forked from mothur/mothur
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathheatmapsim.cpp
executable file
·230 lines (177 loc) · 8.36 KB
/
heatmapsim.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
/*
* 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(string dir, string i, int f) : outputDir(dir), inputfile(i), fontSize(f) {
m = MothurOut::getInstance();
}
//**********************************************************************************************************************
vector<string> HeatMapSim::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> calcs, vector<string> groups) {
try {
EstOutput data;
vector<double> sims;
vector<string> outputNames;
//make file for each calculator selected
for (int k = 0; k < calcs.size(); k++) {
if (m->getControl_pressed()) { return outputNames; }
string filenamesvg = outputDir + util.getRootName(util.getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + calcs[k]->getName() + ".heatmap.sim.svg";
util.openOutputFile(filenamesvg, outsvg);
outputNames.push_back(filenamesvg);
//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() * 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\" font-size=\"" + toString(fontSize) + "\" 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\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" y=\"50\">" + groups[h] + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" y=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" x=\"50\">" + groups[h] + "</text>\n";
}
sims.clear();
double biggest = 0;
double smallest = 10000000;
//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++){
if (m->getControl_pressed()) { outsvg.close(); return outputNames; }
vector<SharedRAbundVector*> subset;
subset.push_back(lookup[i]); subset.push_back(lookup[j]);
//get similairity between groups
data = calcs[k]->getValues(subset);
sims.push_back(1.0 - data[0]);
//save biggest similairity to set relative sim
if ((1.0 - data[0]) > biggest) { biggest = (1.0 - data[0]); }
//save smalllest similairity to set relative sim
if ((1.0 - data[0]) < smallest) { smallest = (1.0 - data[0]); }
}
}
//map biggest similairity found to red
float scalerBig = 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 = scalerBig * 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, smallest);
outsvg << "</g>\n</svg>\n";
outsvg.close();
}
return outputNames;
}
catch(exception& e) {
m->errorOut(e, "HeatMapSim", "getPic");
exit(1);
}
}
//**********************************************************************************************************************
string HeatMapSim::getPic(vector< vector<double> > dists, vector<string> groups) {
try {
vector<double> sims;
string filenamesvg = outputDir + util.getRootName(util.getSimpleName(inputfile)) + "heatmap.sim.svg";
util.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((dists.size() * 150) + 160) + " " + toString((dists.size() * 150) + 160) + "\">\n";
outsvg << "<g>\n";
//white backround
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((dists.size() * 150) + 160) + "\" height=\"" + toString((dists.size() * 150) + 160) + "\"/>";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString((dists.size() * 75) - 40) + "\" y=\"25\">Heatmap for " + inputfile + "</text>\n";
//column labels
for (int h = 0; h < groups.size(); h++) {
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" y=\"50\">" + groups[h] + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" y=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" x=\"50\">" + groups[h] + "</text>\n";
}
double biggest = -1;
double smallest = 10000000;
float scaler;
//get sim for each comparison and save them so you can find the relative similairity
for(int i = 0; i < (dists.size()-1); i++){
for(int j = (i+1); j < dists.size(); j++){
if (m->getControl_pressed()) { outsvg.close(); return filenamesvg; }
float sim = 1.0 - dists[i][j];
sims.push_back(sim);
//save biggest similairity to set relative sim
if (sim > biggest) { biggest = sim; }
//save smalllest similairity to set relative sim
if (sim < smallest) { smallest = sim; }
}
}
//map biggest similairity found to red
scaler = 255.0 / biggest;
int count = 0;
//output similairites to file
for(int i = 0; i < (dists.size()-1); i++){
for(int j = (i+1); j < dists.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 = ((dists.size() * 150) + 120);
printLegend(y, biggest, smallest);
outsvg << "</g>\n</svg>\n";
outsvg.close();
return filenamesvg;
}
catch(exception& e) {
m->errorOut(e, "HeatMapSim", "getPic");
exit(1);
}
}
//**********************************************************************************************************************
void HeatMapSim::printLegend(int y, float maxSim, float minSim) {
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=\"3\" height=\"30\"/>\n";
x += 3;
}
float scaler = (maxSim-minSim) / 5.0;
//prints legend labels
x = 0;
for (int i = 0; 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\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
x += 153;
}
}
catch(exception& e) {
m->errorOut(e, "HeatMapSim", "printLegend");
exit(1);
}
}
//**********************************************************************************************************************