Infer Angles for Single-cell Samples Using Fluorescence Intensities

Source: R/intensity2circle.R

We use FUCCI intensities to infer the position of the cells in cell cycle progression. The result is a vector of angles on a unit circle corresponding to the positions of the cells in cell cycle progression.

intensity2circle(mat, plot.it = FALSE, method = c("trig", "algebraic"))

Arguments

mat

A matrix with two columns giving summarized fluorescence intensities. Rows correspond to samples.
plot.it

TRUE or FALSE. If plot.it = TRUE, plot the fitted results.
method

The method used to fit the circle. method = "trig" uses trignometry to transform intensity measurements from cartesian coordinates to polar coordinates; method = "algebraic" uses an algebraic approach for circle fitting, implemented in the conicfit package.

Value

The inferred angles on a unit circle based on the input intensity measurements.

Examples

library(SingleCellExperiment)
data(sce_top101genes)

# Compute FUCCI scores---the log10-transformed sum of intensities
# corrected for background noise.
ints <- colData(sce_top101genes)[,c("rfp.median.log10sum.adjust",
                                    "gfp.median.log10sum.adjust")]
intensity2circle(ints, plot.it=TRUE, method = "trig")
#>   [1] 1.908566377 4.030550702 1.462869397 6.036322138 0.221865736 2.393217464
#>   [7] 2.565661253 0.018582534 2.151251195 4.432796527 5.680768699 2.363130513
#>  [13] 4.391618848 2.267355620 0.841323142 3.840672482 4.103053332 2.050937786
#>  [19] 5.231315547 0.137910140 2.746779806 2.288868528 4.809227813 1.956300844
#>  [25] 2.072511033 4.872325554 2.107913907 1.887654025 5.703514093 6.215565622
#>  [31] 5.637256525 5.852156461 1.814531834 3.292541718 6.246042631 5.413775540
#>  [37] 2.690151147 0.419094853 2.181825153 0.096908168 0.371674829 5.713011861
#>  [43] 2.275347384 3.980561542 2.068073905 1.717287389 1.977312562 6.226084115
#>  [49] 4.531474668 2.622259335 2.122202994 5.656606980 1.738286624 1.842594881
#>  [55] 5.209373453 3.264240715 6.183291708 5.981413937 2.281405045 2.356540495
#>  [61] 2.079194435 1.832823819 1.881314659 1.890853354 3.793086175 4.627758567
#>  [67] 3.179217580 1.735888798 3.890050031 4.766560426 0.857598118 6.172983580
#>  [73] 3.206852955 6.149025176 2.440828600 2.448755718 6.088574972 0.529588403
#>  [79] 5.612445691 3.201531939 6.145121274 3.845897725 1.893196437 2.100050354
#>  [85] 5.825444659 6.071190448 3.422183706 5.733563608 5.732346366 5.796096070
#>  [91] 3.864814925 0.162150507 6.040652273 2.456712536 2.641609798 2.060763092
#>  [97] 4.861315690 2.591372634 1.828291865 0.071874781 3.347274406 0.297818040
#> [103] 3.947109430 6.004103202 2.008521821 6.062819087 2.933270516 2.219926210
#> [109] 5.538434496 1.213794888 5.692898543 0.000825173 5.101368340 3.296415755
#> [115] 1.480448340 3.005872320 0.481798758 1.354298911 0.340206064 5.966858193
#> [121] 0.191234752 2.036688141 1.481043020 2.071643754 6.215620964 4.964060641
#> [127] 3.219807710 4.708654312 2.505956519 2.045855543 0.492168502 4.637666427
#> [133] 6.108619395 1.873384081 3.116785130 5.357563874 0.310197390 1.834033615
#> [139] 3.192709272 3.107315554 2.231580204 2.772181347 2.872740413 0.100084576
#> [145] 2.256588856 2.469857656 0.159296198 4.986612508 2.524750573 4.397679812
#> [151] 2.149608398 6.118425753 2.340620088 3.626279519 3.760667083 2.740117951
#> [157] 3.698154480 4.650846331 1.932335183 2.329819764 5.496778584 5.805835143
#> [163] 2.274728765 2.973826305 0.541323909 1.830557087 4.435982786 3.883329154
#> [169] 2.355645571 3.112794443 2.845364177 1.696587296 3.295434889 2.263016523
#> [175] 2.211456910 2.305795909 3.664975214 2.503031644 3.737899545 0.390370694
#> [181] 4.021850285 2.395836789 2.442646473 3.450896345 3.393643345 6.141431428
#> [187] 2.395082562 2.262816847 0.571077092 3.727758710 2.161135723 2.149075974
#> [193] 6.062823790 0.242315184 6.063903437 6.192318218 4.869831414 1.424880433
#> [199] 1.400306728 1.751942551 2.679269629 0.720687444 3.583795493 5.065510834
#> [205] 1.956700924 2.638509892 2.411486393 2.311762461 2.375374507 0.012499077
#> [211] 3.917893735 5.499970864 1.834248276 1.575356466 0.106499537 2.340584620
#> [217] 6.183929078 5.420684694 2.467806591 6.004511899 1.024821284 1.937343613
#> [223] 2.681352694 4.355073199 0.513685852 3.618617566 0.283181004 3.844485934
#> [229] 3.157841856 3.303988928 0.064689854 2.526874728 0.337694592 3.236558441
#> [235] 3.767080195 5.345927334 0.695460581 3.634061424 0.905331035 2.745015621
#> [241] 0.875989426 4.943033015 6.233901008 1.891329251 6.269620199 2.905871421
#> [247] 3.429228169 3.756666368 1.070049514 2.344541820 2.335602644 0.756847926
#> [253] 1.725923286 2.430745642 3.577375942 0.075850087 2.800458721 2.005081621
#> [259] 1.063245688 2.143608689 3.943608644 2.418933727 1.991637914 6.112588839
#> [265] 2.788345521 0.201157673 2.805667663 2.741192673 4.140893396 4.121543815
#> [271] 2.727573603 5.083231265 2.148621420 2.069533546 2.901072152 0.969446096
#> [277] 4.690492425 5.111575129 5.476740132 2.229765387 3.833663456 4.413457124
#> [283] 2.717021871 2.680936521 2.018685710 6.157594860 1.649905343 2.039509362
#> [289] 2.392543529 2.107515565 3.039875204 5.796417496 2.105608686 5.245921104
#> [295] 1.926581670 2.155330255 0.036374490 3.007820275 0.007112426 0.463159486
#> [301] 1.703146958 1.799445834 0.307866576 6.262844390 0.175660157 2.840872970
#> [307] 4.820845488 0.997590418 6.262186159 3.501778935 0.153031152 4.776730791
#> [313] 2.859183530 2.705423938 0.162665503 2.758750281 6.218825847 0.062228111
#> [319] 2.740500064 2.491532200 2.659291823 4.668717668 2.386484194 0.948654502
#> [325] 0.504641133 1.287283186 2.279649009 1.428750827 2.854953772 1.551041022
#> [331] 2.395855471 2.051625993 2.403645991 5.034618909 4.438180224 4.636066404
#> [337] 3.210789246 4.089321606 2.079453626 0.677759699 1.852789383 2.565559807
#> [343] 6.153283585 0.838831021 0.051185185 6.234648228 3.955778598 1.251836211
#> [349] 1.259053564 2.087078138 0.725279615 0.643876932 0.550750355 0.540451635
#> [355] 1.931441304 1.349483956 2.046787735 0.966113370 2.331995091 6.266987240
#> [361] 6.042067078 1.574894340 5.768672201 2.478245639 3.821895791 3.139881383
#> [367] 0.315650104 6.006684519 0.393779020 2.211681420 3.532075479 0.091736060
#> [373] 1.725073854 5.229846690 6.130612905 1.033439790 2.675363723 4.819485148
#> [379] 0.445721577 2.290401777 6.074552169 3.695671007 2.529200175 2.409515002
#> [385] 5.155961998 0.070376451 0.193285289 5.123606523 0.485628410 3.112407709
#> [391] 0.549107968 5.943510367 1.925016356 0.412328568 0.321990665 5.078350631
#> [397] 1.975614742 2.230974495 2.276398200 3.790497969 1.735078763 5.109862869
#> [403] 3.508019312 2.379899309 4.297162537 3.169498631 0.464490141 2.226914880
#> [409] 2.079252061 4.393402275 3.563781050 5.024429121 0.610746257 4.038916122
#> [415] 1.996488106 0.091433246 1.927123431 6.250005673 2.233438095 2.158641489
#> [421] 2.625954798 2.244104335 0.765036120 0.174223945 5.311277487 6.028966337
#> [427] 0.062648969 1.945052404 0.985159283 6.121261652 0.568695073 2.510967724
#> [433] 0.081018025 2.249114704 5.867423621 0.100541629 5.033160817 2.252707307
#> [439] 1.662192591 3.131014456 1.876004795 0.645261527 2.817998008 2.679578634
#> [445] 6.164174445 6.197628796 6.222642873 1.439126009 0.833359030 5.805945554
#> [451] 0.343802993 5.861046416 4.234772857 1.978314017 0.002054462 4.266122345
#> [457] 0.992951297 5.175193236 2.946126090 0.147586101 2.105994498 2.076113336
#> [463] 0.288383300 0.421087507 0.131281053 4.218271155 0.520585771 1.932342827
#> [469] 4.885645712 0.283377420 2.392395364 6.254049976 2.728784601 0.627011073
#> [475] 3.048814044 6.216808008 0.193246959 5.741327260 3.650825617 5.964272422
#> [481] 2.022124486 3.272433018 2.321263080 6.203078912 6.243722955 6.194167997
#> [487] 0.081498321 0.220510384 5.993008946 0.158480598 1.616097413 5.779324404
#> [493] 4.428700930 5.822187903 2.616345057 1.095916973 3.033323759 5.716480764
#> [499] 0.078541364 5.341239593 2.979806510 0.897543559 2.284225622 2.260341806
#> [505] 2.145911752 5.591311274 5.595769400 4.147491481 0.404815390 2.824954770
#> [511] 2.905045267 2.809922190 5.195286924 5.701165738 5.626671364 0.559766351
#> [517] 2.945561975 2.019607293 0.146942702 2.453089051 3.881890461 0.226635589
#> [523] 2.140623905 2.431839805 4.402131470 2.293024696 0.081709049 5.832112473
#> [529] 0.289740313 5.137849335 2.907059458 3.764988942 6.020576261 3.953723660
#> [535] 4.710871407 2.809021519 2.783070373 5.635938972 5.094402817 3.672297759
#> [541] 4.697163071 0.122306523 5.119309832 5.402019407 0.352364492 5.842973861
#> [547] 6.136196307 0.818644136 6.226124457 4.870180283 5.704905929 5.122246688
#> [553] 3.672737370 2.487920248 5.993023986 4.105158201 3.388757334 2.337518307
#> [559] 4.717549282 0.007191240 2.485438478 0.710785578 5.170995907 6.066485020
#> [565] 6.219276591 2.093610306 6.277208041 2.515247265 0.110384256 5.945891152
#> [571] 2.223727668 0.316890664 0.359666742 0.312585519 6.055754047 1.932081086
#> [577] 3.027954286 3.769403675 2.257249600 3.359110016 5.903067995 6.013675243
#> [583] 2.626969462 3.665183846 1.417745293 5.974637450 5.150019549 1.990227123
#> [589] 3.142743909 6.058689446 2.310024046 6.123113715 2.419463614 2.910820939
#> [595] 1.511290906 0.609205824 0.216576275 2.957222026 3.427776363 2.281557305
#> [601] 0.037215024 1.910048852 5.832235758 6.151517909 0.415041472 6.126316650
#> [607] 4.300102318 6.060544489 0.615429222 3.510096126 0.220144026 1.527516948
#> [613] 2.285998491 0.172298582 3.367001047 2.042641963 0.665215171 4.095309047
#> [619] 3.940821091 2.589374326 6.004974679 5.659633129 3.585254975 0.144436399
#> [625] 2.624681474 0.293069398 0.240327868 3.656307946 4.020073462 3.035653719
#> [631] 2.470398751 6.004088732 6.153501990 3.073231255 0.003849159 0.742677565
#> [637] 2.665489293 3.234413556 1.805759467 3.502903791 3.080514114 6.124082263
#> [643] 6.006788278 6.235009038 3.114183608 3.586973717 3.755623005 4.100674609
#> [649] 2.283922117 2.718196324 3.881076643 4.650358288 4.128633711 3.162427822
#> [655] 2.828231506 0.762312288 6.177276295 0.956352184 6.089110033 3.131185130
#> [661] 3.298163122 5.697206252 6.279159977 1.640110023 4.631300031 5.491104866
#> [667] 3.397865400 1.070114488 0.400238289 0.107744358 6.009421973 0.389596524
#> [673] 5.844264067 3.923078217 6.142496897 2.603339868 2.335874294 0.138091448
#> [679] 5.663763754 1.741151679 5.537456741 6.022505415 4.054169538 5.629531028
#> [685] 0.977187820 1.437399451 4.163048592 3.024715720 3.094436858 6.141857672
#> [691] 2.687682981 6.268566411 2.767031224 5.783947461 0.053359131 3.559046576
#> [697] 5.597507951 2.277847443 4.770890745 5.783097460 2.017911876 2.000857391
#> [703] 5.064866229 2.378584730 5.545545574 3.308410546 2.321950806 5.895705857
#> [709] 0.867473026 1.419299608 2.589551523 4.203190608 2.987726551 1.989669133
#> [715] 3.511571776 2.534157348 0.317324878 3.065423994 2.388885633 4.770269602
#> [721] 2.606822074 1.910702246 5.948237457 2.911520972 0.396912515 5.774506693
#> [727] 2.765049123 4.095798239 2.063722529 0.453414737 4.360723573 6.234154934
#> [733] 2.373045626 2.159015505 2.035542064 0.826661130 1.942863863 4.010901866
#> [739] 5.083380067 4.925252141 1.066046001 5.147489648 3.219067066 5.292580954
#> [745] 4.855295642 2.627173282 0.156774956 2.029153370 3.139751900 0.626594361
#> [751] 0.019008784 2.585755330 0.114612317 0.919350443 4.787807626 4.492688734
#> [757] 2.945166583 3.463847425 5.270173552 0.358891749 2.088021854 6.255097074
#> [763] 4.596941040 2.009829864 2.667272252 2.667561756 2.951237151 2.637041752
#> [769] 2.410882652 4.848146310 2.233549185 5.773875129 3.349197504 5.831994685
#> [775] 3.229389625 1.906659897 0.251601474 4.702667123 5.104532252 4.180170850
#> [781] 5.825902186 4.478781177 5.513070082 2.384306799 2.368932007 4.806721151
#> [787] 5.990347878 3.882597518 2.850773263 4.277537129 6.240075757 5.250440593
#> [793] 2.197769485 2.194323847 5.937047064 3.352694899 0.213321139 2.043059006
#> [799] 0.994419698 0.264079347 2.995598149 2.150361357 5.885649144 5.988149304
#> [805] 2.411943106 2.342777345 2.366003967 3.715289553 0.072533458 4.972828587
#> [811] 5.720202950 3.700515866 5.627423168 3.514982177 5.660856874 0.020787604
#> [817] 2.789945871 0.329119777 6.211251830 6.216459840 6.014786253 6.184638113
#> [823] 0.722726575 2.396461451 2.718850438 1.614677449 6.018312135 2.057726074
#> [829] 6.273867313 0.343062768 0.331910890 0.041511636 5.976873863 5.932957995
#> [835] 2.963658500 5.809005516 0.074655915 4.332678585 4.421610645 4.417167979
#> [841] 2.487543899 3.852075010 4.192171353 2.106168703 4.274230625 4.265318854
#> [847] 2.266349529 6.193974331 4.945049175 4.354266289 3.771972950 0.289098226
#> [853] 1.783000570 2.013943349 0.333992183 5.969237263 5.314167505 4.061153414
#> [859] 4.300945383 4.788513810 4.213773213 0.495226087 5.473718741 3.118721495
#> [865] 1.139997069 4.209729132 4.508015431 4.212207951 4.293030442 2.188758328
#> [871] 4.298660512 3.900612662 3.875912956 0.695096166 0.130148076 5.620643220
#> [877] 0.581427165 3.750957924 4.354901227 3.948844794 4.060906091 4.554872876
#> [883] 2.060476875 4.125703069 5.753018711 4.239399919 4.505130389 4.430589891