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/*
* heatmapcommand.cpp
* Mothur
*
* Created by Sarah Westcott on 3/25/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "heatmapcommand.h"
//**********************************************************************************************************************
vector<string> HeatMapCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund);
CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prelabund);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "","",false,false); parameters.push_back(pscale);
CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "","",false,false); parameters.push_back(psorted);
CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnumotu);
CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false; allLines = true;
vector<string> tempOutNames;
outputTypes["svg"] = tempOutNames;
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, "HeatMapCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string HeatMapCommand::getHelpString(){
try {
string helpString = "";
helpString += "The heatmap.bin command parameters are shared, relabund, list, rabund, sabund, groups, sorted, scale, numotu, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
helpString += "The sorted parameter allows you to order the otus displayed, default=shared, meaning display the shared otus first. Other options for sorted are none, meaning the exact representation of your otus, \n";
helpString += "topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n";
helpString += "The scale parameter allows you to choose the range of color your bin information will be displayed with.\n";
helpString += "The numotu parameter allows you to display only the top N otus, by default all the otus are displayed. You could choose to look at the top 10, by setting numotu=10. The default for sorted is topotu when numotu is used.\n";
helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and are also separated by dashes.\n";
helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
helpString += "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n";
helpString += "Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n";
helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
helpString += "The default value for scale is log10; your other options are log2 and linear.\n";
helpString += "The heatmap.bin command outputs a .svg file for each label you specify.\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "HeatMapCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string HeatMapCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "svg") { pattern = "[filename],svg"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "HeatMapCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
HeatMapCommand::HeatMapCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { format = "list"; inputfile = listfile; current->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund");
if (sabundfile == "not open") { abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
else { format = "sabund"; inputfile = sabundfile; current->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund");
if (rabundfile == "not open") { abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
else { format = "rabund"; inputfile = rabundfile; current->setRabundFile(rabundfile); }
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { format = "sharedfile"; inputfile = sharedfile; current->setSharedFile(sharedfile); }
relabundfile = validParameter.validFile(parameters, "relabund");
if (relabundfile == "not open") { abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
else { format = "relabund"; inputfile = relabundfile; current->setRelAbundFile(relabundfile); }
if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
//is there are current file available for any of these?
//give priority to shared, then list, then rabund, then sabund
//if there is a current shared file, use it
sharedfile = current->getSharedFile();
if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else {
listfile = current->getListFile();
if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter.\n"); }
else {
rabundfile = current->getRabundFile();
if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter.\n"); }
else {
sabundfile = current->getSabundFile();
if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter.\n"); }
else {
relabundfile = current->getRelAbundFile();
if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter.\n"); }
else {
m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file.\n");
abort = true;
}
}
}
}
}
}
if (outputdir == ""){ outputdir = util.hasPath(inputfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
groups = validParameter.valid(parameters, "groups");
if (groups == "not found") { groups = ""; }
else {
util.splitAtDash(groups, Groups);
if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }
}
string temp = validParameter.valid(parameters, "numotu"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, numOTU);
temp = validParameter.valid(parameters, "fontsize"); if (temp == "not found") { temp = "24"; }
util.mothurConvert(temp, fontSize);
sorted = validParameter.valid(parameters, "sorted");
if (sorted == "not found") {
//if numOTU is used change default
if (numOTU != 0) { sorted = "topotu"; }
else { sorted = "shared"; }
}
scale = validParameter.valid(parameters, "scale"); if (scale == "not found") { scale = "log10"; }
if ((sorted != "none") && (sorted != "shared") && (sorted != "topotu") && (sorted != "topgroup")) { m->mothurOut(sorted + " is not a valid sorting option. Sorted options are: none, shared, topotu, topgroup\n"); abort=true; }
}
}
catch(exception& e) {
m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
exit(1);
}
}
//**********************************************************************************************************************
int HeatMapCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
InputData input(inputfile, format, Groups);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
HeatMap heatmap(sorted, scale, numOTU, fontSize, outputdir, inputfile);
if (format == "sharedfile") {
SharedRAbundVectors* lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookup->getNamesGroups();
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
string outputFileName = heatmap.getPic(lookup); delete lookup;
outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
}
}else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
RAbundVector* rabund = util.getNextRAbund(input, allLines, userLabels, processedLabels, lastLabel);
while (rabund != nullptr) {
if (m->getControl_pressed()) { delete rabund; break; }
string outputFileName = heatmap.getPic(rabund); delete rabund;
outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
rabund = util.getNextRAbund(input, allLines, userLabels, processedLabels, lastLabel);
}
}else if (format == "relabund") {
SharedRAbundFloatVectors* lookup = util.getNextRelabund(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookup->getNamesGroups();
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
string outputFileName = heatmap.getPic(lookup); delete lookup;
outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
lookup = util.getNextRelabund(input, allLines, userLabels, processedLabels, lastLabel);
}
}
if (m->getControl_pressed()) {
for (int i = 0; i < outputNames.size(); i++) { if (outputNames[i] != "control") { util.mothurRemove(outputNames[i]); } } outputTypes.clear(); return 0;
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "HeatMapCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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