375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1350F9E433D008EF9B8 /* readotu.cpp */; };
375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1370F9E433D008EF9B8 /* readphylip.cpp */; };
377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 377326630FAF16E0007ABB8B /* concensuscommand.cpp */; };
+ 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */; };
+ 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */; };
378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */; };
378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */; };
378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */; };
375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = SOURCE_ROOT; };
377326630FAF16E0007ABB8B /* concensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = concensuscommand.cpp; sourceTree = SOURCE_ROOT; };
377326640FAF16E0007ABB8B /* concensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = concensuscommand.h; sourceTree = SOURCE_ROOT; };
+ 378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = "<group>"; };
+ 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = "<group>"; };
+ 378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = "<group>"; };
+ 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = "<group>"; };
378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = SOURCE_ROOT; };
378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = SOURCE_ROOT; };
378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = SOURCE_ROOT; };
373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */,
375873ED0F7D646F0040F377 /* heatmap.h */,
375873EE0F7D646F0040F377 /* heatmap.cpp */,
+ 378598720FDD4C1500EF9D03 /* heatmapsim.h */,
+ 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */,
37D927E60F21331F001D4494 /* inputdata.h */,
37D927E50F21331F001D4494 /* inputdata.cpp */,
7E412F420F8D213C00381DD0 /* libshuff.h */,
37D928A90F2133E5001D4494 /* commands */ = {
isa = PBXGroup;
children = (
- 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */,
- 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */,
- 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
- 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
37D927CD0F21331F001D4494 /* command.hpp */,
378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
375873F10F7D64800040F377 /* heatmapcommand.h */,
375873F00F7D64800040F377 /* heatmapcommand.cpp */,
+ 378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
+ 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */,
37D927E40F21331F001D4494 /* helpcommand.h */,
37D927E30F21331F001D4494 /* helpcommand.cpp */,
375873F40F7D648F0040F377 /* libshuffcommand.h */,
372E126F0F26365B0095CF7E /* readotucommand.cpp */,
37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
+ 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
+ 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
371B30B30FD7EE67000414CA /* screenseqscommand.h */,
371B30B20FD7EE67000414CA /* screenseqscommand.cpp */,
3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */,
37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
211C38370F961E1F00FEE541 /* treegroupscommand.h */,
211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
+ 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */,
+ 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */,
3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
374610760F40645300460C57 /* unifracweightedcommand.h */,
371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */,
7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */,
7E09C5360FDA7F65002ECAE5 /* trimseqscommand.cpp in Sources */,
+ 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */,
+ 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
#include "unifracweightedcommand.h"
#include "libshuffcommand.h"
#include "heatmapcommand.h"
+#include "heatmapsimcommand.h"
#include "filterseqscommand.h"
#include "mothur.h"
#include "venncommand.h"
else if(commandName == "get.sabund") { command = new GetSAbundCommand(); }
else if(commandName == "get.rabund") { command = new GetRAbundCommand(); }
else if(commandName == "libshuff") { command = new LibShuffCommand(); }
- else if(commandName == "heatmap") { command = new HeatMapCommand(); }
+ else if(commandName == "heatmap.bin") { command = new HeatMapCommand(); }
+ else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(); }
else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(); }
else if(commandName == "venn") { command = new VennCommand(); }
else if(commandName == "bin.seqs") { command = new BinSeqCommand(); }
}
}
- if ((commandName == "heatmap") || (commandName == "venn")) {
+ if ((commandName == "heatmap.bin") || (commandName == "venn") || (commandName == "heatmap.sim")) {
if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
- cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap or venn commands." << endl; return false;
+ cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap.bin, heatmap.sim or venn commands." << endl; return false;
}
}
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
+ if((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared") || (commandName == "heatmap.sim")) {
if((calc == "default") || (calc == "")) {
calc = "jclass-thetayc";
}
}
- string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.svg";
+ string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.bin.svg";
openOutputFile(filenamesvg, outsvg);
//svg image
}
}
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.svg";
+ string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.bin.svg";
openOutputFile(filenamesvg, outsvg);
//svg image
--- /dev/null
+/*
+ * heatmapsim.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 6/8/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "heatmapsim.h"
+#include "sharedjabund.h"
+#include "sharedsorabund.h"
+#include "sharedjclass.h"
+#include "sharedsorclass.h"
+#include "sharedjest.h"
+#include "sharedsorest.h"
+#include "sharedthetayc.h"
+#include "sharedthetan.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+
+//**********************************************************************************************************************
+HeatMapSim::HeatMapSim(){
+ try {
+ globaldata = GlobalData::getInstance();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void HeatMapSim::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> calcs) {
+ try {
+ EstOutput data;
+ vector<double> sims;
+
+ //make file for each calculator selected
+ for (int m = 0; m < calcs.size(); m++) {
+
+ string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + calcs[m]->getName() + ".heatmap.sim.svg";
+ openOutputFile(filenamesvg, outsvg);
+
+ //svg image
+ outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString((lookup.size() * 150) + 160) + " " + toString((lookup.size() * 150) + 160) + "\">\n";
+ outsvg << "<g>\n";
+
+ //white backround
+ outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((lookup.size() * 150) + 160) + "\" height=\"" + toString((lookup.size() * 150) + 160) + "\"/>";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 75) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
+
+ //column labels
+ for (int h = 0; h < lookup.size(); h++) {
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" y=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" x=\"50\">" + lookup[h]->getGroup() + "</text>\n";
+ }
+
+ sims.clear();
+ double biggest = -1;
+ float scaler;
+
+ //get sim for each comparison and save them so you can find the relative similairity
+ for(int i = 0; i < (lookup.size()-1); i++){
+ for(int j = (i+1); j < lookup.size(); j++){
+
+ vector<SharedRAbundVector*> subset;
+ subset.push_back(lookup[i]); subset.push_back(lookup[j]);
+
+ //get similairity between groups
+ data = calcs[m]->getValues(subset);
+ sims.push_back(data[0]);
+
+ //save biggest similairity to set relative sim
+ if (data[0] > biggest) { biggest = data[0]; }
+ }
+ }
+
+ //map biggest similairity found to red
+ scaler = 255.0 / biggest;
+
+ int count = 0;
+ //output similairites to file
+ for(int i = 0; i < (lookup.size()-1); i++){
+ for(int j = (i+1); j < lookup.size(); j++){
+
+ //find relative color
+ int color = scaler * sims[count];
+ //draw box
+ outsvg << "<rect fill=\"rgb(" + toString(color) + ",0,0)\" stroke=\"rgb(" + toString(color) + ",0,0)\" x=\"" + toString((i*150)+80) + "\" y=\"" + toString((j*150)+75) + "\" width=\"150\" height=\"150\"/>\n";
+ count++;
+ }
+ }
+
+ int y = ((lookup.size() * 150) + 120);
+ printLegend(y, biggest);
+
+ outsvg << "</g>\n</svg>\n";
+ outsvg.close();
+
+ }
+
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSim class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMapSim class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void HeatMapSim::printLegend(int y, float maxSim) {
+ try {
+
+ //output legend and color labels
+ //go through map and give each score a color value
+ string color;
+ int x = 10;
+
+ //prints legend
+ for (int i = 1; i < 255; i++) {
+ color = toHex(int((float)(i)));
+ outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
+ x += 1;
+ }
+
+ float scaler = maxSim / 5.0;
+
+ //prints legend labels
+ x = 10;
+ for (int i = 1; i<=5; i++) {
+ float label = scaler*i;
+ label = int(label * 1000 + 0.5);
+ label /= 1000.0;
+ string text = toString(label, 3);
+
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
+ x += 60;
+ }
+ }
+
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSim class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMapSim class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+//**********************************************************************************************************************
+
+
+
+
--- /dev/null
+#ifndef HEATMAPSIM_H
+#define HEATMAPSIM_H
+/*
+ * heatmapsim.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 6/8/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "sharedrabundvector.h"
+#include "datavector.hpp"
+#include "globaldata.hpp"
+#include "calculator.h"
+
+/***********************************************************************/
+
+class HeatMapSim {
+
+ public:
+ HeatMapSim();
+ ~HeatMapSim(){};
+
+ void getPic(vector<SharedRAbundVector*>, vector<Calculator*>);
+
+ private:
+ void printLegend(int, float);
+
+ GlobalData* globaldata;
+ string format, groupComb;
+ ofstream outsvg;
+
+};
+
+/***********************************************************************/
+
+#endif
+
--- /dev/null
+/*
+ * heatmapsimcommand.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 6/8/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "heatmapsimcommand.h"
+#include "sharedjabund.h"
+#include "sharedsorabund.h"
+#include "sharedjclass.h"
+#include "sharedsorclass.h"
+#include "sharedjest.h"
+#include "sharedsorest.h"
+#include "sharedthetayc.h"
+#include "sharedthetan.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+
+
+//**********************************************************************************************************************
+
+HeatMapSimCommand::HeatMapSimCommand(){
+ try {
+ globaldata = GlobalData::getInstance();
+ validCalculator = new ValidCalculators();
+ heatmap = new HeatMapSim();
+
+ int i;
+ for (i=0; i<globaldata->Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("heat", globaldata->Estimators[i]) == true) {
+ if (globaldata->Estimators[i] == "jabund") {
+ heatCalculators.push_back(new JAbund());
+ }else if (globaldata->Estimators[i] == "sorabund") {
+ heatCalculators.push_back(new SorAbund());
+ }else if (globaldata->Estimators[i] == "jclass") {
+ heatCalculators.push_back(new Jclass());
+ }else if (globaldata->Estimators[i] == "sorclass") {
+ heatCalculators.push_back(new SorClass());
+ }else if (globaldata->Estimators[i] == "jest") {
+ heatCalculators.push_back(new Jest());
+ }else if (globaldata->Estimators[i] == "sorest") {
+ heatCalculators.push_back(new SorEst());
+ }else if (globaldata->Estimators[i] == "thetayc") {
+ heatCalculators.push_back(new ThetaYC());
+ }else if (globaldata->Estimators[i] == "thetan") {
+ heatCalculators.push_back(new ThetaN());
+ }else if (globaldata->Estimators[i] == "morisitahorn") {
+ heatCalculators.push_back(new MorHorn());
+ }else if (globaldata->Estimators[i] == "braycurtis") {
+ heatCalculators.push_back(new BrayCurtis());
+ }
+ }
+ }
+
+ //reset calc for next command
+ globaldata->setCalc("");
+
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMapSimCommand class function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+HeatMapSimCommand::~HeatMapSimCommand(){
+ delete input;
+ delete read;
+ delete heatmap;
+}
+
+//**********************************************************************************************************************
+
+int HeatMapSimCommand::execute(){
+ try {
+ int count = 1;
+
+ //if the users entered no valid calculators don't execute command
+ if (heatCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
+
+ //you have groups
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
+ vector<SharedRAbundVector*> lastLookup = lookup;
+
+ if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;}
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+ set<int> userLines = globaldata->lines;
+
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lookup, heatCalculators);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
+ }
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastLookup, heatCalculators);
+
+ processedLabels.insert(lastLookup[0]->getLabel());
+ userLabels.erase(lastLookup[0]->getLabel());
+ }
+
+ //prevent memory leak
+ if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
+ lastLookup = lookup;
+
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
+ count++;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
+ cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lastLookup, heatCalculators);
+ }
+
+ for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+
+ //reset groups parameter
+ globaldata->Groups.clear();
+ globaldata->setGroups("");
+
+ return 0;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMapSimCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
--- /dev/null
+#ifndef HEATMAPSIMCOMMAND_H
+#define HEATMAPSIMCOMMAND_H
+
+/*
+ * heatmapsimcommand.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 6/8/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "readotu.h"
+#include "validcalculator.h"
+#include "heatmapsim.h"
+
+class GlobalData;
+
+class HeatMapSimCommand : public Command {
+
+public:
+ HeatMapSimCommand();
+ ~HeatMapSimCommand();
+ int execute();
+
+private:
+ GlobalData* globaldata;
+ ReadOTUFile* read;
+ InputData* input;
+ vector<SharedRAbundVector*> lookup;
+ vector<Calculator*> heatCalculators;
+ ValidCalculators* validCalculator;
+ HeatMapSim* heatmap;
+
+};
+
+#endif
+
cout << "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01." << "\n";
cout << "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual." << "\n";
cout << "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters)." << "\n" << "\n";
- }else if (globaldata->helpRequest == "heatmap") {
- cout << "The heatmap command can only be executed after a successful read.otu command." << "\n";
- cout << "The heatmap command parameters are groups, sorted, scale, line and label. No parameters are required, but you may not use line and label at the same time." << "\n";
+ }else if (globaldata->helpRequest == "heatmap.bin") {
+ cout << "The heatmap.bin command can only be executed after a successful read.otu command." << "\n";
+ cout << "The heatmap.bin command parameters are groups, sorted, scale, line and label. No parameters are required, but you may not use line and label at the same time." << "\n";
cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
cout << "The sorted parameter allows you to choose to see the file with the shared otus at the top or the otus in the order they appear in your input file. " << "\n";
cout << "The scale parameter allows you to choose the range of color your bin information will be displayed with." << "\n";
cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
- cout << "The heatmap command should be in the following format: heatmap(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
- cout << "Example heatmap(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n";
+ cout << "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, line=yourLines, label=yourLabels)." << "\n";
+ cout << "Example heatmap.bin(groups=A-B-C, line=1-3-5, sorted=F, scale=log10)." << "\n";
cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
cout << "The default value for sorted is T meaning you want the shared otus on top, you may change it to F meaning the exact representation of your input file." << "\n";
cout << "The default value for scale is log10; your other options are log2 and linear." << "\n";
- cout << "The heatmap command outputs a .svg file for each line or label you specify." << "\n";
+ cout << "The heatmap.bin command outputs a .svg file for each line or label you specify." << "\n";
cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
}else if (globaldata->helpRequest == "venn") {
cout << "The venn command can only be executed after a successful read.otu command." << "\n";
sabund = inputSabund->getSAbundVector();
globaldata->sabund = sabund; //saving to be used by summary command.
rabund = inputRabund->getRAbundVector();
- globaldata->rabund = rabund; //saving to be used by heatmap command.
+ globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
list = inputList->getListVector();
globaldata->gListVector = list;
}else if (globaldata->getFormat() == "shared") {
initialBoot();
initialDistance();
initialMatrix();
+ initialHeat();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
cout << endl;
return false; }
+ }else if (parameter == "heat") {
+ //is it valid
+ if ((heat.find(calculator)) != (heat.end())) {
+ return true;
+ }else {
+ cout << calculator << " is not a valid estimator for the heatmap.sim command and will be disregarded. Valid estimators are ";
+ for (it = heat.begin(); it != heat.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
}else if (parameter == "boot") {
//is it valid
if ((boot.find(calculator)) != (boot.end())) {
exit(1);
}
}
+/********************************************************************/
+void ValidCalculators::initialHeat() {
+ try {
+ heat["jabund"] = "jabund";
+ heat["sorabund"] = "sorabund";
+ heat["jclass"] = "jclass";
+ heat["sorclass"] = "sorclass";
+ heat["jest"] = "jest";
+ heat["sorest"] = "sorest";
+ heat["thetayc"] = "thetayc";
+ heat["thetan"] = "thetan";
+ heat["morisitahorn"] = "morisitahorn";
+ heat["braycurtis"] = "braycurtis";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialHeat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function initialHeat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
/********************************************************************/
void ValidCalculators::initialMatrix() {
try {
map<string, string> vennshared;
map<string, string> treegroup;
map<string, string> matrix;
+ map<string, string> heat;
map<string, string> boot;
map<string, string> distance;
map<string, string>::iterator it;
void initialMatrix();
void initialBoot();
void initialDistance();
+ void initialHeat();
};
#endif
commands["unifrac.unweighted"] = "unifrac.unweighted";
commands["libshuff"] = "libshuff";
commands["tree.shared"] = "tree.shared";
- commands["heatmap"] = "heatmap";
+ commands["heatmap.bin"] = "heatmap.bin";
+ commands["heatmap.sim"] = "heatmap.sim";
commands["venn"] = "venn";
commands["get.group"] = "get.group";
commands["get.label"] = "get.label";
commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
string heatmapArray[] = {"groups","line","label","sorted","scale"};
- commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+ commandParameters["heatmap.bin"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+
+ string heatmapSimArray[] = {"groups","line","label"};
+ commandParameters["heatmap.sim"] = addParameters(heatmapSimArray, sizeof(heatmapSimArray)/sizeof(string));
string filterseqsArray[] = {"fasta", "trump", "soft", "hard", "vertical"};
commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
projects / mothur.git / commitdiff