Extraction methods
# S4 method for DiffusionMap names(x) # S4 method for DPT names(x) # S4 method for DiffusionMap,character,missing [[(x, i, j, ...) # S4 method for DPT,character,missing [[(x, i, j, ...) # S4 method for DiffusionMap $(x, name) # S4 method for DPT $(x, name)
x |
|
---|---|
i, name | Name of a diffusion component 'DCx', 'DPTx', 'Branch' or column from the data |
j | N/A |
... | ignored |
The names or data row, see respective generics.
Extract, names
for the generics. DiffusionMap accessors, DiffusionMap methods, coercions for more methods
#> 10 11 12 13 14 15 #> -0.050599180 -0.050308628 -0.042713978 -0.046807417 -0.049715209 -0.048400715 #> 16 17 18 19 20 21 #> -0.042794319 -0.049326107 -0.051274456 -0.046960905 -0.047207376 -0.049309236 #> 22 23 24 25 26 27 #> -0.048646571 -0.050355256 -0.050906675 -0.044202454 -0.048328323 -0.051601460 #> 28 29 30 31 32 33 #> -0.049368552 -0.040047039 -0.040232348 -0.037844182 -0.040955466 -0.042788661 #> 34 35 36 37 38 39 #> -0.039669942 -0.039894296 -0.039830137 -0.039561181 -0.039909813 -0.039868809 #> 40 41 42 43 44 45 #> -0.037581091 -0.038907847 -0.040463287 -0.035690189 -0.037576199 -0.040815359 #> 46 47 48 49 50 51 #> -0.037994255 -0.037805560 -0.041339504 -0.039813597 -0.038513457 -0.039024878 #> 52 53 54 55 56 57 #> -0.029427772 -0.030676396 -0.032689042 -0.033585219 -0.034516885 -0.029910563 #> 58 59 60 61 62 63 #> -0.028258455 -0.031462904 -0.031964117 -0.031589127 -0.030518188 -0.031276915 #> 64 65 66 67 68 69 #> -0.032069408 -0.035921774 -0.034645908 -0.036547290 -0.035734692 -0.033103654 #> 70 71 72 74 75 76 #> -0.035212047 -0.035088970 -0.032808082 -0.031039585 -0.034565939 -0.033010685 #> 77 78 79 80 81 82 #> -0.025877333 -0.037562655 -0.033538823 -0.034571299 -0.033199550 -0.033766867 #> 83 84 85 86 87 88 #> -0.029939475 -0.034270426 -0.031689056 -0.035961786 -0.033173410 -0.033487202 #> 89 90 91 92 93 94 #> -0.035251871 -0.035811212 -0.035013881 -0.032924413 -0.032700341 -0.034170579 #> 95 96 97 98 99 100 #> -0.035094766 -0.020783010 -0.029274864 -0.022228471 -0.013951941 -0.021346627 #> 101 102 103 104 105 106 #> -0.013383619 -0.013271922 -0.012378082 -0.022047943 -0.025999825 -0.009650161 #> 107 108 109 110 111 112 #> -0.018003574 -0.022559760 -0.016824467 -0.030923340 -0.016242399 0.004050374 #> 113 114 115 116 117 118 #> -0.009477270 -0.020355765 -0.015760410 -0.023491745 -0.020526968 -0.029756536 #> 119 120 121 122 123 124 #> -0.024154631 -0.018462632 -0.027761951 -0.028102383 -0.019302251 -0.024009325 #> 125 126 127 128 129 130 #> -0.021226730 -0.027173812 -0.023567814 -0.017164880 -0.020036246 -0.017789847 #> 131 132 133 134 135 136 #> -0.024441629 -0.025744632 -0.023093016 -0.021762549 -0.014414671 -0.025274578 #> 137 138 139 140 141 142 #> -0.020395282 -0.023455554 -0.011771350 -0.020767499 -0.023171035 -0.023712503 #> 143 144 145 146 147 148 #> -0.027766009 -0.028477730 -0.026895293 -0.023433548 -0.027908985 -0.024899257 #> 149 150 151 152 153 154 #> -0.025465358 -0.021495527 -0.025796085 -0.023909434 -0.023941512 -0.024188943 #> 155 156 157 158 159 160 #> -0.026800286 -0.023664947 -0.024962072 -0.027190267 -0.024831547 -0.025921935 #> 161 162 163 164 165 166 #> -0.023872284 -0.006859106 -0.023713551 -0.031410383 -0.025213636 -0.019339227 #> 167 168 169 170 171 172 #> -0.024225904 -0.025614210 -0.021615299 -0.031582620 0.069476193 -0.037218558 #> 173 174 175 176 177 178 #> 0.073284522 0.072851265 -0.040620402 -0.040719247 0.065723808 -0.039476971 #> 179 180 181 182 183 184 #> -0.040049437 -0.040540926 0.068066466 0.068876155 -0.037469394 0.066921313 #> 185 186 187 188 189 190 #> -0.039742320 -0.036252788 -0.042775267 -0.040405081 -0.038338314 -0.039347390 #> 191 192 193 194 195 196 #> -0.037970462 0.066505906 0.052288328 0.057169263 -0.033223039 -0.035067844 #> 197 198 199 200 201 202 #> 0.043334929 0.009603867 -0.036470599 0.050481059 0.071152493 -0.037164133 #> 203 204 205 206 207 208 #> 0.059443404 -0.034896789 -0.038046880 -0.036739525 -0.034407949 0.068941815 #> 209 210 211 212 213 214 #> 0.060667790 0.068401424 0.059643490 0.062793771 -0.037947175 -0.035776751 #> 215 216 217 218 219 220 #> -0.038597263 0.060051552 0.068697101 -0.037255375 -0.042026118 -0.038048436 #> 221 222 223 224 225 226 #> -0.039085163 0.049428532 0.068384861 0.060562170 -0.034694749 0.065474045 #> 227 228 229 230 231 232 #> 0.060731458 -0.030881962 -0.039703307 -0.042211621 0.046961257 0.068450110 #> 233 234 235 236 237 238 #> 0.067572443 -0.035803488 -0.036883343 -0.036661443 0.068730147 -0.037785704 #> 239 240 241 242 243 244 #> 0.056713689 0.036570565 -0.031216520 0.061622104 -0.027842321 0.067867887 #> 245 246 247 248 249 250 #> 0.065112615 -0.038511715 0.059779180 -0.035350105 0.044014237 -0.039946093 #> 251 252 253 254 255 256 #> 0.063857669 0.039661375 0.057683506 0.064223074 0.059836314 0.058760564 #> 257 258 259 260 261 262 #> -0.037680175 0.039661707 0.062554132 0.056932435 0.067623037 -0.035534672 #> 263 264 265 267 268 270 #> 0.059939070 0.062840199 -0.033301263 0.051646616 0.028325104 0.068022127 #> 271 272 273 274 275 277 #> -0.034404134 0.069722609 0.068739588 -0.036723355 -0.034854542 0.062484384 #> 278 279 281 282 283 284 #> 0.056744108 0.060172856 -0.003359837 -0.035811299 0.066330023 -0.043430962 #> 285 286 287 288 289 290 #> 0.072476583 -0.044312310 -0.040392912 -0.042710589 -0.042132470 -0.044430500 #> 291 292 293 294 295 296 #> 0.071075826 -0.042250044 0.069058026 -0.042408101 0.062639594 -0.042724608 #> 297 298 299 300 301 302 #> 0.064192904 0.058998904 0.068890944 0.068583243 0.071194634 0.070908725 #> 303 304 305 306 307 308 #> 0.068794867 -0.039489474 -0.042488806 -0.045452139 0.063075218 0.055357089 #> 309 310 311 312 313 314 #> -0.043824300 0.071387627 0.071323125 0.070555480 0.058051599 0.069173486 #> 315 316 317 318 319 320 #> 0.067579832 0.064814918 0.052910295 0.072080666 0.071950204 0.071616403 #> 321 322 323 324 325 326 #> 0.071228608 0.066313892 -0.043647901 -0.039475449 -0.020645196 -0.043592119 #> 327 328 329 330 331 332 #> 0.061546285 0.067496592 0.072339230 0.068642230 0.069333110 0.070457284 #> 333 334 335 336 337 338 #> 0.067124773 0.064515812 0.066538695 -0.040692800 0.068560122 -0.041838230 #> 339 340 341 342 343 344 #> -0.034840527 0.069959892 0.071257825 0.067796786 0.070430975 0.068906218 #> 345 346 347 348 349 350 #> 0.066693314 0.072757752 -0.036902354 -0.027039399 0.070230346 0.070691041 #> 351 352 353 354 355 356 #> 0.066211418 0.068015770 0.067967945 0.070523044 0.072839678 0.058298828 #> 357 358 359 360 361 362 #> 0.064632010 0.063788199 0.066908744 0.066222604 -0.045088691 0.067059791 #> 363 364 365 366 367 368 #> 0.071629143 0.071461336 -0.043571283 -0.046466112 -0.047052955 -0.041808235 #> 369 370 371 372 373 374 #> -0.039723224 -0.039477662 -0.044231974 0.072612401 -0.042884293 0.070505913 #> 375 376 377 378 379 380 #> -0.040377423 -0.047365795 0.065802912 0.068360682 0.069192971 0.069078809 #> 381 382 383 384 385 386 #> 0.060554366 0.066035445 0.072307966 0.070236574 0.070507345 0.068690118 #> 387 388 389 390 391 392 #> 0.066840318 0.066943003 0.066497682 0.068935001 -0.045796593 0.070090652 #> 393 394 395 396 397 398 #> -0.040737153 0.070634827 -0.044411659 0.065039007 -0.044227335 0.070626882 #> 399 400 401 402 403 404 #> 0.072200891 -0.043679038 0.073524670 0.070282625 0.060613863 0.061929508 #> 405 406 407 408 409 410 #> 0.058093238 -0.044631804 -0.043645186 0.069678924 -0.046029854 -0.043987114 #> 411 412 413 414 415 416 #> -0.044685066 -0.047145101 -0.044837620 -0.044606008 0.061823041 0.071851081 #> 417 418 419 420 421 422 #> 0.071561253 0.069355341 0.033800118 -0.003025556 -0.045191964 -0.047473934 #> 423 424 425 426 427 428 #> -0.047675181 -0.045877773 -0.044962649 -0.040028280 -0.043789769 -0.043291572 #> 429 430 431 432 433 434 #> -0.028072342 -0.045800379 -0.048257623 -0.043588728 -0.044329643 -0.043955483 #> 435 436 437 438 439 440 #> -0.044587684 -0.041524132 -0.040406389 0.060001575 0.066290992 0.065863174 #> 441 442 #> 0.062216956 0.065394597dm$Actb # A gene expression vector#> 10 11 12 13 14 15 16 17 18 19 #> -0.5750 -0.4350 0.4600 0.6100 1.9700 2.2850 1.7850 1.4950 1.9350 -0.8200 #> 20 21 22 23 24 25 26 27 28 29 #> -1.3350 -0.5950 -0.6000 2.6600 1.2050 1.4250 0.8150 2.0750 -0.5200 -4.2450 #> 30 31 32 33 34 35 36 37 38 39 #> 0.5700 -0.0850 2.7850 1.8800 2.1700 1.3900 1.2600 0.8350 -0.7450 -0.2800 #> 40 41 42 43 44 45 46 47 48 49 #> 0.8050 2.6150 3.5875 1.9700 1.3850 0.9300 -0.2200 -1.0250 -0.3800 0.8650 #> 50 51 52 53 54 55 56 57 58 59 #> 0.6000 -0.9675 3.0050 -0.8750 -0.3350 -3.1350 -1.4300 -2.4750 -1.1950 0.9050 #> 60 61 62 63 64 65 66 67 68 69 #> 3.4650 -0.1650 -3.1200 -2.6650 -2.6700 0.2350 1.2850 0.9300 0.8550 0.0550 #> 70 71 72 74 75 76 77 78 79 80 #> 0.5350 -0.7950 -0.5700 1.3450 -2.0850 -0.2350 3.2200 0.3550 -0.7600 1.2200 #> 81 82 83 84 85 86 87 88 89 90 #> 0.3950 -0.6550 -3.2100 -2.3400 -2.2450 0.3000 1.3150 0.2250 2.6050 1.9850 #> 91 92 93 94 95 96 97 98 99 100 #> -1.2850 -1.8600 -1.3000 -0.9050 0.6950 3.3550 -1.6650 -1.7150 -0.2000 -2.8500 #> 101 102 103 104 105 106 107 108 109 110 #> -2.8050 -2.4550 -3.5300 -0.1000 -1.0550 -1.8400 -0.2400 -1.9650 -1.9200 -2.5700 #> 111 112 113 114 115 116 117 118 119 120 #> -2.2550 -1.0700 -1.3900 -0.5500 -1.4000 -1.9300 -2.2000 -1.5550 -2.7050 -2.0400 #> 121 122 123 124 125 126 127 128 129 130 #> -2.9500 -0.1300 0.0650 -0.9550 -0.7850 0.3950 -2.3400 -0.9250 -1.3150 -2.0800 #> 131 132 133 134 135 136 137 138 139 140 #> 2.1000 0.1250 -0.2750 -0.0950 2.2650 -0.7800 -5.8350 0.0700 -1.6950 0.5250 #> 141 142 143 144 145 146 147 148 149 150 #> -0.1700 1.0300 0.4700 -0.7200 -0.4050 -2.3450 -2.7300 -1.7850 0.8350 0.9175 #> 151 152 153 154 155 156 157 158 159 160 #> 1.2500 -0.2750 -0.9200 -1.6600 -2.7350 -2.0500 0.2350 -0.6700 -1.5075 0.4250 #> 161 162 163 164 165 166 167 168 169 170 #> -1.9050 -1.8950 -3.9950 -0.9800 -3.2150 -1.2950 -0.0050 -0.6550 -1.2850 -2.7700 #> 171 172 173 174 175 176 177 178 179 180 #> -4.4550 -3.4700 -3.7750 -4.8850 -0.9600 -0.8850 -2.1250 -0.7650 -2.2550 -1.9700 #> 181 182 183 184 185 186 187 188 189 190 #> -4.7550 -4.3750 -3.7950 -3.6200 -1.1750 -1.4000 -0.1900 -0.9650 -0.5550 -3.9800 #> 191 192 193 194 195 196 197 198 199 200 #> -2.9200 -5.5650 -1.4500 -2.6850 -3.0950 -0.6650 -0.2450 -4.8250 -3.4800 -3.4500 #> 201 202 203 204 205 206 207 208 209 210 #> -4.3450 -1.2150 -0.0150 -1.6650 -2.1050 -1.0500 -3.6600 -4.6350 -3.4150 -4.0500 #> 211 212 213 214 215 216 217 218 219 220 #> -1.9400 -1.3550 -2.7100 -0.8300 -2.3750 -2.4400 -3.1200 -1.8850 -2.7000 -0.3500 #> 221 222 223 224 225 226 227 228 229 230 #> -0.5900 -0.7500 -2.9200 -2.3000 -2.9050 -3.9450 -3.1000 -3.6100 -0.9900 -0.5150 #> 231 232 233 234 235 236 237 238 239 240 #> -1.4150 -1.6050 -0.9950 -2.5700 -2.2650 -3.0750 -3.5500 -0.2600 -3.9750 -2.6450 #> 241 242 243 244 245 246 247 248 249 250 #> -1.0750 -1.4350 -3.2800 -7.3150 -3.1200 -2.0450 -0.5050 -0.1000 -0.4000 -0.8800 #> 251 252 253 254 255 256 257 258 259 260 #> -2.8700 -3.1850 -4.5250 -3.1200 -2.5750 -1.1350 0.4175 0.4500 -1.8550 -2.8500 #> 261 262 263 264 265 267 268 270 271 272 #> -3.4800 -4.3800 -4.7950 -2.8550 -0.7700 -3.7975 -0.1200 -3.9800 -1.3050 -5.1400 #> 273 274 275 277 278 279 281 282 283 284 #> -3.0600 -2.4900 -1.2250 -0.8550 -1.2000 -1.2500 -3.3900 -2.5500 -4.4250 -2.2750 #> 285 286 287 288 289 290 291 292 293 294 #> -4.6550 0.4700 0.1350 -0.6450 0.1550 -1.3350 -0.8300 -3.2650 -3.8250 -2.9350 #> 295 296 297 298 299 300 301 302 303 304 #> -1.9000 0.8950 -1.3000 -0.0400 -1.9650 -2.4350 -5.4000 -3.5100 -3.2550 0.5700 #> 305 306 307 308 309 310 311 312 313 314 #> 1.3750 0.5250 -1.3350 -1.2350 -1.9450 -5.4000 -4.6100 -3.5750 -1.7050 -1.0150 #> 315 316 317 318 319 320 321 322 323 324 #> -3.6550 -3.2850 -0.1600 -5.1500 -4.7850 -3.5550 -4.9600 -1.2400 -0.3150 -1.1000 #> 325 326 327 328 329 330 331 332 333 334 #> 0.0900 0.1850 -1.0100 -2.8700 -3.6550 -4.8300 -2.7600 -2.4700 -3.5300 -3.2900 #> 335 336 337 338 339 340 341 342 343 344 #> -3.2900 -2.5550 -3.7450 -1.6700 -1.8600 -2.9000 -2.0350 -2.3450 -2.4150 -1.0150 #> 345 346 347 348 349 350 351 352 353 354 #> -2.4600 -4.2150 -1.6550 0.5200 -3.5100 -3.2450 -1.9550 -1.4250 -1.4850 -4.3300 #> 355 356 357 358 359 360 361 362 363 364 #> -7.2550 -3.7800 -3.9550 -0.3450 -1.5600 -1.1600 -1.2600 -1.5000 -2.8550 -3.8750 #> 365 366 367 368 369 370 371 372 373 374 #> -1.3400 -0.2750 2.0450 2.1675 0.8700 1.3950 1.0400 -3.5500 -0.9950 -2.1900 #> 375 376 377 378 379 380 381 382 383 384 #> 0.5850 0.9700 -1.7175 -0.1350 -2.9350 -1.6550 -4.7250 -2.7900 -4.7450 -3.6750 #> 385 386 387 388 389 390 391 392 393 394 #> -0.9050 -2.4350 -2.6750 -3.6400 -3.8150 -3.8700 -2.4950 -4.8550 -0.8500 -2.1650 #> 395 396 397 398 399 400 401 402 403 404 #> -1.2950 -1.6750 -1.0150 -3.0700 -5.7450 -3.2350 -6.4450 -3.7700 -2.4550 -1.9500 #> 405 406 407 408 409 410 411 412 413 414 #> -0.7100 -0.6450 -1.4250 -5.4800 -2.3600 -1.5250 0.5100 0.4150 -0.7650 0.1350 #> 415 416 417 418 419 420 421 422 423 424 #> -0.0850 -4.1450 -4.2100 -2.6000 -0.5550 2.7350 1.7850 -0.8850 -0.5250 1.3700 #> 425 426 427 428 429 430 431 432 433 434 #> -0.3400 -1.9950 -1.8450 -1.9000 5.2100 -0.1250 0.7100 1.1300 -0.1050 -0.1800 #> 435 436 437 438 439 440 441 442 #> -1.2600 0.2950 -1.7400 -0.9000 -1.1700 -1.3000 -1.7700 -1.1000dm$num_cells # Phenotype metadata#> [1] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 4 4 4 4 4 #> [26] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 8 8 8 8 8 8 8 8 #> [51] 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 #> [76] 8 8 8 8 8 8 8 8 8 8 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 #> [101] 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 #> [126] 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 #> [151] 16 16 16 16 16 16 16 16 16 16 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 #> [176] 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 #> [201] 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 #> [226] 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 #> [251] 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 64 64 64 64 64 64 #> [276] 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 #> [301] 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 #> [326] 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 #> [351] 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 #> [376] 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 #> [401] 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 #> [426] 64 64 64#> NULLdm$DPT1#> NULL