forked from johannesgerer/jburkardt-f
-
Notifications
You must be signed in to change notification settings - Fork 2
/
gene_cluster.html
336 lines (299 loc) · 9.59 KB
/
gene_cluster.html
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
<html>
<head>
<title>
GENE_CLUSTER - Cluster Genetic Expression Data
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
GENE_CLUSTER <br> Cluster Genetic Expression Data
</h1>
<hr>
<p>
<b>GENE_CLUSTER</b>
is a FORTRAN90 program which
divides a set of genetic data into clusters.
</p>
<p>
The data comes from genetic expression experiments.
</p>
<p>
Each cluster will be defined in terms of a representative data
vector, and the clustering minimizes the sum of
the squares of the "distances" of each data point to its cluster
representative. Here, the "distance" may be either the Euclidean
distance or a similarity measure based on angles.
</p>
<p>
The data to be examined is assumed to be stored in a file.
</p>
<p>
The file is assumed to contain a number of records, with each
record stored on its own line.
</p>
<p>
Each record, in turn, contains a fixed number of data values
that describe a particular gene expression experiment.
</p>
<p>
Each record will be regarded as a point in N dimensional space.
</p>
<p>
The program will try to cluster the data, that is, to organize
the data by defining a number of cluster centers, which are
also points in N dimensional space, and assigning each record
to the cluster associated with a particular center.
</p>
<p>
The method of assigning data aims to minimize the cluster energy,
which is taken to be the sum of the squares of the distances of
each data point from its cluster center.
</p>
<p>
In some contexts, it makes sense to use the usual Euclidean sort
of distance. In others, it may make more sense to replace each
data record by a normalized version, and to assign distance
by computing angles between the unit vectors.
</p>
<h3 align = "center">
Licensing:
</h3>
<p>
The computer code and data files described and made available on this web page
are distributed under
<a href = "../../txt/gnu_lgpl.txt">the GNU LGPL license.</a>
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../f77_src/asa136/asa136.html">
ASA136</a>,
a FORTRAN77 library which
is an implementation of the K-Means algorithm.
</p>
<p>
<a href = "../../f_src/cities/cities.html">
CITIES</a>,
a FORTRAN90 library which
defines various problems associated with a set of
"cities" on a map.
</p>
<p>
<a href = "../../f_src/kmeans/kmeans.html">
KMEANS</a>,
a FORTRAN90 library which
contains several implementations of
the K-Means algorithm.
</p>
<p>
<a href = "../../f_src/lau_np/lau_np.html">
LAU_NP</a>,
a FORTRAN90 library which
contains heuristic algorithms for the
K-center and K-median problems.
</p>
<p>
<a href = "../../f_src/spaeth/spaeth.html">
SPAETH</a>,
a FORTRAN90 library which
can cluster data according to various
principles.
</p>
<p>
<a href = "../../f_src/spaeth2/spaeth2.html">
SPAETH2</a>,
a FORTRAN90 library which
can cluster data according to various
principles.
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "gene_cluster.f90">gene_cluster.f90</a>, the source code.
</li>
<li>
<a href = "gene_cluster.sh">gene_cluster.sh</a>,
commands to compile and load the source code.
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
Genetic expression data files include:
<ul>
<li>
<a href = "i1039.txt">i1039.txt</a>, 1152 lines of data.
</li>
<li>
<a href = "i1650.txt">i1650.txt</a>, 180 lines of data.
</li>
<li>
<a href = "i2032.txt">i2032.txt</a>, 1481 lines of data.
</li>
<li>
<a href = "i2282.txt">i2282.txt</a>, 11016 lines of data.
</li>
<li>
<a href = "i29111.txt">i29111.txt</a>, 1031 lines of data.
</li>
<li>
<a href = "i29486.txt">i29486.txt</a>, 8526 lines of data.
</li>
</ul>
</p>
<p>
For data set 1039, there are the following files:
<ul>
<li>
<a href = "gene_cluster_1039_input.txt">gene_cluster_1039_input.txt</a>, an
input file describing the run to be made;
</li>
<li>
<a href = "gene_cluster_1039_output.txt">gene_cluster_1039_output.txt</a>, the
output file containing the results;
</li>
<li>
<a href = "normal_1039.txt">normal_1039.txt</a>, a table of the
energy versus number of clusters, for normalized data;
</li>
<li>
<a href = "normal_1039.png">normal_1039.png</a>,
a <a href = "../../data/png/png.html">PNG</a> image of
a plot of the
energy versus number of clusters, for normalized data;
</li>
<li>
<a href = "normal2_1039.txt">normal2_1039.txt</a>, a table of the
energy versus the inverse number of clusters, for normalized data;
</li>
<li>
<a href = "normal2_1039.png">normal2_1039.png</a>,
a <a href = "../../data/png/png.html">PNG</a> image of
a plot of the
energy versus the inverse number of clusters, for normalized data;
</li>
<li>
<a href = "unnormal_1039.txt">unnormal_1039.txt</a>, a table of the
energy versus number of clusters, for unnormalized data;
</li>
<li>
<a href = "unnormal_1039.png">unnormal_1039.png</a>,
a <a href = "../../data/png/png.html">PNG</a> image of
a plot of the
energy versus number of clusters, for unnormalized data;
</li>
<li>
<a href = "unnormal2_1039.txt">unnormal2_1039.txt</a>, a table of the
energy versus the inverse number of clusters, for unnormalized data;
</li>
</ul>
</p>
<p>
For data set 1650, there are the following files:
<ul>
<li>
<a href = "gene_cluster_1650_input.txt">gene_cluster_1650_input.txt</a>, an
input file describing the run to be made;
</li>
<li>
<a href = "gene_cluster_1650_output.txt">gene_cluster_1650_output.txt</a>, the
output file containing the results;
</li>
<li>
<a href = "normal_1650.txt">normal_1650.txt</a>, a table of the
energy versus number of clusters, for normalized data;
</li>
<li>
<a href = "normal2_1650.txt">normal2_1650.txt</a>, a table of the
energy versus the inverse number of clusters, for normalized data;
</li>
<li>
<a href = "unnormal_1650.txt">unnormal_1650.txt</a>, a table of the
energy versus number of clusters, for unnormalized data;
</li>
<li>
<a href = "unnormal2_1650.txt">unnormal2_1650.txt</a>, a table of the
energy versus the inverse number of clusters, for unnormalized data;
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>MAIN</b> is the main program for GENE_CLUSTER.
</li>
<li>
<b>ANALYSIS</b> computes the energy for a range of number of clusters.
</li>
<li>
<b>CLUSTER_ITERATION</b> seeks the minimal energy of a cluster of a given size.
</li>
<li>
<b>DATA_TO_GNUPLOT</b> writes data to a file suitable for processing by GNUPLOT.
</li>
<li>
<b>ENERGY_COMPUTATION</b> computes the total energy of a given clustering.
</li>
<li>
<b>FILE_COLUMN_COUNT</b> counts the number of columns in the first line of a file.
</li>
<li>
<b>FILE_LINE_COUNT</b> counts the number of lines in a file.
</li>
<li>
<b>GET_UNIT</b> returns a free FORTRAN unit number.
</li>
<li>
<b>I4_INPUT</b> prints a prompt string and reads an integer from the user.
</li>
<li>
<b>I4_RANGE_INPUT</b> reads a pair of integers from the user, representing a range.
</li>
<li>
<b>I4_UNIFORM</b> returns a scaled pseudorandom I4.
</li>
<li>
<b>NEAREST_POINT</b> finds the center point nearest a data point.
</li>
<li>
<b>POINT_GENERATE</b> generates data points for the problem.
</li>
<li>
<b>POINT_PRINT</b> prints out the values of the data points.
</li>
<li>
<b>S_INPUT</b> prints a prompt string and reads a string from the user.
</li>
<li>
<b>S_REP_CH</b> replaces all occurrences of one character by another.
</li>
<li>
<b>S_TO_I4</b> reads an integer value from a string.
</li>
<li>
<b>S_WORD_COUNT</b> counts the number of "words" in a string.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../f_src.html">
the FORTRAN90 source codes</a>.
</p>
<hr>
<i>
Last revised on 12 November 2006.
</i>
</body>
</html>