double)counter / (double) iters;
string pString = "";
if(pValue < 1/(double)iters){ pString = '<' + toString(1/(double)iters); }
else { pString = toString(pValue); }
//print anova table
it = groupSampleMap.begin();
AMOVAFile << it->first;
m->mothurOut(it->first);
it++;
for(it;it!=groupSampleMap.end();it++){
AMOVAFile << '-' << it->first;
m->mothurOut('-' + it->first);
}
AMOVAFile << "\tAmong\tWithin\tTotal" << endl;
m->mothurOut("\tAmong\tWithin\tTotal\n");
AMOVAFile << "SS\t" << ssAmongOrig << '\t' << ssWithinOrig << '\t' << ssTotalOrig << endl;
m->mothurOut("SS\t" + toString(ssAmongOrig) + '\t' + toString(ssWithinOrig) + '\t' + toString(ssTotalOrig) + '\n');
int dfAmong = numGroups - 1; double MSAmong = ssAmongOrig / (double) dfAmong;
int dfWithin = totalNumSamples - numGroups; double MSWithin = ssWithinOrig / (double) dfWithin;
int dfTotal = totalNumSamples - 1; double Fs = MSAmong / MSWithin;
AMOVAFile << "df\t" << dfAmong << '\t' << dfWithin << '\t' << dfTotal << endl;
m->mothurOut("df\t" + toString(dfAmong) + '\t' + toString(dfWithin) + '\t' + toString(dfTotal) + '\n');
AMOVAFile << "MS\t" << MSAmong << '\t' << MSWithin << endl << endl;
m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n\n");
AMOVAFile << "Fs:\t" << Fs << endl;
m->mothurOut("Fs:\t" + toString(Fs) + '\n');
AMOVAFile << "p-value: " << pString;
m->mothurOut("p-value: " + pString);
if(pValue < alpha){
AMOVAFile << "*";
m->mothurOut("*");
}
AMOVAFile << endl << endl;
m->mothurOutEndLine();m->mothurOutEndLine();
return pValue;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "runAMOVA");
exit(1);
}
}
//**********************************************************************************************************************
map<string, vector<int> > AmovaCommand::getRandomizedGroups(map<string, vector<int> > origMapping){
try{
vector<int> sampleIndices;
vector<int> samplesPerGroup;
map<string, vector<int> >::iterator it;
for(it=origMapping.begin();it!=origMapping.end();it++){
vector<int> indices = it->second;
samplesPerGroup.push_back(indices.size());
sampleIndices.insert(sampleIndices.end(), indices.begin(), indices.end());
}
random_shuffle(sampleIndices.begin(), sampleIndices.end());
int index = 0;
map<string, vector<int> > randomizedGroups = origMapping;
for(it=randomizedGroups.begin();it!=randomizedGroups.end();it++){
for(int i=0;i<it->second.size();i++){
it->second[i] = sampleIndices[index++];
}
}
return randomizedGroups;
}
catch (exception& e) {
m->errorOut(e, "AmovaCommand", "getRandomizedGroups");
exit(1);
}
}
//**********************************************************************************************************************
double AmovaCommand::calcSSTotal(map<string, vector<int> >& groupSampleMap) {
try {
vector<int> indices;
map<string, vector<int> >::iterator it;
for(it=groupSampleMap.begin();it!=groupSampleMap.end();it++){
indices.insert(indices.end(), it->second.begin(), it->second.end());
}
sort(indices.begin(), indices.end());
int numIndices =indices.size();
double ssTotal = 0.0;
for(int i=1;i<numIndices;i++){
int row = indices[i];
for(int j=0;j<i;j++){
ssTotal += distanceMatrix[row][indices[j]];
}
}
ssTotal /= numIndices;
return ssTotal;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "calcSSTotal");
exit(1);
}
}
//**********************************************************************************************************************
double AmovaCommand::calcSSWithin(map<string, vector<int> >& groupSampleMap) {
try {
double ssWithin = 0.0;
map<string, vector<int> >::iterator it;
for(it=groupSampleMap.begin();it!=groupSampleMap.end();it++){
double withinGroup = 0;
vector<int> samples = it->second;
for(int i=0;i<samples.size();i++){
int row = samples[i];
for(int j=0;j<samples.size();j++){
int col = samples[j];
if(col < row){
withinGroup += distanceMatrix[row][col];
}
}
}
ssWithin += withinGroup / samples.size();
}
return ssWithin;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "calcSSWithin");
exit(1);
}
}
//**********************************************************************************************************************