7 Plotting Basics
We explore plotting using dilution series data as an example
7.1 Libraries
The package ggpmisc will only be used once in this chapter. It provides additional functions for the annotating and plotting of fitted models
7.2 Import Datasets
We import a lipidomics dataset in a flat table with additinal columns indicating QC types, injection volumes, and dilution series number
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| DataFileName | QCtype | CurveNo | InjVol | CE 16:0 | CE 16:1 | CE 16:2 | CE 17:0 | CE 17:1 | CE 18:0 | CE 18:1 | CE 18:1 d7 (ISTD) | CE 18:2 | CE 18:3 | CE 20:1 | CE 20:2 | CE 20:3 | CE 20:4 | CE 20:5 | CE 22:0 | CE 22:1 | CE 22:4 | CE 22:5 | CE 22:6 | CE 24:4 | Cer d18:0/16:0 | Cer d18:0/18:0 | Cer d18:0/20:0 | Cer d18:0/22:0 | Cer d18:0/22:0 [284] | Cer d18:0/24:1 | Cer d18:0/24:1 [284] | Cer d18:1/16:0 | Cer d18:1/16:0 d31 (ISTD) | Cer d18:1/17:0 | Cer d18:1/18:0 | Cer d18:1/20:0 | Cer d18:1/22:0 | Cer d18:1/24:0 | Cer d18:1/24:1 | Cer d18:1/25:0 | Cer d18:1/26:0 | Cer d18:2/22:0 | Cer d18:2/24:1 | COH [161) | COH [95) | DG 14:0_18:1 [-14:0] | DG 14:0_18:1 [-18:1] | DG 14:0_18:2 [-14:0] | DG 14:0_18:2 [-18:2] | DG 15:0_18:1 d7 (ISTD) [-15:0] | DG 15:0_18:1 d7 (ISTD) [-18:1] | DG 16:0_16:0 [-16:0] | DG 16:0_16:1 [-16:0] | DG 16:0_16:1 [-16:1] | DG 16:0_18:1 [-16:0] | DG 16:0_18:1 [-18:1] | DG 16:0_18:2 [-16:0] | DG 16:0_18:2 [-18:2] | DG 16:0_20:3 [-20:3] | DG 16:0_20:4 [-20:4] | DG 16:0_22:5 [-22:5] | DG 16:0_22:6 [-22:6] | DG 16:1_18:1 [-16:1] | DG 16:1_18:1 [-18:1] | DG 18:0_18:1 [-18:0] | DG 18:0_18:1 [-18:1] | DG 18:0_18:2 [-18:0] | DG 18:0_18:2 [-18:2] | DG 18:0_20:4 [-20:4] | DG 18:1_18:1 [-18:1] | DG 18:1_18:2 [-18:1] | DG 18:1_18:2 [-18:2] | DG 18:1_18:3 [-18:3] | DG 18:1_20:3 [-20:3] | DG 18:1_20:4 [-18:1] | DG 18:1_20:4 [-20:4] | DG 18:2_18:2 [-18:2] | DG 18:2_20:3 [-20:3] | DG 18:2_20:4 [-20:4] | Diisooctyl Phthalate | GM3 d18:1/16:0 | GM3 d18:1/18:0 | GM3 d18:1/20:0 | GM3 d18:1/22:0 | GM3 d18:1/24:0 | GM3 d18:1/24:1 | Hex2Cer d18:1/16:0 | Hex2Cer d18:1/16:0 d3 (ISTD) | Hex2Cer d18:1/18:0 | Hex2Cer d18:1/20:0 | Hex2Cer d18:1/22:0 | Hex2Cer d18:1/24:0 | Hex2Cer d18:1/24:1 | Hex3Cer d18:1/16:0 | Hex3Cer d18:1/18:0 | Hex3Cer d18:1/20:0 | Hex3Cer d18:1/22:0 | Hex3Cer d18:1/24:0 | Hex3Cer d18:1/24:1 | HexCer d18:1/16:0 | HexCer d18:1/16:0 d3 (ISTD) | HexCer d18:1/18:0 | HexCer d18:1/20:0 | HexCer d18:1/22:0 | HexCer d18:1/24:0 | HexCer d18:1/24:1 | LPC 14:0 | LPC 15:0 | LPC 16:1 | LPC 17:0 | LPC 17:1 | LPC 18:0 | LPC 18:1 | LPC 18:1 d7 (ISTD) | LPC 18:2 | LPC 18:3 | LPC 19:0 | LPC 19:1 | LPC 20:0 | LPC 20:1 | LPC 20:2 | LPC 20:3 | LPC 20:4 | LPC 20:5 | LPC 22:0 | LPC 22:1 | LPC 22:5 | LPC 22:6 | LPC 24:0 | LPC 26:0 | LPC O-16:0 | LPC O-18:0 | LPC O-18:1 | LPC O-20:0 | LPC O-20:1 | LPC O-22:0 | LPC O-22:1 | LPC O-24:0 | LPC P-16:0 | LPC P-18:0 | LPC P-18:1 | LPC P-20:0 | LPE 16:0 | LPE 18:0 | LPE 18:1 | LPE 18:1 d7 (ISTD) | LPE 18:2 | LPE 20:4 | LPE 22:6 | LPE P-16:0 | LPE P-18:0 | LPE P-18:1 | LPI 20:4 | LPS 16:0 | LPS 18:0 | LPS 18:1 | LPS 18:2 | PC 31:0 | PC 31:1 | PC 32:0 | PC 32:1 | PC 32:2 | PC 32:3 | PC 33:1 | PC 33:1 d7 (ISTD) | PC 33:2 | PC 34:0 | PC 34:1 | PC 34:2 | PC 34:2 + 2O | PC 34:2 + OO-34:3 +2OP-34:2 +2O | PC 34:3 | PC 34:4 | PC 34:5 | PC 35:1 | PC 35:2 | PC 35:3 | PC 35:4 | PC 35:5 | PC 36:1 | PC 36:2 | PC 36:3 | PC 36:4 a | PC 36:4 b | PC 36:5 | PC 36:6 | PC 36:7 | PC 37:4 | PC 37:5 | PC 37:6 | PC 38:3 | PC 38:4 | PC 38:5|PC 38:6 [M+2] | PC 38:6 | PC 38:7 | PC 38:8 | PC 39:5 | PC 39:6 | PC 39:7 | PC 40:4|PC 40:5 [M+2]|PC 40:6 [M+4] | PC 40:5|PC 40:6 [M+2] | PC 40:6 | PC 40:7 | PC 40:8 | PC O-32:0 | PC O-32:1 | PC O-32:2 | PC O-34:1 | PC O-34:2 | PC O-34:4 | PC O-36:1 | PC O-36:2 | PC O-36:4 | PC O-36:5 | PC O-38:4 | PC O-38:5 | PC O-38:6 | PC O-40:5 | PC O-40:6 | PC O-40:7 | PC P-32:0 | PC P-32:1 | PC P-34:1 | PC P-34:2 | PC P-34:3 | PC P-36:2 | PC P-36:4 | PC P-36:5 | PC P-38:4 | PC P-38:5 | PC P-40:5 | PC P-40:6 | PE 32:1 | PE 33:1 d7 (ISTD) | PE 34:0 | PE 34:1 | PE 34:2 | PE 34:3 | PE 35:1 | PE 35:2 | PE 36:1 | PE 36:2 | PE 36:3|PE 36:4 [M+2] | PE 36:4 a | PE 36:4 b | PE 36:5 | PE 37:5 | PE 38:3 | PE 38:4 | PE 38:5 | PE 38:6 | PE 40:4 | PE 40:5|PE 40:6 [M+2] | PE 40:6 | PE 40:7 | PE O-34:1 | PE O-34:2 | PE O-36:2 | PE O-36:3 | PE O-36:5 | PE O-38:4 | PE O-38:5 | PE O-40:5 | PE O-40:6 | PE O-40:7 | PE P-16:0/18:1 [FA] | PE P-16:0/18:1 [head group] | PE P-16:0/18:2 [FA] | PE P-16:0/18:2 [head group] | PE P-16:0/20:4 [FA] | PE P-16:0/20:4 [head group] | PE P-16:0/22:5 [FA] | PE P-16:0/22:5 [head group] | PE P-16:0/22:6 [FA] | PE P-16:0/22:6 [head group] | PE P-18:0/18:1 [FA] | PE P-18:0/18:1 [head group] | PE P-18:0/18:2 [FA] | PE P-18:0/18:2 [head group] | PE P-18:0/20:4 [FA] | PE P-18:0/20:4 [head group] | PE P-18:0/22:5 [FA] | PE P-18:0/22:5 [head group] | PE P-18:0/22:6 [FA] | PE P-18:0/22:6 [head group] | PE P-20:0/20:4 [FA] | PE P-20:0/20:4 [head group] | PE P-34:1 [-141] | PE P-34:2 [-141] | PE P-36:2 [-141] | PE P-36:3 [-141] | PE P-36:4 [-141] | PE P-38:4 [-141] | PE P-38:5 [-141] | PE P-38:6 [-141] | PE P-40:5 [-141] | PE P-40:6 [-141] | PG 33:1 d7 (ISTD) | PG 34:1 | PG 36:1 | PG 36:2 | PI 32:0 | PI 32:1 | PI 33:1 d7 (ISTD) | PI 34:0 | PI 34:1 | PI 34:2 | PI 35:1 | PI 35:2 | PI 36:1 | PI 36:2 | PI 36:3|PI 36:4 [M+2] | PI 36:4 | PI 36:5 | PI 37:4 | PI 38:3 | PI 38:4 | PI 38:5 | PI 38:6 | PI 40:4 | PI 40:5|PI 40:6 M+2 | PI 40:6 | polysiloxane 7 | polysiloxane 8 | PS 33:1 d7 (ISTD) | SM 30:1 | SM 31:1 | SM 32:0 | SM 32:1 | SM 32:2 | SM 33:1 | SM 34:0 | SM 34:1 | SM 34:2 | SM 34:3 | SM 35:1 | SM 35:2 | SM 36:1 | SM 36:2 | SM 36:2 d9 (ISTD) | SM 36:3 | SM 38:1 | SM 38:2 | SM 38:3 | SM 39:1 | SM 40:1 | SM 40:2 | SM 40:3|PC 36:4 M+1 | SM 41:1 | SM 42:1 | SM 42:2 | SM 42:3 | SM 43:1 | SM 44:1 | SM 44:2 | TG 48:0 | TG 48:0 [-16:0] | TG 48:1 | TG 48:1 [-18:1] | TG 48:1 d7 (ISTD) | TG 48:1 d7 [-15:0] (ISTD) | TG 48:2 | TG 48:2 [-14:1] | TG 48:2 [-16:0] | TG 48:2 [-16:1] | TG 48:2 [-18:1] | TG 48:3 | TG 48:3 [-16:1] | TG 48:3 [-18:2] | TG 49:1 | TG 49:1 [-15:0] | TG 49:1 [-16:0] | TG 49:1 [-18:1] | TG 50:0 | TG 50:0 [-18:0] | TG 50:1 | TG 50:1 [-14:0] | TG 50:1 [-18:1] | TG 50:2 | TG 50:2 [-18:0] | TG 50:2 [-18:1] | TG 50:2 [-18:2] | TG 50:3 | TG 50:3 [-14:1] | TG 50:3 [-16:1] | TG 50:3 [-18:1] | TG 50:4 | TG 50:4 [-14:0] | TG 51:0 [-16:0] | TG 51:0 [-17:0] | TG 51:1 | TG 51:1 [-18:1] | TG 51:2 | TG 51:2 [-15:0] | TG 51:2 [-16:0] | TG 51:2 [-18:1] | TG 52:1 | TG 52:1 [-18:0] | TG 52:2 | TG 52:2 [-16:0] | TG 52:3 | TG 52:3 [-16:1] | TG 52:3 [-18:2] | TG 52:4 | TG 52:4 [-16:0] | TG 52:4 [-18:1] | TG 53:2 | TG 53:2 [-17:0] | TG 54:1 | TG 54:1 [-18:1] | TG 54:2 | TG 54:2 [-18:0] | TG 54:3 | TG 54:3 [-18:1] | TG 54:4 | TG 54:4 [-18:0] | TG 54:4 [-18:2] | TG 54:5 | TG 54:5 [-18:1] | TG 54:6 | TG 54:6 [-18:2] | TG 56:6 | TG 56:6 [-20:4] | TG 56:8 | TG 56:8 [-20:4] | TG 58:8 | TG 58:8 [-22:6] |
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| 007_ExtrBLK+ISTD01.d | PBLK | NA | 1.0 | 286 | 176 | 3 | 138 | 62 | 59 | 3428 | 689555 | 10116 | 376 | 274 | 69 | 149 | 4192 | 1447 | 68 | 13 | 8 | 541 | 677 | 95 | 299 | 151 | 370 | 879 | 84 | 747 | 60 | 296 | 52921 | 76 | 504 | 445 | 561 | 2002 | 601 | 115 | 577 | 81 | 50 | 930 | 758 | 68 | 227 | 27 | 72 | 46210 | 35538 | 12075 | 27 | 443 | 986 | 755 | 114 | 788 | NA | 17 | 33 | 74 | 680 | 1121 | 366 | 347 | 186 | 446 | 90 | 2580 | 1276 | 1677 | 102 | 77 | 0 | 79 | 575 | 86 | 6 | 10884476 | 296 | 40 | NA | 11 | 3 | 15 | 130 | 19588 | 169 | 11 | 77 | 43 | 5 | 101 | 11 | 14 | 18 | 4 | 18 | 4 | 81 | 483 | NA | 11 | 35 | 173 | 343 | 1899 | 1641 | 1394 | 194 | 45993 | 14271 | 743063 | 8866 | 261 | 315 | 342 | 52 | 306 | 313 | 773 | 4746 | 404 | 84 | 46 | 776 | 374 | 21 | 3978 | 554 | 243 | 567 | 2 | 24 | NA | 7 | 10 | 118 | 146 | 19 | 5 | 197 | 203 | 473 | 30320 | 273 | 105 | 116 | 5 | 52 | 5 | 9 | 3 | 36 | 9 | 14 | 2337 | 127 | 5482 | 4179 | 1014 | 56 | 2544 | 5364027 | 2055 | 3028 | 50186 | 220121 | 8836 | 3371 | 12841 | 3739 | 439 | 7315 | 6255 | 3550 | 4741 | 555 | 44677 | 193527 | 66604 | 8948 | 74075 | 15242 | 1398 | 139 | 7389 | 4445 | 715 | 29878 | 218128 | 116602 | 31502 | 1950 | 1604 | 1697 | 1368 | 664 | 10408 | 28746 | 32564 | 3049 | 1174 | 727 | 154 | 223 | 3945 | 1504 | 63496 | 120 | 1971 | 10601 | 2625 | 3839 | 10068 | 1570 | 599 | 33 | 749 | 667 | 124 | 2145 | 1528 | 63496 | 947 | 3496 | 2430 | 2586 | 2146 | 84 | 103 | 119 | 85385 | 37 | 732 | 1521 | 1501 | 75 | 4 | 593 | 3321 | 769 | 141 | 948 | 82 | 3 | 24 | 1387 | 643 | 354 | 56 | 150 | 125 | 3 | 12 | 2 | 112 | 63 | 5 | 377 | 15 | 85 | NA | NA | 84 | 46 | 12 | 24 | 250 | 185 | 47 | 10 | 41 | 5 | 40 | 27 | 38 | 11 | 189 | 62 | 167 | 7 | 152 | 53 | 8 | 6 | NA | 3 | 6 | 6 | NA | 15 | 28 | 9 | 6 | 65 | 274588 | 134 | 11 | 1276 | 300 | 39 | 43018 | 74 | 186 | 564 | NA | 5 | 87 | 890 | 33 | 169 | 39 | 121 | 344 | 3313 | 428 | 74 | 171 | 174 | 4 | 70768 | 180139 | 25363 | 58 | 77 | 64 | 1406 | 170 | 1618 | 3123 | 55411 | 4064 | 17 | 1835 | 55 | 10333 | 4775 | 582952 | 105 | 4115 | 6898 | 391 | 2878 | 13648 | 3948 | 64752 | 6403 | 5377 | 14692 | 615 | 803 | 324 | 315 | 69292 | 157096 | 87824 | 14097 | 1223048 | 1155057 | 79678 | 2246 | 9701 | 38124 | 7483 | 19294 | 10544 | 1721 | 310114 | 12002 | 14803 | 10859 | 82977 | 59094 | 73204 | 1860 | 32582 | 82248 | 1562 | 18063 | 6893 | 27208 | 729 | 12103 | 5169 | 8014 | 96 | 6051 | 5371 | 59691 | 7676 | 32008 | 1599 | 3712 | 8119 | 62496 | 13275 | 93624 | 26525 | 57316 | 5563 | 11115 | 39649 | 3334 | 2364 | 12603 | 1530 | 31678 | 2391 | 44729 | 7425 | 66343 | 33337 | 545312 | 704 | 1584 | 61815 | 3630 | 20502 | 1958 | 12937 | 572 | 7188 | 267 | 11468 | 51 |
| 009_NIST_NIST01.d | NIST | NA | 1.0 | 127473 | 63573 | 1354 | 4352 | 10483 | 25764 | 2783175 | 738212 | 13162658 | 268666 | 2432 | 22891 | 750424 | 4331803 | 440531 | 159 | 289 | 33936 | 119603 | 469990 | 2819 | 2032 | 2507 | 3130 | 13689 | 4089 | 163978 | 3598 | 20578 | 58137 | 407 | 9578 | 9657 | 109670 | 474960 | 128787 | 5898 | 5495 | 13298 | 15250 | 62026 | 75898 | 4694 | 6308 | 2939 | 4740 | 23752 | 25514 | 25321 | 9300 | 7985 | 65222 | 86007 | 36817 | 72652 | 3515 | 11053 | 3842 | 2715 | 19179 | 15307 | 9694 | 10912 | 9669 | 9996 | 3978 | 166263 | 102995 | 127856 | 14601 | 6590 | 2967 | 26302 | 53036 | 3774 | 9941 | 12028398 | 22791 | 6010 | 3205 | 4061 | 4856 | 4056 | 106803 | 19758 | 1327 | 219 | 5130 | 6301 | 18680 | 22473 | 8010 | 506 | 3691 | 5062 | 6070 | 201817 | 65013 | 6262 | 3772 | 39476 | 64282 | 41399 | 137314 | 81574 | 346927 | 130496 | 24036 | 3794250 | 2898079 | 1028806 | 3046211 | 50027 | 9119 | 5646 | 9732 | 19749 | 27292 | 231721 | 750717 | 37843 | 2648 | 1431 | 56154 | 101253 | 3547 | 12303 | 108525 | 25048 | 86960 | 4571 | 4829 | 4705 | 5904 | 10741 | 35194 | 3148 | 4106 | 3780 | 19083 | 25955 | 20755 | 32941 | 32608 | 14350 | 6862 | 2360 | 2322 | 961 | 970 | 3520 | 732 | 375 | 353 | 107170 | 12343 | 2144857 | 4292903 | 281378 | 5590 | 524947 | 6948171 | 577516 | 291150 | 26218795 | 72538161 | 499424 | 481548 | 2793917 | 154926 | 8551 | 622151 | 1094257 | 326459 | 142848 | 3259 | 2673755 | 28758469 | 16938446 | 3594098 | 19641161 | 1585119 | 33128 | 675 | 588800 | 175758 | 27043 | 4266329 | 11203851 | 8258775 | 13240020 | 84571 | 3575 | 245280 | 82061 | 13853 | 426518 | 1049393 | 1769673 | 619813 | 75505 | 300743 | 93996 | 13065 | 577991 | 834438 | 243929 | 40578 | 176994 | 2335966 | 93378 | 812063 | 1756614 | 62520 | 159494 | 120383 | 146460 | 253160 | 53650 | 411874 | 1222791 | 243929 | 216928 | 1354951 | 85965 | 379378 | 697564 | 126608 | 39892 | 18069 | 72411 | 1591 | 70238 | 114781 | 11020 | 2543 | 3712 | 51482 | 289573 | 96921 | 33207 | 165189 | 8842 | 1431 | 36141 | 307092 | 113882 | 430302 | 9090 | 32529 | 77145 | 22208 | 5985 | 8418 | 8972 | 9036 | 1882 | 37007 | 49305 | 7587 | 5891 | 7340 | 7787 | 12375 | 25305 | 23644 | 92100 | 95195 | 30551 | 17864 | 52029 | 30229 | 10421 | 9987 | 45057 | 58485 | 171670 | 168714 | 13585 | 14555 | 35227 | 38250 | 8036 | 9595 | 2377 | 6919 | 15024 | 42958 | 12554 | 37074 | 47238 | 16703 | 12986 | 10628 | 309207 | 2827 | 1351 | 8581 | 4483 | 14210 | 52508 | 8924 | 77584 | 83305 | 1663 | 4135 | 89470 | 234090 | 62510 | 58141 | 1040 | 4738 | 248874 | 564977 | 52061 | 8225 | 28222 | 28282 | 16498 | 90063 | 139562 | 79878 | 29418 | 15895 | 40053 | 987604 | 80064 | 576029 | 3841275 | 36009635 | 2099380 | 13225 | 661530 | 76583 | 4254255 | 5493318 | 2042574 | 153261 | 2204192 | 1053841 | 133281 | 704683 | 4426105 | 3414587 | 21053767 | 1445846 | 2265186 | 7185614 | 3458279 | 104401 | 9260 | 37478 | 1713850 | 2579195 | 4259047 | 1609938 | 1088468 | 1077786 | 2996868 | 201403 | 1147437 | 929866 | 833735 | 940461 | 182196 | 309810 | 606252 | 141427 | 240862 | 183495 | 1980468 | 1297072 | 12311881 | 130839 | 7056648 | 16533433 | 93602 | 4895184 | 2716242 | 8832187 | 81948 | 2630841 | 1440570 | 2009639 | 234563 | 55377 | 38042 | 793988 | 321167 | 1370133 | 137899 | 315528 | 560791 | 10189061 | 3297740 | 38252501 | 11964607 | 37500101 | 1261912 | 10354682 | 24520756 | 4653990 | 2635978 | 904734 | 212152 | 1392636 | 315694 | 7311102 | 2153844 | 12461871 | 8145577 | 12948806 | 367959 | 924028 | 11723013 | 1918808 | 5831344 | 843191 | 3314241 | 356905 | 1117741 | 121504 | 610872 | 62389 |
| 010_TQC-0perc.d | RQC | 1 | 0.0 | 176 | 208 | 43 | 69 | 32 | 21 | 775 | 88 | 4449 | 394 | 13 | NA | 324 | 2995 | 540 | 70 | 47 | 9 | 328 | 485 | NA | 262 | 96 | 345 | 785 | 20 | 920 | 43 | 499 | 163 | NA | 59 | 245 | 576 | 1951 | 107 | 97 | 650 | NA | 59 | 65 | 1216 | 83 | 48 | 73 | 76 | 67 | 81 | 13056 | 74 | 182 | 1053 | 1488 | 297 | 531 | NA | 33 | NA | 71 | 145 | 115 | 163 | 416 | 120 | 336 | 183 | 2292 | 807 | 1589 | 381 | NA | 0 | 96 | 406 | NA | 0 | 9621854 | 121 | 0 | 75 | 0 | 7 | 6 | 53 | 0 | 5 | 46 | 0 | 19 | 17 | 153 | 86 | 7 | 0 | 7 | 0 | 0 | 126 | NA | NA | 21 | 5 | 21 | 288 | 255 | 1081 | 812 | 154 | 27944 | 9967 | 1206 | 7387 | 193 | 125 | 212 | 82 | 184 | 110 | 426 | 2931 | 249 | 92 | 12 | 359 | 247 | 56 | 39 | 522 | 156 | 281 | 5 | 8 | 21 | 18 | 60 | 153 | 18 | 66 | 40 | 254 | 153 | 525 | 50 | 136 | 38 | 125 | 13 | 11 | NA | 11 | 7 | 11 | NA | 5 | 508 | 154 | 3808 | 3178 | 1497 | 36 | 2043 | 7977 | 544 | 997 | 42277 | 130082 | 3146 | 3582 | 8252 | 2438 | 420 | 3193 | 2540 | 1136 | 1505 | 228 | 43477 | 145681 | 36696 | 11968 | 44258 | 7001 | 672 | 110 | 3820 | 2047 | 445 | 15850 | 100563 | 48640 | 15930 | 1041 | 333 | 1068 | 556 | NA | 3655 | 9078 | 14142 | 1077 | 777 | 412 | 105 | 71 | 1880 | 536 | 35 | 116 | 1185 | 6927 | 1132 | 3068 | 4810 | 293 | 186 | 514 | 32 | 76 | 71 | 556 | 1597 | 35 | 1086 | 1844 | NA | 1563 | 1008 | 390 | 267 | 0 | 87 | 16 | 1248 | 1787 | 929 | 234 | 66 | 195 | 2276 | 708 | 341 | 97 | 284 | 6 | 22 | 1422 | 117 | 62 | 50 | 139 | 150 | 4 | 23 | 3 | 68 | 4 | 10 | 82 | 42 | 204 | 2 | 52 | NA | 9 | 5 | 65 | 279 | 44 | 0 | 69 | NA | 20 | 64 | 143 | 97 | 5 | 255 | 52 | 110 | 45 | 82 | 5 | 22 | 46 | 4 | 4 | 7 | 13 | NA | 134 | 1 | 0 | NA | NA | 133 | 166 | 0 | 1363 | 0 | 20 | 100 | 0 | 345 | 559 | NA | 68 | 2 | 268 | 306 | 433 | 55 | 0 | 67 | 2487 | 207 | 45 | 74 | 317 | 121 | 133566 | 435796 | NA | 59 | 63 | NA | 1103 | 53 | 1888 | 1196 | 45361 | 3665 | 30 | 1734 | 500 | 7304 | 2388 | 606 | 253 | 4118 | 1414 | 613 | 722 | 14459 | 6812 | 46493 | 3662 | 6282 | 15077 | 198 | 305 | 203 | 299 | 84832 | 130952 | 77481 | 13927 | 55692 | 485 | 72017 | 2107 | 9871 | 31049 | 7373 | 15593 | 8308 | 1625 | 67786 | 13271 | 17665 | 8660 | 71660 | 31531 | 73428 | 963 | 29587 | 84100 | 2063 | 20463 | 6554 | 32747 | 536 | 10082 | 4977 | NA | 30 | 4944 | 2760 | 32404 | 7362 | 24266 | 2011 | 4011 | 9419 | 46059 | 10004 | 83604 | 18932 | 42201 | 5155 | 15668 | 17497 | 3106 | 2170 | 11341 | 1221 | 25696 | 2122 | 28169 | 4117 | 45821 | 24443 | 22263 | 491 | 1666 | 14707 | 2711 | 21203 | 1189 | 9077 | 210 | 8244 | 148 | 7214 | 117 |
| 011_TQC-20perc.d | RQC | 1 | 0.2 | 61694 | 20572 | 1334 | 1793 | 6066 | 12630 | 1254932 | 122316 | 10162065 | 298819 | 1096 | 13190 | 355471 | 9214056 | 923462 | 83 | 41 | 27013 | 158402 | 490973 | 186 | 1353 | 1015 | 992 | 1856 | 518 | 21905 | 563 | 12154 | 12449 | 432 | 12612 | 7216 | 29933 | 61119 | 43403 | 1813 | 1238 | 2063 | 2478 | 67872 | 73909 | 824 | 1516 | 908 | 5 | 4762 | 4914 | 15414 | 1528 | 1187 | 9772 | 12150 | 10529 | 15260 | 825 | 5732 | 1862 | 1452 | 4205 | 4831 | 3845 | 4948 | 3980 | 6617 | 4510 | 44752 | 26787 | 34749 | 6103 | 2610 | 1208 | 9334 | 11170 | 865 | 8181 | 10404085 | 20565 | 7126 | 1653 | 1816 | 902 | 4125 | 23108 | 2958 | 2393 | 468 | 1010 | 1340 | 1201 | 3702 | 2402 | 619 | 387 | 519 | 728 | 42680 | 19104 | 1274 | 827 | 1704 | 2699 | 1737 | 39034 | 26830 | 187399 | 105172 | 15929 | 4638519 | 1126016 | 159574 | 930585 | 28405 | 17858 | 5507 | 5969 | 17237 | 17624 | 73068 | 495662 | 41901 | 1820 | 1342 | 68524 | 48665 | 1857 | 1550 | 37452 | 17252 | 40956 | 613 | 705 | 158 | 221 | 155 | 6778 | 1371 | 1083 | 966 | 10633 | 28832 | 9210 | 6740 | 7561 | 3868 | 1424 | 708 | 1940 | 641 | 274 | 714 | 1036 | 199 | 43 | 50683 | 5206 | 508068 | 693799 | 147071 | 7335 | 205200 | 1325752 | 199052 | 203669 | 6609328 | 29442224 | 756090 | 469800 | 1353212 | 77345 | 5025 | 487661 | 658999 | 251582 | 97587 | 3950 | 3694307 | 25860400 | 7523694 | 1451904 | 12283106 | 1354230 | 43142 | 1691 | 839878 | 296705 | 21466 | 3117178 | 24244982 | 12609444 | 5991185 | 153116 | 18565 | 127489 | 109214 | 11159 | 816180 | 2457044 | 3210928 | 527581 | 108967 | 78736 | 55214 | 13136 | 236840 | 183855 | 58394 | 22161 | 86525 | 1017511 | 133620 | 397755 | 1186140 | 154760 | 111815 | 118739 | 66732 | 37681 | 5551 | 111762 | 226915 | 58394 | 62617 | 320892 | 59986 | 174464 | 191838 | 51790 | 9855 | 4059 | 13910 | 1200 | 20037 | 40466 | 5735 | 1542 | 5198 | 20770 | 147044 | 52985 | 21955 | 60167 | 6198 | 1723 | 9818 | 210873 | 70869 | 182277 | 6369 | 29116 | 32769 | 12379 | 1692 | 2323 | 9762 | 2278 | 674 | 40687 | 32843 | 34161 | 7262 | 8337 | 792 | 898 | 1162 | 2324 | 6873 | 9560 | 6843 | 3517 | 9900 | 6187 | 2519 | 2215 | 6004 | 5316 | 26777 | 38186 | 7873 | 7506 | 5864 | 7466 | 521 | 427 | 116 | 366 | 1564 | 5837 | 1919 | 6078 | 15802 | 1573 | 13824 | 2680 | 50535 | 2737 | 489 | 9130 | 1712 | 1571 | 9490 | 15992 | 16417 | 23906 | 2078 | 2374 | 34472 | 66359 | 24239 | 36026 | 1114 | 3296 | 72903 | 298856 | 32144 | 3350 | 18084 | 13935 | 4693 | 202140 | 567223 | 16956 | 2934 | 4176 | 3487 | 116392 | 9371 | 230925 | 840399 | 7792418 | 459229 | 2809 | 366413 | 31604 | 1211164 | 1477662 | 275813 | 20060 | 303689 | 162667 | 30349 | 151902 | 493389 | 287821 | 12822011 | 347213 | 333465 | 1189392 | 59863 | 24272 | 4147 | 13270 | 691319 | 1067563 | 1138106 | 451759 | 347005 | 265272 | 587806 | 37355 | 152370 | 174334 | 180093 | 214514 | 48780 | 46771 | 407948 | 75885 | 124483 | 126712 | 1034646 | 586888 | 3872574 | 81522 | 1910499 | 3964718 | 67644 | 1451011 | 739644 | 1727153 | 25737 | 483618 | 360356 | 483880 | 36490 | 39829 | 29394 | 550179 | 158819 | 702224 | 69656 | 135707 | 288183 | 3711590 | 1614807 | 14927621 | 4037398 | 17539953 | 827120 | 3341124 | 5594760 | 928052 | 896321 | 604613 | 167787 | 722626 | 161911 | 3006890 | 1187016 | 7798572 | 4307841 | 11490319 | 360533 | 572420 | 5415961 | 966709 | 2483365 | 315246 | 2821175 | 374205 | 824005 | 100156 | 581948 | 43145 |
| 012_TQC-40perc.d | RQC | 1 | 0.4 | 117673 | 48622 | 1584 | 4550 | 12252 | 39588 | 2607941 | 315312 | 20199519 | 358757 | 3010 | 28641 | 615644 | 12485971 | 2182075 | 22 | 18 | 48920 | 339380 | 742016 | 1088 | 2857 | 3067 | 1466 | 3157 | 905 | 51812 | 981 | 15892 | 14277 | 1099 | 29760 | 15453 | 67207 | 142054 | 107122 | 3960 | 2146 | 3720 | 7831 | 69443 | 75636 | 2137 | 2048 | 1057 | 1045 | 10021 | 12896 | 19260 | 2397 | 3472 | 26870 | 37350 | 23633 | 29960 | 2126 | 11101 | 4436 | 1793 | 10244 | 10281 | 9138 | 9298 | 10737 | 14924 | 12429 | 89279 | 83036 | 74684 | 15247 | 5168 | 3441 | 19901 | 32067 | 5170 | 16341 | 10581631 | 58123 | 17612 | 3504 | 1217 | 2103 | 2156 | 58051 | 9087 | 6000 | 1219 | 3486 | 3053 | 3810 | 6222 | 3030 | 730 | 1408 | 1772 | 841 | 86015 | 52621 | 2457 | 3211 | 5596 | 6574 | 4951 | 89832 | 67649 | 429799 | 251299 | 38777 | 14838903 | 2954297 | 439570 | 2326507 | 64211 | 46124 | 13270 | 14168 | 52770 | 41843 | 186901 | 1327072 | 104006 | 4475 | 4069 | 174737 | 124183 | 5326 | 6499 | 83963 | 41191 | 88453 | 2048 | 1683 | 578 | 581 | 426 | 15963 | 3803 | 2469 | 1657 | 25231 | 68525 | 20087 | 13823 | 17964 | 8760 | 3073 | 1649 | 4835 | 1102 | 540 | 2127 | 2642 | 389 | 71 | 94942 | 13501 | 1291580 | 2022692 | 383311 | 14765 | 487825 | 3132381 | 557533 | 580772 | 13509625 | 53795455 | 1980420 | 1304889 | 4409903 | 206510 | 13448 | 1328407 | 1945259 | 543379 | 282428 | 10074 | 9844450 | 48720121 | 13790204 | 5014062 | 30950762 | 4635226 | 97396 | 3902 | 2386817 | 951059 | 55754 | 7625670 | 40784021 | 24718897 | 15246895 | 335989 | 37261 | 390578 | 249937 | 31709 | 1808005 | 4415291 | 6599016 | 1345593 | 356688 | 222909 | 152480 | 26521 | 731712 | 365189 | 164873 | 59171 | 236241 | 2368822 | 292476 | 1316157 | 2322290 | 216129 | 363011 | 187248 | 144267 | 71669 | 16449 | 302754 | 498029 | 164873 | 184480 | 848949 | 134693 | 369634 | 525392 | 179693 | 17709 | 5336 | 39522 | 2514 | 36898 | 82520 | 12722 | 5439 | 7179 | 55161 | 273642 | 114984 | 61084 | 135118 | 15179 | 8077 | 29162 | 416860 | 153189 | 397746 | 19739 | 50842 | 60793 | 28857 | 10002 | 3458 | 23793 | 4289 | 1608 | 88303 | 68892 | 74045 | 10752 | 13565 | 2300 | 2581 | 2015 | 3555 | 16283 | 23990 | 20928 | 11038 | 18572 | 11400 | 5157 | 5434 | 12282 | 13699 | 63213 | 83452 | 20527 | 21725 | 15600 | 23616 | 981 | 687 | 505 | 1121 | 3908 | 11139 | 4188 | 14255 | 36887 | 3646 | 30128 | 2901 | 103162 | 4790 | 1461 | 16959 | 3435 | 4539 | 21631 | 22318 | 42756 | 56618 | 4037 | 4010 | 88201 | 201309 | 43831 | 79562 | 2538 | 9759 | 219411 | 651807 | 79351 | 8537 | 52609 | 39001 | 13983 | 249091 | 466880 | 32406 | 7144 | 10316 | 8864 | 281206 | 24138 | 621646 | 1942572 | 27612222 | 984462 | 5721 | 963459 | 79113 | 2731227 | 3271466 | 872857 | 49650 | 951864 | 343967 | 63586 | 480738 | 1356196 | 880350 | 26167824 | 944484 | 760560 | 2595089 | 156848 | 67324 | 12250 | 34241 | 1106826 | 1499276 | 1958793 | 878979 | 721557 | 630266 | 1369952 | 92952 | 325846 | 409738 | 369498 | 471095 | 105790 | 119907 | 505906 | 116102 | 195811 | 186531 | 2064964 | 1278469 | 6308232 | 122047 | 3152024 | 7508103 | 131067 | 2883614 | 1073917 | 4378084 | 69767 | 1247724 | 800924 | 1123044 | 80643 | 76914 | 65275 | 849991 | 309751 | 1166669 | 86571 | 210298 | 436332 | 8728511 | 3398622 | 18913822 | 6316448 | 26768309 | 1509715 | 5763033 | 15066447 | 2493426 | 2551634 | 1232388 | 337260 | 1861349 | 483059 | 9173035 | 2772530 | 11508134 | 7918162 | 17142880 | 574890 | 922970 | 14148146 | 2612867 | 5794736 | 771570 | 5317616 | 548092 | 2069017 | 264968 | 1363608 | 126308 |
| 013_TQC-60perc.d | RQC | 1 | 0.6 | 156974 | 46748 | 2024 | 8108 | 16930 | 68171 | 3470512 | 430598 | 21175237 | 358670 | 5194 | 36523 | 941156 | 15466319 | 3178876 | 20 | 166 | 64374 | 295298 | 1019271 | 1093 | 2455 | 5664 | 1760 | 4773 | 1366 | 77299 | 1577 | 22712 | 29252 | 1029 | 30987 | 24735 | 94740 | 221862 | 170846 | 5837 | 3192 | 5717 | 12955 | 68640 | 76589 | 3317 | 5656 | 1124 | 1821 | 13733 | 19908 | 25348 | 3376 | 4540 | 36722 | 52281 | 30847 | 49311 | 2678 | 17022 | 8098 | 3713 | 14773 | 14711 | 13376 | 14782 | 14595 | 20999 | 18957 | 158583 | 113541 | 113038 | 16069 | 8255 | 4624 | 34243 | 39471 | 6560 | 17744 | 10800520 | 81852 | 26201 | 4035 | 2407 | 1712 | 5366 | 99707 | 15004 | 5621 | 2314 | 4274 | 3171 | 5472 | 10077 | 3194 | 905 | 1590 | 1699 | 2311 | 112728 | 92340 | 4039 | 4879 | 8147 | 9650 | 8163 | 139576 | 112760 | 659549 | 379460 | 61269 | 27286319 | 5041635 | 729528 | 3873034 | 95940 | 71581 | 22550 | 23901 | 94750 | 68859 | 315268 | 2167424 | 161473 | 7005 | 5334 | 294022 | 199385 | 7451 | 9408 | 154936 | 63400 | 162642 | 2787 | 3170 | 916 | 805 | 963 | 21785 | 5807 | 3963 | 2511 | 37996 | 99375 | 29740 | 21580 | 28558 | 13401 | 4862 | 2401 | 6981 | 2063 | 943 | 4056 | 4060 | 927 | 535 | 118345 | 26905 | 1770885 | 3171171 | 582064 | 22358 | 554965 | 4069666 | 869196 | 922882 | 18847354 | 61237414 | 3395370 | 1782637 | 7180931 | 342895 | 22164 | 2027915 | 2370170 | 970208 | 372987 | 12580 | 17980909 | 58785218 | 21383288 | 7037327 | 36135439 | 7153772 | 151948 | 5232 | 3295363 | 1295516 | 113871 | 11388561 | 45945289 | 30144206 | 22873131 | 555058 | 63994 | 606785 | 320774 | 50194 | 2802510 | 5778767 | 10096374 | 1789018 | 495586 | 353759 | 190798 | 39208 | 1199459 | 383518 | 240126 | 97139 | 410953 | 3429512 | 363644 | 1975318 | 3041881 | 213588 | 568661 | 186321 | 221778 | 138100 | 30523 | 437824 | 606467 | 240126 | 296127 | 1383135 | 151409 | 563884 | 715009 | 243522 | 32973 | 9492 | 69562 | 4743 | 48045 | 118034 | 17683 | 6246 | 15036 | 96662 | 353890 | 173216 | 67780 | 179887 | 20553 | 9808 | 47188 | 420527 | 234726 | 442814 | 26002 | 68646 | 84319 | 28701 | 13232 | 3948 | 33482 | 4666 | 1389 | 145695 | 82052 | 128864 | 14449 | 19943 | 4912 | 3259 | 5766 | 7267 | 27032 | 29049 | 30729 | 16266 | 23765 | 13039 | 8406 | 8311 | 19429 | 17165 | 122088 | 99755 | 28542 | 27565 | 24146 | 22617 | 1310 | 1456 | 1638 | 1144 | 7663 | 27329 | 3005 | 24735 | 58184 | 4093 | 54603 | 4377 | 205893 | 7216 | 2831 | 20434 | 6478 | 7855 | 34181 | 24434 | 59813 | 105520 | 5927 | 7393 | 69090 | 247296 | 73219 | 139031 | 4424 | 14417 | 236097 | 1242914 | 109192 | 13836 | 42954 | 49338 | 21254 | 65323 | 154719 | 35757 | 10606 | 14660 | 12594 | 445081 | 34161 | 937595 | 2552058 | 42448905 | 1466065 | 11104 | 1092522 | 117699 | 3872093 | 4521678 | 1210793 | 88135 | 1402276 | 418103 | 83241 | 821261 | 1935472 | 1388413 | 32999765 | 1551228 | 1163204 | 4298622 | 842475 | 101599 | 16069 | 46857 | 1162439 | 1822452 | 2843614 | 1077254 | 642714 | 862320 | 2002130 | 140325 | 577704 | 540820 | 599313 | 775705 | 162782 | 176731 | 559338 | 130203 | 199692 | 213629 | 2492710 | 1454644 | 7378543 | 159023 | 4355694 | 8366068 | 148504 | 3550924 | 1304357 | 6436755 | 95553 | 1391568 | 1157419 | 1738345 | 147102 | 104962 | 104262 | 1076069 | 380672 | 1277747 | 140647 | 268994 | 555391 | 12427530 | 3799514 | 29606799 | 7141771 | 31676652 | 1659674 | 7283898 | 20518296 | 3218666 | 2917170 | 1388816 | 366257 | 3204483 | 708824 | 9984047 | 4211767 | 16790868 | 8627074 | 22094513 | 591913 | 1106370 | 16952617 | 3448999 | 9164283 | 1337916 | 6502633 | 830651 | 3026281 | 364772 | 1687461 | 133587 |
7.3 Prepare Data
# Convert to long format
d_long <- d_orig|>
pivot_longer(cols = -DataFileName:-InjVol,
names_to = "Lipid" ,
values_to = "Area")
# Get a table with RQCs only and sort by Lipid
d_rqc <- d_long |>
filter(QCtype == "RQC") |>
arrange(Lipid)
#Have a look at the table using View(d_rqc)7.4 Plot a single curve
#Select data from one single lipid from dilution curve
d_forplot <- d_rqc |> filter(Lipid == "LPC 16:1", CurveNo == 1)| DataFileName | QCtype | CurveNo | InjVol | Lipid | Area |
|---|---|---|---|---|---|
| 010_TQC-0perc.d | RQC | 1 | 0.0 | LPC 16:1 | 1081 |
| 011_TQC-20perc.d | RQC | 1 | 0.2 | LPC 16:1 | 187399 |
| 012_TQC-40perc.d | RQC | 1 | 0.4 | LPC 16:1 | 429799 |
| 013_TQC-60perc.d | RQC | 1 | 0.6 | LPC 16:1 | 659549 |
| 014_TQC-80perc.d | RQC | 1 | 0.8 | LPC 16:1 | 905868 |
| 015_TQC-100perc.d | RQC | 1 | 1.0 | LPC 16:1 | 1085113 |
7.5 Plotting one curve
ggplot(d_forplot, aes(x = InjVol, y = Area)) +
geom_point(size =5, color="red") +
#geom_line() +
scale_x_continuous(name = "Injection Volume", limits = c(-0.1, NA)) +
labs(title = "Response of LPC 16:1", y = "Peak Area [CPS]") +
geom_smooth(method = "lm",se = TRUE, color = "blue", linetype = "dotted") +
theme_light()
7.6 Plotting multiple curves
#Select data from one single lipid from ALL dilution curves
d_forplot_2 <- d_rqc |> filter(Lipid == "LPC 16:1")
ggplot(d_forplot_2, aes(x = InjVol, y = Area, color = factor(CurveNo))) +
geom_point(size =5) +
scale_x_continuous(name = "Injection Volume", limits = c(0, NA)) +
labs(title = "Response of LPC 16:1", y = "Peak Area [CPS]") +
geom_smooth(method = "lm", se = FALSE, linetype = "dotted") +
theme_light()
7.7 Faceted plot from different lipids of one curve
#Select data from all LPCs from dilution curve 1
d_forplot_3 <- d_rqc |> filter(str_detect(Lipid, "LPC 2"), CurveNo == 2)
ggplot(d_forplot_3, aes(x = InjVol, y = Area, color = factor(CurveNo))) +
geom_point(size = 2) +
scale_x_continuous(name = "Injection Volume", limits = c(0, NA)) +
labs(title = "Response Curves", y = "Peak Area [CPS]") +
geom_smooth(method = "lm", se = FALSE, linetype = "dotted", size = 0.6) +
facet_wrap(~Lipid, scales = "free") +
theme_light(base_size = 8)
7.8 Add \(R^2\) to the plots
# Plot
ggplot(data = d_forplot_3, aes(x = InjVol, y = Area,
group = factor(CurveNo))) +
stat_poly_line() +
stat_poly_eq(
aes(
label = after_stat(rr.label),
color = if_else(after_stat(r.squared) < 0.96, "red", "black")
),
size = 2.4,
lineheight = 1111.5) +
scale_color_identity() +
scale_y_continuous(limits = c(0, NA)) +
facet_wrap( ~ Lipid, scales = "free") +
geom_point() + theme_light(base_size = 6)#> Warning: Removed 62 rows containing missing values (geom_smooth).
7.9 Faceted plot from different lipids of all curves
#Select data from all LPCs from dilution curve 1
d_forplot_4 <- d_rqc |> filter(str_detect(Lipid, "LPC 2"))
ggplot(d_forplot_4, aes(x = InjVol, y = Area,
color = factor(CurveNo))) +
geom_point(size = 2) +
scale_x_continuous(name = "Injection Volume", limits = c(0, NA)) +
labs(title = "Response Curves", y = "Peak Area [CPS]") +
geom_smooth(method = "lm", se = FALSE,
linetype = "dotted", size = 0.6) +
facet_wrap(~Lipid, scales = "free") +
theme_light(base_size = 8)
7.10 Faceted plots over multiple pages
One option is to use `ggforce::facet_wrap_paginate()` but this function can be slow and has some bugs with large datasets. Here an alternative way using *purrr::map()*
# Define function to plot 1 page
plot_page <-
function(d, rows_page, columns_page) {
ggplot(data = d, aes(x = InjVol , y = Area, group = factor(CurveNo))) +
stat_poly_line() +
stat_poly_eq(aes(
label = after_stat(rr.label),
color = ifelse(after_stat(r.squared) < 0.80, "red", "darkgreen")
), size = 1.4) +
scale_color_identity() +
scale_y_continuous(limits = c(0, NA)) +
facet_wrap(vars(Lipid),
scales = "free",
nrow = rows_page,
ncol = columns_page) +
geom_point() + theme_light(base_size = 6)
}
# Select all LPCs
d_forplot_5 <- d_rqc |> filter(str_detect(Lipid, "LPC "), CurveNo == 2)
# Interate through pages
rows_page = 4
columns_page = 5
d_rqc_grp <- d_forplot_5 %>%
left_join(tibble(Lipid = unique(.$Lipid)) |>
mutate(grp = ceiling(row_number() / (rows_page * columns_page)))) %>%
group_by(grp) %>%
nest() %>%
mutate(plt = map(data, ~ plot_page(.,rows_page = rows_page, columns_page = 5)))
# Print pages
d_rqc_grp$plt#> Warning: Removed 101 rows containing missing values (geom_smooth).#> Warning: Removed 1 rows containing non-finite values (stat_poly_line).#> Warning: Removed 1 rows containing non-finite values (stat_poly_eq).#> Warning: Removed 56 rows containing missing values (geom_smooth).#> Warning: Removed 1 rows containing missing values (geom_point).
