+++ /dev/null
-/*
- * heatmap.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 3/25/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "heatmap.h"
-
-//**********************************************************************************************************************
-HeatMap::HeatMap(string sort, string scale, int num, int fsize, string dir, string i){
- try {
- m = MothurOut::getInstance();
-// format = globaldata->getFormat();
- sorted = sort;
- scaler = scale;
- outputDir = dir;
- numOTU = num;
- fontSize = fsize;
- inputfile = i;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "HeatMap");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-string HeatMap::getPic(RAbundVector* rabund) {
- try {
-
- int numBinsToDisplay = rabund->getNumBins();
-
- if (numOTU != 0) { //user want to display a portion of the otus
- if (numOTU < numBinsToDisplay) { numBinsToDisplay = numOTU; }
- }
-
- //sort lookup so shared bins are on top
- if (sorted != "none") { sortRabund(rabund); }
-
- float maxRelAbund = 0.0;
-
- for(int i=0;i<rabund->size();i++){
- float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
- if(relAbund > maxRelAbund){ maxRelAbund = relAbund; }
- }
-
- vector<string> scaleRelAbund(numBinsToDisplay, "");
-
- for(int i=0;i<numBinsToDisplay;i++){
- float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
-
- if (m->control_pressed) { return "control"; }
-
- if (rabund->get(i) != 0) { //don't want log value of 0.
- if (scaler == "log10") {
- scaleRelAbund[i] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund))) + "0000";
- }else if (scaler == "log2") {
- scaleRelAbund[i] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund))) + "0000";
- }else if (scaler == "linear") {
- scaleRelAbund[i] = toHex(int(255 * relAbund / maxRelAbund)) + "0000";
- }else { //if user enters invalid scaler option.
- scaleRelAbund[i] = toHex(int(255 * log10(relAbund / log10(maxRelAbund)))) + "0000";
- }
- }
- else { scaleRelAbund[i] = "FFFFFF"; }
- }
-
-
- string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + rabund->getLabel() + ".heatmap.bin.svg";
- m->openOutputFile(filenamesvg, outsvg);
-
- //svg image
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((numBinsToDisplay*5 + 120)) + "\">\n";
- outsvg << "<g>\n";
-
- //white backround
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(300) + "\" height=\"" + toString((numBinsToDisplay*5 + 120)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" text-anchor=\"middle\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund->getLabel() + "</text>\n";
-
- //output legend and color labels
- string color;
- int x = 0;
- int y = 103 + (numBinsToDisplay*5);
- printLegend(y, maxRelAbund);
-
- y = 70;
-
- for (int i = 0; i < scaleRelAbund.size(); i++) {
- if (m->control_pressed) { outsvg.close(); return "control"; }
-
- outsvg << "<rect fill=\"#" + scaleRelAbund[i] + "\" stroke=\"#" + scaleRelAbund[i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
- y += 5;
- }
-
- outsvg << "</g>\n</svg>\n";
- outsvg.close();
-
- return filenamesvg;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "getPic");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
- try {
-
- int numBinsToDisplay = lookup[0]->size();
-
- if (numOTU != 0) { //user want to display a portion of the otus
- if (numOTU < numBinsToDisplay) { numBinsToDisplay = numOTU; }
- }
-
- //sort lookup so shared bins are on top
- if (sorted != "none") { sortSharedVectors(lookup); }
-
- vector<vector<string> > scaleRelAbund;
- vector<float> maxRelAbund(lookup[0]->size(), 0.0);
- float superMaxRelAbund = 0;
-
- for(int i = 0; i < lookup.size(); i++){
- for(int j=0; j<lookup[i]->size(); j++){
-
- float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
- if(relAbund > maxRelAbund[i]){ maxRelAbund[i] = relAbund; }
- }
- if(maxRelAbund[i] > superMaxRelAbund){ superMaxRelAbund = maxRelAbund[i]; }
- }
-
- scaleRelAbund.resize(lookup.size());
- for(int i=0;i<lookup.size();i++){
- scaleRelAbund[i].assign(numBinsToDisplay, "");
- for(int j=0;j<numBinsToDisplay;j++){
- if (m->control_pressed) { return "control"; }
- float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
-
- if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
- if (scaler == "log10") {
- scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
- }else if (scaler == "log2") {
- scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
- }else if (scaler == "linear") {
- scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
- }else { //if user enters invalid scaler option.
- scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
- }
- }else { scaleRelAbund[i][j] = "FFFFFF"; }
-
- }
- }
-
- string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
- m->openOutputFile(filenamesvg, outsvg);
-
- //svg image
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((numBinsToDisplay*5 + 120)) + "\">\n";
- outsvg << "<g>\n";
-
- //white backround
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((numBinsToDisplay*5 + 120)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" text-anchor=\"middle\" x=\"" + toString((lookup.size() * 150) - 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\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
- }
-
- //output legend and color labels
- string color;
- int x = 0;
- int y = 103 + (numBinsToDisplay*5);
- printLegend(y, superMaxRelAbund);
-
- y = 70;
- for (int i = 0; i < numBinsToDisplay; i++) {
- for (int j = 0; j < scaleRelAbund.size(); j++) {
- if (m->control_pressed) { outsvg.close(); return "control"; }
-
- outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
- x += 300;
- }
- x = 0;
- y += 5;
- }
-
- outsvg << "</g>\n</svg>\n";
- outsvg.close();
-
- return filenamesvg;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "getPic");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
- try {
-
- vector<SharedRAbundVector*> looktemp;
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- /****************** find order of otus **********************/
- if (sorted == "shared") {
- place = orderShared(lookup);
- }else if (sorted == "topotu") {
- place = orderTopOtu(lookup);
- }else if (sorted == "topgroup") {
- place = orderTopGroup(lookup);
- }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine(); return 1; }
-
-
- /******************* create copy of lookup *********************/
- //create and initialize looktemp as a copy of lookup
- for (int i = 0; i < lookup.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
- temp->setLabel(lookup[i]->getLabel());
- temp->setGroup(lookup[i]->getGroup());
- //copy lookup i's info
- for (int j = 0; j < lookup[i]->size(); j++) {
- temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
- }
- looktemp.push_back(temp);
- }
-
- /************************ fill lookup in order given by place *********************/
- //for each bin
- for (int i = 0; i < looktemp[0]->size(); i++) { //place
- //fill lookup // 2 -> 1
- for (int j = 0; j < looktemp.size(); j++) { // 3 -> 2
- int newAbund = looktemp[j]->getAbundance(i); // 1 -> 3
- lookup[j]->set(place[i], newAbund, looktemp[j]->getGroup()); //binNumber, abundance, group
- }
- }
-
- //delete looktemp -- Sarah look at - this is causing segmentation faults
- for (int j = 0; j < looktemp.size(); j++) {
-// delete looktemp[j];
- }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "sortSharedVectors");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-map<int, int> HeatMap::orderShared(vector<SharedRAbundVector*>& lookup){
- try {
-
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- vector<int> sharedBins;
- vector<int> uniqueBins;
-
- //for each bin
- for (int i = 0; i < lookup[0]->size(); i++) {
- int count = 0;
-
- //is this bin shared
- for (int j = 0; j < lookup.size(); j++) { if (lookup[j]->getAbundance(i) != 0) { count++; } }
-
- if (count < 2) { uniqueBins.push_back(i); }
- else { sharedBins.push_back(i); }
- }
-
- //fill place
- for (int i = 0; i < sharedBins.size(); i++) { place[sharedBins[i]] = i; }
- for (int i = 0; i < uniqueBins.size(); i++) { place[uniqueBins[i]] = (sharedBins.size() + i); }
-
- return place;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "orderShared");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-map<int, int> HeatMap::orderTopOtu(vector<SharedRAbundVector*>& lookup){
- try {
-
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- vector<binCount> totals;
-
- //for each bin
- for (int i = 0; i < lookup[0]->size(); i++) {
- int total = 0;
-
- for (int j = 0; j < lookup.size(); j++) { total += lookup[j]->getAbundance(i); }
-
- binCount temp(i, total);
-
- totals.push_back(temp);
- }
-
- sort(totals.begin(), totals.end(), comparebinCounts);
-
- //fill place
- for (int i = 0; i < totals.size(); i++) { place[totals[i].bin] = i; }
-
- return place;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "orderTopOtu");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-map<int, int> HeatMap::orderTopGroup(vector<SharedRAbundVector*>& lookup){
- try {
-
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- vector < vector<binCount> > totals; //totals[0] = bin totals for group 0, totals[1] = bin totals for group 1, ...
- totals.resize(lookup.size());
-
- //for each bin
- for (int i = 0; i < lookup[0]->size(); i++) {
- for (int j = 0; j < lookup.size(); j++) {
- binCount temp(i, (lookup[j]->getAbundance(i)));
- totals[j].push_back(temp);
- }
- }
-
- for (int i = 0; i < totals.size(); i++) { sort(totals[i].begin(), totals[i].end(), comparebinCounts); }
-
- //fill place
- //grab the top otu for each group adding it if its not already added
- int count = 0;
- for (int i = 0; i < totals[0].size(); i++) {
-
- for (int j = 0; j < totals.size(); j++) {
- it = place.find(totals[j][i].bin);
-
- if (it == place.end()) { //not added yet
- place[totals[j][i].bin] = count;
- count++;
- }
- }
- }
-
- return place;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "orderTopGroup");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-void HeatMap::printLegend(int y, float maxbin) {
- 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;
- }
-
- //prints legend labels
- x = 10;
- for (int i = 1; i<=5; i++) {
- float label;
- if(scaler== "log10") { label = maxbin * log10(51*i) / log10(255); }
- else if(scaler== "log2") { label = maxbin * log2(51*i) / log2(255); }
- else if(scaler== "linear") { label = maxbin * 51 * i / 255; }
- else { label = maxbin * log10(51*i) / log10(255); }
- 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) {
- m->errorOut(e, "HeatMap", "printLegend");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-string HeatMap::getPic(vector<SharedRAbundFloatVector*> lookup) {
- try {
-
- int numBinsToDisplay = lookup[0]->size();
-
- if (numOTU != 0) { //user want to display a portion of the otus
- if (numOTU < numBinsToDisplay) { numBinsToDisplay = numOTU; }
- }
-
- //sort lookup so shared bins are on top
- if (sorted != "none") { sortSharedVectors(lookup); }
-
- vector<vector<string> > scaleRelAbund;
- vector<float> maxRelAbund(lookup.size(), 0.0);
- float superMaxRelAbund = 0;
-
- for(int i = 0; i < lookup.size(); i++){
- for(int j=0; j<lookup[i]->size(); j++){
-
- float relAbund = lookup[i]->getAbundance(j);
- if(relAbund > maxRelAbund[i]){ maxRelAbund[i] = relAbund; }
- }
- if(maxRelAbund[i] > superMaxRelAbund){ superMaxRelAbund = maxRelAbund[i]; }
- }
-
- scaleRelAbund.resize(lookup.size());
- for(int i=0;i<lookup.size();i++){
- scaleRelAbund[i].assign(numBinsToDisplay, "");
- for(int j=0;j<numBinsToDisplay;j++){
- if (m->control_pressed) { return "control"; }
- float relAbund = lookup[i]->getAbundance(j);
-
- if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
- if (scaler == "log10") {
- scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
- }else if (scaler == "log2") {
- scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
- }else if (scaler == "linear") {
- scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
- }else { //if user enters invalid scaler option.
- scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i])))) + "0000";
- }
- }else { scaleRelAbund[i][j] = "FFFFFF"; }
-
- }
- }
-
- string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
- m->openOutputFile(filenamesvg, outsvg);
-
- //svg image
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((numBinsToDisplay*5 + 120)) + "\">\n";
- outsvg << "<g>\n";
-
- //white backround
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((numBinsToDisplay*5 + 120)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" text-anchor=\"middle\" x=\"" + toString((lookup.size() * 150) - 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\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
- }
-
- //output legend and color labels
- string color;
- int x = 0;
- int y = 103 + (numBinsToDisplay*5);
- printLegend(y, superMaxRelAbund);
-
- y = 70;
- for (int i = 0; i < numBinsToDisplay; i++) {
- for (int j = 0; j < scaleRelAbund.size(); j++) {
- if (m->control_pressed) { outsvg.close(); return "control"; }
-
- outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
- x += 300;
- }
- x = 0;
- y += 5;
- }
-
- outsvg << "</g>\n</svg>\n";
- outsvg.close();
-
- return filenamesvg;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "getPic");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
- try {
-
- vector<SharedRAbundFloatVector*> looktemp;
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- /****************** find order of otus **********************/
- if (sorted == "shared") {
- place = orderShared(lookup);
- }else if (sorted == "topotu") {
- place = orderTopOtu(lookup);
- }else if (sorted == "topgroup") {
- place = orderTopGroup(lookup);
- }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine(); return 1; }
-
-
- /******************* create copy of lookup *********************/
- //create and initialize looktemp as a copy of lookup
- for (int i = 0; i < lookup.size(); i++) {
- SharedRAbundFloatVector* temp = new SharedRAbundFloatVector(lookup[i]->getNumBins());
- temp->setLabel(lookup[i]->getLabel());
- temp->setGroup(lookup[i]->getGroup());
- //copy lookup i's info
- for (int j = 0; j < lookup[i]->size(); j++) {
- temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
- }
- looktemp.push_back(temp);
- }
-
- /************************ fill lookup in order given by place *********************/
- //for each bin
- for (int i = 0; i < looktemp[0]->size(); i++) { //place
- //fill lookup // 2 -> 1
- for (int j = 0; j < looktemp.size(); j++) { // 3 -> 2
- float newAbund = looktemp[j]->getAbundance(i); // 1 -> 3
- lookup[j]->set(place[i], newAbund, looktemp[j]->getGroup()); //binNumber, abundance, group
- }
- }
-
- //delete looktemp -- Sarah look at - this is causing segmentation faults
- for (int j = 0; j < looktemp.size(); j++) {
-// delete looktemp[j];
- }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "sortSharedVectors");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int HeatMap::sortRabund(RAbundVector*& r){
- try {
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- /****************** find order of otus **********************/
- vector<binCount> totals;
-
- //for each bin
- for (int i = 0; i < r->getNumBins(); i++) {
- binCount temp(i, r->get(i));
-
- totals.push_back(temp);
- }
-
- sort(totals.begin(), totals.end(), comparebinCounts);
-
- //fill place
- for (int i = 0; i < totals.size(); i++) { place[totals[i].bin] = i; }
-
- /******************* create copy of lookup *********************/
- //create and initialize rtemp as a copy of r
-
- RAbundVector* rtemp = new RAbundVector(r->getNumBins());
- for (int i = 0; i < r->size(); i++) { rtemp->set(i, r->get(i)); }
- rtemp->setLabel(r->getLabel());
-
- /************************ fill lookup in order given by place *********************/
- //for each bin
- for (int i = 0; i < rtemp->size(); i++) { //place
- //fill lookup // 2 -> 1
- // 3 -> 2
- int newAbund = rtemp->get(i); // 1 -> 3
- r->set(place[i], newAbund); //binNumber, abundance
- }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "sortRabund");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-map<int, int> HeatMap::orderShared(vector<SharedRAbundFloatVector*>& lookup){
- try {
-
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- vector<int> sharedBins;
- vector<int> uniqueBins;
-
- //for each bin
- for (int i = 0; i < lookup[0]->size(); i++) {
- int count = 0;
-
- //is this bin shared
- for (int j = 0; j < lookup.size(); j++) { if (lookup[j]->getAbundance(i) != 0) { count++; } }
-
- if (count < 2) { uniqueBins.push_back(i); }
- else { sharedBins.push_back(i); }
- }
-
- //fill place
- for (int i = 0; i < sharedBins.size(); i++) { place[sharedBins[i]] = i; }
- for (int i = 0; i < uniqueBins.size(); i++) { place[uniqueBins[i]] = (sharedBins.size() + i); }
-
- return place;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "orderShared");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-map<int, int> HeatMap::orderTopOtu(vector<SharedRAbundFloatVector*>& lookup){
- try {
-
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- vector<binCountFloat> totals;
-
- //for each bin
- for (int i = 0; i < lookup[0]->size(); i++) {
- int total = 0;
-
- for (int j = 0; j < lookup.size(); j++) { total += lookup[j]->getAbundance(i); }
-
- binCountFloat temp(i, total);
-
- totals.push_back(temp);
- }
-
- sort(totals.begin(), totals.end(), comparebinFloatCounts);
-
- //fill place
- for (int i = 0; i < totals.size(); i++) { place[totals[i].bin] = i; }
-
- return place;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "orderTopOtu");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-map<int, int> HeatMap::orderTopGroup(vector<SharedRAbundFloatVector*>& lookup){
- try {
-
- map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
- map<int, int>::iterator it;
-
- vector < vector<binCountFloat> > totals; //totals[0] = bin totals for group 0, totals[1] = bin totals for group 1, ...
- totals.resize(lookup.size());
-
- //for each bin
- for (int i = 0; i < lookup[0]->size(); i++) {
- for (int j = 0; j < lookup.size(); j++) {
- binCountFloat temp(i, (lookup[j]->getAbundance(i)));
- totals[j].push_back(temp);
- }
- }
-
- for (int i = 0; i < totals.size(); i++) { sort(totals[i].begin(), totals[i].end(), comparebinFloatCounts); }
-
- //fill place
- //grab the top otu for each group adding it if its not already added
- int count = 0;
- for (int i = 0; i < totals[0].size(); i++) {
-
- for (int j = 0; j < totals.size(); j++) {
- it = place.find(totals[j][i].bin);
-
- if (it == place.end()) { //not added yet
- place[totals[j][i].bin] = count;
- count++;
- }
- }
- }
-
- return place;
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMap", "orderTopGroup");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
-
-
-
projects / mothur.git / blobdiff