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Last data update: 2014.03.03
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R: Plot hydrogen bond timeseries
Plot hydrogen bond timeseries
Description
Timeseries plot of hydrogen bonds (various selections possible). In addition to the timeseries file, the summary file is also necessary.
Usage
hbond_ts( timeseries,
summary,
acceptorRange = NA,
donorRange = NA,
plotOccurences = FALSE,
scalingFactorPlot = NA,
printNames = FALSE,
namesToSingle = FALSE,
printAtoms = FALSE,
timeUnit = NA,
snapshotsPerTimeInt = 1000,
timeRange = NA,
hbondIndices = NA,
barePlot = FALSE,
... )
Arguments
timeseries |
Table, containing the timeseries information (e.g. produced by load_hbond_ts()).
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summary |
Table, containing the summary information (e.g. produced by load_hbond()).
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acceptorRange |
Vector of acceptor resdiues, which are to be plotted.
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donorRange |
Vector of donor residues, which are to be plotted.
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plotOccurences |
Specifies, whether the overall summary should also be plotted in a subplot on the right hand side.
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scalingFactorPlot |
To manually set the scaling factor (if necessary).
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printNames |
Enables human readable names rather than the hbond identifiers.
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namesToSingle |
If printNames is TRUE, this flags enables one letter codes.
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printAtoms |
Enables atom names in hydrogen bond identification on the y-axis.
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timeUnit |
Specifies the time unit on the x-axis.
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snapshotsPerTimeInt |
Specifies, how many snapshots make up one time unit (see above).
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timeRange |
Selects a certain time range specified by a vector.
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hbondIndices |
List, containing vectors to select hbonds by their identifiers.
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barePlot |
Boolean, indicating whether the plot is to be made without any additional information.
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... |
Additional arguments (ellipsis).
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Author(s)
Christian Margreitter
Examples
# see "extdata/hbond_example.txt.gz" and "extdata/hbond_ts_example.txt.gz" for format information
hbond_ts( load_hbond_ts( system.file( "extdata/hbond_ts_example.txt.gz",
package = "MDplot" ) ),
load_hbond( system.file( "extdata/hbond_example.txt.gz",
package = "MDplot" ) ) )
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MDplot)
Loading required package: MASS
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MDplot/hbond_ts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hbond_ts
> ### Title: Plot hydrogen bond timeseries
> ### Aliases: hbond_ts
> ### Keywords: hbond hydrogen bond timeseries
>
> ### ** Examples
>
> # see "extdata/hbond_example.txt.gz" and "extdata/hbond_ts_example.txt.gz" for format information
> hbond_ts( load_hbond_ts( system.file( "extdata/hbond_ts_example.txt.gz",
+ package = "MDplot" ) ),
+ load_hbond( system.file( "extdata/hbond_example.txt.gz",
+ package = "MDplot" ) ) )
hbondID occurence [%]
[1,] 1 1.54
[2,] 2 3.04
[3,] 3 3.17
[4,] 4 69.87
[5,] 5 0.01
[6,] 6 3.94
[7,] 7 0.01
[8,] 8 0.02
[9,] 9 0.00
[10,] 10 0.00
[11,] 11 0.01
[12,] 12 0.00
[13,] 13 35.30
[14,] 14 94.76
[15,] 15 0.05
[16,] 16 0.00
[17,] 17 0.37
[18,] 18 0.21
[19,] 19 93.12
[20,] 20 0.02
[21,] 21 0.00
[22,] 22 3.47
[23,] 23 0.36
[24,] 24 0.00
[25,] 25 0.24
[26,] 26 0.01
[27,] 27 0.00
[28,] 28 0.00
[29,] 29 0.00
[30,] 30 0.03
[31,] 31 0.01
[32,] 32 0.00
[33,] 33 0.09
[34,] 34 0.00
[35,] 35 0.01
[36,] 36 0.07
[37,] 37 0.08
[38,] 38 0.00
[39,] 39 0.05
[40,] 40 92.21
[41,] 41 0.19
[42,] 42 0.01
[43,] 43 0.00
[44,] 44 0.00
[45,] 45 0.00
[46,] 46 0.04
[47,] 47 0.78
[48,] 48 0.14
[49,] 49 0.02
[50,] 50 0.05
[51,] 51 92.04
[52,] 52 0.64
[53,] 53 0.03
[54,] 54 0.00
[55,] 55 93.68
[56,] 56 1.79
[57,] 57 0.00
[58,] 58 0.00
[59,] 59 0.00
[60,] 60 0.04
[61,] 61 0.01
[62,] 62 0.02
[63,] 63 0.00
[64,] 64 4.66
[65,] 65 0.04
[66,] 66 0.09
[67,] 67 0.00
[68,] 68 0.00
[69,] 69 0.00
[70,] 70 0.00
[71,] 71 0.00
[72,] 72 0.00
[73,] 73 0.00
[74,] 74 0.00
[75,] 75 0.17
[76,] 76 0.00
[77,] 77 0.00
[78,] 78 0.00
[79,] 79 0.07
[80,] 80 1.27
[81,] 81 75.53
[82,] 82 3.15
[83,] 83 0.00
[84,] 84 0.00
[85,] 85 0.00
[86,] 86 0.00
[87,] 87 0.02
[88,] 88 0.07
[89,] 89 0.00
[90,] 90 0.50
[91,] 91 0.12
[92,] 92 65.95
[93,] 93 0.00
[94,] 94 0.00
[95,] 95 0.00
[96,] 96 0.00
[97,] 97 0.25
[98,] 98 0.00
[99,] 99 0.00
[100,] 100 0.00
[101,] 101 0.00
[102,] 102 0.00
[103,] 103 0.01
[104,] 104 0.00
[105,] 105 0.00
[106,] 106 0.00
[107,] 107 0.00
[108,] 108 0.00
[109,] 109 0.00
[110,] 110 0.00
[111,] 111 0.00
[112,] 112 0.00
[113,] 113 0.00
[114,] 114 0.00
[115,] 115 0.00
[116,] 116 0.00
[117,] 117 0.00
[118,] 118 0.00
[119,] 119 0.17
[120,] 120 0.79
[121,] 121 0.02
[122,] 122 0.61
[123,] 123 0.19
[124,] 124 0.00
[125,] 125 0.00
[126,] 126 0.00
[127,] 127 0.02
[128,] 128 61.62
[129,] 129 0.00
[130,] 130 0.00
[131,] 131 0.00
[132,] 132 0.00
[133,] 133 25.60
[134,] 134 0.00
[135,] 135 0.00
[136,] 136 0.00
[137,] 137 0.00
[138,] 138 0.00
[139,] 139 0.00
[140,] 140 0.00
[141,] 141 0.00
[142,] 142 0.00
[143,] 143 0.00
[144,] 144 83.47
[145,] 145 0.04
[146,] 146 0.00
[147,] 147 0.18
[148,] 148 4.65
[149,] 149 0.02
[150,] 150 0.05
[151,] 151 0.03
[152,] 152 0.00
[153,] 153 25.84
[154,] 154 97.05
[155,] 155 0.23
[156,] 156 0.00
[157,] 157 79.59
[158,] 158 0.01
[159,] 159 0.93
[160,] 160 0.00
[161,] 161 0.19
[162,] 162 0.00
[163,] 163 0.08
[164,] 164 0.00
[165,] 165 32.01
[166,] 166 95.61
[167,] 167 0.07
[168,] 168 0.00
[169,] 169 0.03
[170,] 170 0.00
[171,] 171 0.01
[172,] 172 1.06
[173,] 173 0.06
[174,] 174 0.69
[175,] 175 0.02
[176,] 176 0.21
[177,] 177 89.16
[178,] 178 0.08
[179,] 179 0.11
[180,] 180 82.70
[181,] 181 0.03
[182,] 182 0.46
[183,] 183 0.79
[184,] 184 0.00
[185,] 185 0.03
[186,] 186 0.00
[187,] 187 0.00
[188,] 188 27.01
[189,] 189 98.29
[190,] 190 0.18
[191,] 191 0.00
[192,] 192 1.01
[193,] 193 0.02
[194,] 194 0.04
[195,] 195 0.17
[196,] 196 0.01
[197,] 197 0.11
[198,] 198 90.80
[199,] 199 0.00
[200,] 200 0.02
[201,] 201 0.00
[202,] 202 0.04
[203,] 203 0.01
[204,] 204 0.03
[205,] 205 0.12
[206,] 206 86.53
[207,] 207 0.60
[208,] 208 0.00
[209,] 209 1.20
[210,] 210 0.49
[211,] 211 1.73
[212,] 212 75.61
[213,] 213 0.00
[214,] 214 7.22
[215,] 215 0.02
[216,] 216 0.00
[217,] 217 0.01
[218,] 218 28.84
[219,] 219 97.14
[220,] 220 0.12
[221,] 221 0.00
[222,] 222 0.02
[223,] 223 0.01
[224,] 224 79.89
[225,] 225 0.01
[226,] 226 2.58
[227,] 227 0.00
[228,] 228 0.67
[229,] 229 0.17
[230,] 230 0.01
[231,] 231 0.01
[232,] 232 30.07
[233,] 233 96.63
[234,] 234 0.10
[235,] 235 0.01
[236,] 236 0.20
[237,] 237 93.06
[238,] 238 0.01
[239,] 239 0.03
[240,] 240 0.81
[241,] 241 0.07
[242,] 242 0.97
[243,] 243 0.10
[244,] 244 0.01
[245,] 245 86.08
[246,] 246 0.09
[247,] 247 0.15
[248,] 248 0.04
[249,] 249 2.20
[250,] 250 0.04
[251,] 251 0.01
[252,] 252 0.02
[253,] 253 22.17
[254,] 254 97.94
[255,] 255 0.24
[256,] 256 0.02
[257,] 257 0.24
[258,] 258 0.08
[259,] 259 92.40
[260,] 260 0.01
[261,] 261 0.00
[262,] 262 0.02
[263,] 263 0.59
[264,] 264 0.01
[265,] 265 0.02
[266,] 266 0.05
[267,] 267 0.00
[268,] 268 0.04
[269,] 269 0.01
[270,] 270 0.00
[271,] 271 0.14
[272,] 272 87.61
[273,] 273 1.38
[274,] 274 0.01
[275,] 275 0.02
[276,] 276 0.75
[277,] 277 0.23
[278,] 278 0.00
[279,] 279 0.00
[280,] 280 0.00
[281,] 281 0.00
[282,] 282 0.00
[283,] 283 68.94
[284,] 284 0.05
[285,] 285 0.00
[286,] 286 0.00
[287,] 287 0.00
[288,] 288 0.70
[289,] 289 0.00
[290,] 290 0.00
[291,] 291 0.00
[292,] 292 0.00
[293,] 293 4.29
[294,] 294 0.00
[295,] 295 0.01
[296,] 296 0.00
[297,] 297 0.00
[298,] 298 0.00
[299,] 299 0.00
[300,] 300 0.00
[301,] 301 39.35
[302,] 302 79.93
[303,] 303 0.09
[304,] 304 0.00
[305,] 305 0.00
[306,] 306 0.03
[307,] 307 0.00
[308,] 308 0.02
[309,] 309 0.00
[310,] 310 0.00
[311,] 311 4.53
[312,] 312 72.01
[313,] 313 0.01
[314,] 314 0.00
[315,] 315 0.00
[316,] 316 0.00
[317,] 317 0.00
[318,] 318 0.00
[319,] 319 0.00
[320,] 320 1.05
[321,] 321 12.24
[322,] 322 0.02
[323,] 323 0.00
[324,] 324 0.00
[325,] 325 0.00
[326,] 326 0.00
[327,] 327 0.00
[328,] 328 0.01
[329,] 329 0.00
[330,] 330 0.09
[331,] 331 0.00
[332,] 332 75.29
[333,] 333 0.02
[334,] 334 0.00
[335,] 335 0.00
[336,] 336 0.00
[337,] 337 0.17
[338,] 338 0.00
[339,] 339 0.02
[340,] 340 0.00
[341,] 341 0.00
[342,] 342 0.00
[343,] 343 3.76
[344,] 344 0.02
[345,] 345 0.00
[346,] 346 0.00
[347,] 347 36.36
[348,] 348 96.97
[349,] 349 0.04
[350,] 350 0.00
[351,] 351 0.00
[352,] 352 0.00
[353,] 353 0.01
[354,] 354 0.00
[355,] 355 0.00
[356,] 356 74.28
[357,] 357 0.02
[358,] 358 0.00
[359,] 359 1.41
[360,] 360 0.00
[361,] 361 0.00
[362,] 362 0.88
[363,] 363 0.00
[364,] 364 0.14
[365,] 365 0.01
[366,] 366 0.00
[367,] 367 32.51
[368,] 368 95.07
[369,] 369 0.04
[370,] 370 0.00
[371,] 371 0.00
[372,] 372 0.00
[373,] 373 0.08
[374,] 374 0.01
[375,] 375 86.43
[376,] 376 0.19
[377,] 377 0.00
[378,] 378 0.00
[379,] 379 0.00
[380,] 380 0.29
[381,] 381 1.29
[382,] 382 0.02
[383,] 383 0.01
[384,] 384 0.02
[385,] 385 0.02
[386,] 386 0.04
[387,] 387 0.01
[388,] 388 0.00
[389,] 389 0.06
[390,] 390 82.19
[391,] 391 0.03
[392,] 392 0.19
[393,] 393 0.11
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> dev.off()
null device
1
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providing 
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