├── LICENSE ├── README.md ├── data_B.csv ├── data_Cmu_E10.5.csv ├── data_Cmu_E11.5.csv ├── data_Cmu_E8.5.csv ├── data_Cmu_E9.5.csv ├── data_Cwt_E10.5.csv ├── data_Cwt_E11.5.csv ├── data_Cwt_E8.5.csv ├── data_Cwt_E9.5.csv ├── data_D1.csv ├── data_D2.csv ├── data_Ea.csv ├── data_Eb.csv ├── data_Ec.csv ├── data_F.csv ├── figure_example.R ├── figure_example.pdf ├── figure_example.png ├── figure_example.svg ├── image1.jpg └── image2.png /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # scifig_plot_examples_R 2 | Scientific publication figure plotting examples with R. 3 | 4 | ![figure_example](https://github.com/marco-meer/scifig_plot_examples_R/blob/main/figure_example.png) 5 | -------------------------------------------------------------------------------- /data_B.csv: -------------------------------------------------------------------------------- 1 | n,fraction1,fraction2,err1,err2 2 | 3,0.01,0.005,0.002,0.001 3 | 4,0.05,0.04,0.01,0.008 4 | 5,0.24,0.225,0.04,0.04 5 | 6,0.45,0.53,0.06,0.05 6 | 7,0.19,0.14,0.034,0.03 7 | 8,0.045,0.04,0.009,0.008 8 | 9,0.01,0.02,0.002,0.004 9 | 10,0.005,0,0.001,0 10 | -------------------------------------------------------------------------------- /data_Cmu_E10.5.csv: -------------------------------------------------------------------------------- 1 | 65.8205529524502 2 | 41.6531035937204 3 | 83.152551557937 4 | 49.8115199468345 5 | 49.7305565969044 6 | 44.9995256006525 7 | 45.1256605549988 8 | 54.4260875488319 9 | 59.3898067636063 10 | 55.2654589200939 11 | 59.1173471779051 12 | 46.235427610441 13 | 57.6267963516239 14 | 48.5291927139915 15 | 68.6366348486041 16 | 74.2734952793967 17 | 60.6487719565292 18 | 84.786057725313 19 | 48.5480400989702 20 | 65.3386633487001 21 | 52.3899352375807 22 | 48.6507554603649 23 | 57.5822109522762 24 | 67.8970383500416 25 | 45.0397364373011 26 | 36.5613573799657 27 | 60.0366499016365 28 | 52.6932735705296 29 | 53.9281089566023 30 | 67.5736606957021 31 | 53.9476022283962 32 | 54.2741479383546 33 | 70.4077851758678 34 | 54.6481556145846 35 | 60.4091424302168 36 | 49.1581406653753 37 | 59.655677151569 38 | 57.092707914815 39 | 44.6581069131501 40 | 54.8138933538391 41 | 55.310677780828 42 | 68.9534191538903 43 | 50.6759544087888 44 | 65.1494597486622 45 | 52.0866432423026 46 | 48.7163381473606 47 | 56.9623907788505 48 | 53.0820740059476 49 | 63.8609173377662 50 | 69.3508728072075 51 | 43.918594861742 52 | 40.1339485419691 53 | 47.9636860176302 54 | 52.3626294120593 55 | 47.6899666215299 56 | 66.70934623327 57 | 47.6036564420278 58 | 46.4462375984477 59 | 37.1354633751926 60 | 28.4352412345882 61 | 49.317284429323 62 | 39.7967553834712 63 | 51.1200504829997 64 | 89.9445381630164 65 | 58.9838425665504 66 | 48.9544765236798 67 | 39.4502495746855 68 | 53.1342817405542 69 | 77.4269573461966 70 | 49.4436483287547 71 | 82.239850092544 72 | 70.58437635767 73 | 30.262491641059 74 | 64.3093089866025 75 | 60.2999565031281 76 | 72.3560256197538 77 | 40.5564946289917 78 | 55.3711507422376 79 | 56.0267992773933 80 | 56.5769380613516 81 | 66.9992559088336 82 | 59.5371870721189 83 | 63.3197974950725 84 | 53.4387071182716 85 | 53.8879690976582 86 | 64.2194530009369 87 | 38.13817438162 88 | 46.6385040560028 89 | 53.5027322154622 90 | 53.0976496113571 91 | 46.0243049939109 92 | 55.431571319898 93 | 60.9328007658431 94 | 60.8185985209417 95 | 55.6353020926962 96 | 48.7799678522732 97 | 52.5451326562458 98 | 54.5798650090393 99 | 61.774285453737 100 | 57.0345994953582 101 | 37.5665098680396 102 | 51.4414802520879 103 | 50.3611512216014 104 | 61.3682749102604 105 | 55.4435480146538 106 | 64.8662834741187 107 | 62.841494873935 108 | 46.2169685002261 109 | 57.5914131965011 110 | 58.0086668582521 111 | -------------------------------------------------------------------------------- /data_Cmu_E11.5.csv: -------------------------------------------------------------------------------- 1 | 59.1890088518618 2 | 56.2107835047841 3 | 55.2994926733609 4 | 70.7916698405769 5 | 64.7330529679417 6 | 48.2574994441115 7 | 63.2107626882808 8 | 55.8564954899177 9 | 54.5760807254418 10 | 51.3230864223238 11 | 60.2021409743821 12 | 63.4194391191852 13 | 48.3437334986212 14 | 52.7239783061468 15 | 56.8960726372144 16 | 58.0139878340251 17 | 67.0538371096838 18 | 56.6622318629482 19 | 60.5850110851269 20 | 59.2510534999053 21 | 50.4949741224361 22 | 57.0558476030154 23 | 61.0584025897667 24 | 52.7791703590774 25 | 64.4631659684564 26 | 52.2445438695031 27 | 56.7234439395831 28 | 44.5300127340189 29 | 50.9568980312489 30 | 58.5473725355373 31 | 60.5454816944244 32 | 57.3988404666032 33 | 66.7227183053284 34 | 60.4688087395229 35 | 56.2592131452591 36 | 55.0777274410811 37 | 57.383926844346 38 | 67.5864019282867 39 | 65.4738619046073 40 | 66.9529866798847 41 | 58.3114215280906 42 | 56.5273850456214 43 | 56.2353365698152 44 | 61.684464515395 45 | 55.3505158559685 46 | 46.3484877537309 47 | 55.6909136265621 48 | 72.1333458665144 49 | 54.9871118794021 50 | 63.009606324092 51 | 57.097978297995 52 | 55.4169629881021 53 | 51.5280071936532 54 | 48.5373743865034 55 | 55.7150222248605 56 | 49.2113588380889 57 | 53.795783611417 58 | 62.179585698278 59 | 57.5116264374945 60 | 43.8912875539574 61 | 68.1005600287051 62 | 63.0091092848727 63 | 61.5165781695328 64 | 60.0060966410832 65 | 53.4578934689505 66 | 57.631665252223 67 | 59.3242253821183 68 | 58.9981706659672 69 | 64.668851282844 70 | 55.4409232072789 71 | -------------------------------------------------------------------------------- /data_Cmu_E8.5.csv: -------------------------------------------------------------------------------- 1 | 40.0376253078157 2 | 34.4494870737266 3 | 33.4971571900859 4 | 37.9076623810452 5 | 38.3799653610893 6 | 39.4948119596739 7 | 39.8803763629151 8 | 48.0129233665844 9 | 32.9249865794136 10 | 40.5200505165726 11 | 40.9368041901928 12 | 49.4189987182495 13 | 45.3459455596609 14 | 45.155245507597 15 | 38.5315921920013 16 | 48.7421625990379 17 | 50.1490461451389 18 | 40.1161666571257 19 | 49.7231699091656 20 | 37.7391126683174 21 | 46.137918759145 22 | 42.1751325231794 23 | 43.4554162345088 24 | 35.477688506143 25 | 40.7509010376925 26 | 34.4153490978095 27 | 42.0358914711044 28 | 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-------------------------------------------------------------------------------- /data_Cwt_E8.5.csv: -------------------------------------------------------------------------------- 1 | 42.0231534315441 2 | 48.6086180192145 3 | 59.4429177651021 4 | 44.4709256444671 5 | 45.8791913778026 6 | 37.4391162510815 7 | 54.7078670427408 8 | 41.0501181430666 9 | 49.734092289716 10 | 34.4469714336658 11 | 48.258485118967 12 | 43.5922012057071 13 | 44.7419989753021 14 | 54.6933371333323 15 | 41.585945933396 16 | 41.3540581756515 17 | 52.2104634382051 18 | 39.3616396472208 19 | 52.4730752750606 20 | 44.3560106336907 21 | 37.5961172612138 22 | 40.6611276988538 23 | 34.9619321940111 24 | 47.7481711836869 25 | 45.42066827862 26 | 49.8801374172677 27 | 37.169415367784 28 | 60.210092772453 29 | 51.7422913980254 30 | 46.7829983593404 31 | 32.4666700472315 32 | 45.6094999763088 33 | 49.7975795544 34 | 52.4634561840654 35 | 62.6511586856736 36 | 44.7136663069121 37 | 58.6623770527958 38 | 55.3744761891473 39 | 38.3057820825054 40 | 36.1431924300171 41 | 48.7639073645354 42 | 34.6329690311057 43 | 38.320546745845 44 | 30.6188826878588 45 | 56.7984974704626 46 | 57.0226659930928 47 | 42.4077752093245 48 | 44.8110095808989 49 | 44.9310255230851 50 | 41.6995893218805 51 | -------------------------------------------------------------------------------- /data_Cwt_E9.5.csv: -------------------------------------------------------------------------------- 1 | 57.1716435652241 2 | 66.6619363671157 3 | 50.9149524056221 4 | 68.2699436334885 5 | 55.4179671396149 6 | 70.8967115659325 7 | 53.7661806615795 8 | 57.1088484406355 9 | 67.0282384500332 10 | 69.1677135887322 11 | 65.3236151221537 12 | 69.314786869523 13 | 73.5047989126147 14 | 67.4578549115102 15 | 55.5665267387901 16 | 43.2787939697393 17 | 53.7692862506144 18 | 47.0875777784363 19 | 87.1876833515417 20 | 65.1251532898355 21 | 55.398542826564 22 | 86.5986058282673 23 | 64.6808962996307 24 | 50.8768680595717 25 | 69.0664807059441 26 | 75.3992924613927 27 | 59.5186633945559 28 | 82.0897978552346 29 | 64.0129391396651 30 | 66.0178119974159 31 | 62.5265638131648 32 | 56.4424888438124 33 | 68.4412305883574 34 | 79.9237326244011 35 | 52.1762352709889 36 | 62.499827288029 37 | 44.639344226227 38 | 38.8058142245449 39 | 90.464571822197 40 | 66.6376732234725 41 | 45.2547748649069 42 | 65.9969528978274 43 | 61.3484694507117 44 | 71.8804500697977 45 | 55.6118159612999 46 | 58.2683788127051 47 | 55.0902609329985 48 | 59.8413015331919 49 | 60.7681692057057 50 | 56.4418134041207 51 | 81.9744921930709 52 | 74.9007051794205 53 | 65.2037830240915 54 | 89.3019732062328 55 | 67.9720769382965 56 | 63.9704573298836 57 | 56.2640472429427 58 | 70.4765331405108 59 | 72.0803615882728 60 | 97.38311078785 61 | 67.5117822403502 62 | 69.9598216457999 63 | 67.5752386906301 64 | 43.5569726803623 65 | 86.2183632343331 66 | 44.6256489398663 67 | 70.3836236877045 68 | 68.3613421459321 69 | 53.4047360385456 70 | 75.3587631347632 71 | 65.8167893084434 72 | 36.8450247733279 73 | 58.2474048119503 74 | 54.3452409994274 75 | 70.8922017162769 76 | 75.6368604823219 77 | 57.7599208668081 78 | 57.6675516160412 79 | 55.6706053877368 80 | 59.6140127829331 81 | 60.494869551775 82 | 49.9067876841389 83 | 69.0189573610317 84 | 71.3180180493523 85 | 59.6346299667848 86 | 69.7754672178052 87 | 50.5619814793529 88 | 44.9354512046786 89 | 49.201037564726 90 | 57.7760372311394 91 | -------------------------------------------------------------------------------- /data_D1.csv: -------------------------------------------------------------------------------- 1 | width,shear_stress 2 | 20,0.00174 3 | 6,0.01622 4 | 2,0.16065 5 | 1,0.65696 6 | 4,0.02312 7 | -------------------------------------------------------------------------------- /data_D2.csv: -------------------------------------------------------------------------------- 1 | width,velocity 2 | 0.6000000,0.01726544 3 | 0.7484218,0.01507592 4 | 0.9335587,0.02141866 5 | 1.1644929,0.02538495 6 | 1.4525532,0.04250598 7 | 1.8118708,0.03747275 8 | 2.2600728,0.05833458 9 | 2.8191464,0.07434515 10 | 3.5165178,0.09323235 11 | 4.3863979,0.12565372 12 | 5.4714599,0.11249062 13 | 6.8249334,0.19224849 14 | 8.5132152,0.21529261 15 | 10.619127,0.28611650 16 | 13.245977,0.29305465 17 | 16.522631,0.42021676 18 | 20.609830,0.55698482 19 | 25.708077,0.76004248 20 | 32.067477,0.78390300 21 | 40.000000,0.83415913 22 | -------------------------------------------------------------------------------- /data_Ea.csv: -------------------------------------------------------------------------------- 1 | t,C,err 2 | 12,0.27,0.03 3 | 24,0.19,0.02 4 | 36,0.17,0.01 5 | 48,0.13,0.04 6 | 60,0.09,0.03 7 | 72,0.10,0.01 8 | 84,0.09,0.02 9 | 96,0.07,0.02 10 | -------------------------------------------------------------------------------- /data_Eb.csv: -------------------------------------------------------------------------------- 1 | t,C,pos_err,neg_err 2 | 12,0.16,0.03,0.01 3 | 24,0.11,0.02,0.02 4 | 36,0.08,0.01,0.03 5 | 48,0.06,0.02,0.02 6 | 60,0.07,0.03,0.03 7 | 72,0.06,0.01,0.01 8 | 84,0.03,0.02,0.02 9 | 96,0.01,0.02,0.02 10 | -------------------------------------------------------------------------------- /data_Ec.csv: -------------------------------------------------------------------------------- 1 | t,C,neg_err_C,pos_err_C,neg_err_t,pos_err_t 2 | 12,0.37,0.03,0.01,2,2 3 | 24,0.31,0.02,0.02,3,1 4 | 36,0.22,0.01,0.03,2,4 5 | 48,0.23,0.02,0.02,4,2 6 | 60,0.16,0.03,0.03,0,2 7 | 72,0.14,0.01,0.01,2,5 8 | 84,0.13,0.02,0.02,5,4 9 | 96,0.11,0.02,0.02,1,3 10 | -------------------------------------------------------------------------------- /data_F.csv: -------------------------------------------------------------------------------- 1 | K,n,amplitude,duration 2 | 32.5860247920663,3.0650181119781,21.9544436003387,2.32421435318404 3 | 9.01264402390275,2.35883555318762,60.1612164031412,1.00290492935782 4 | 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10.0061684996977,2.14832107689842,51.8987475395389,0.328482888944973 239 | 14.8835591918557,1.44290862034343,27.5280213139187,2.09422281438883 240 | 6.36518114610714,1.418885696892,22.8249130711724,1.00900160163728 241 | 6.55387435784005,0.867976385552192,20.2589693774759,1.9481614605587 242 | 18.7398101351414,1.48146268719019,20.6023781696612,2.57928571113558 243 | 5.29860230618999,1.5755894819387,33.499706349847,1.25519140233096 244 | 9.83486049361585,2.11560770530364,55.9414276507127,0.288323291829843 245 | 8.78986907701208,1.95064051187461,58.501782881899,0.279013766225967 246 | 6.95380094869131,1.4667430968825,20.7799182217287,0.891610721546531 247 | 8.31050080722044,1.43285319512272,43.1279279754577,0.999092665437524 248 | 6.76146958732735,1.57223352255101,59.1589718384256,0.806261040283981 249 | 6.49591871504192,2.29852749077167,36.8405667239904,1.66013940677807 250 | 5.58546135087014,1.80907799390353,58.5513133957796,1.29187518063333 251 | 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-------------------------------------------------------------------------------- /figure_example.R: -------------------------------------------------------------------------------- 1 | 2 | # Set working directory 3 | setwd(getwd()) 4 | 5 | # Libraries/packages 6 | 7 | library(ggplot2) # Grammar of graphics 8 | library(patchwork) # Arranging multiple plots into a grid 9 | library(png) # Load JPEG, PNG and TIFF format 10 | library(scales) # Generic plot scaling methods 11 | library(viridis) # Default color maps from 'matplotlib' 12 | library(grid) # A rewrite of the graphics layout capabilities 13 | library(magick) # graphics and image processing 14 | library(rsvg) # Render svg image into a high quality bitmap 15 | library(ggforce) # Collection of additional ggplot stats + geoms 16 | library(latex2exp) # Use LaTeX Expressions in Plots 17 | 18 | # global font size 19 | base_size=12 20 | 21 | # Manual theme for most panels 22 | # documentation: https://ggplot2.tidyverse.org/reference/theme.html 23 | my_theme <- function() { 24 | theme( 25 | aspect.ratio = 1, 26 | axis.line =element_line(colour = "black"), 27 | 28 | # shift axis text closer to axis bc ticks are facing inwards 29 | axis.text.x = element_text(size = base_size*0.8, color = "black", 30 | lineheight = 0.9, 31 | margin=unit(c(0.3,0.3,0.3,0.3), "cm")), 32 | axis.text.y = element_text(size = base_size*0.8, color = "black", 33 | lineheight = 0.9, 34 | margin=unit(c(0.3,0.3,0.3,0.3), "cm")), 35 | 36 | axis.ticks = element_line(color = "black", size = 0.2), 37 | axis.title.x = element_text(size = base_size, 38 | color = "black", 39 | margin = margin(t = -5)), 40 | # t (top), r (right), b (bottom), l (left) 41 | axis.title.y = element_text(size = base_size, 42 | color = "black", angle = 90, 43 | margin = margin(r = -5)), 44 | axis.ticks.length = unit(-0.3, "lines"), 45 | legend.background = element_rect(color = NA, 46 | fill = NA), 47 | legend.key = element_rect(color = "black", 48 | fill = "white"), 49 | legend.key.size = unit(0.5, "lines"), 50 | legend.key.height =NULL, 51 | legend.key.width = NULL, 52 | legend.text = element_text(size = 0.6*base_size, 53 | color = "black"), 54 | legend.title = element_text(size = 0.6*base_size, 55 | face = "bold", 56 | hjust = 0, 57 | color = "black"), 58 | legend.text.align = NULL, 59 | legend.title.align = NULL, 60 | legend.direction = "vertical", 61 | legend.box = NULL, 62 | panel.background = element_rect(fill = "white", 63 | color = NA), 64 | panel.grid.major = element_blank(), 65 | panel.grid.minor = element_blank(), 66 | plot.title = element_text(size = base_size, 67 | color = "black"), 68 | ) 69 | 70 | 71 | } 72 | 73 | # Panel A ---- 74 | 75 | img1 <- magick::image_flip(magick::image_read("./image1.jpg")) 76 | img2 <- magick::image_flip(magick::image_read("./image2.png")) 77 | 78 | panel_A <- ggplot() + 79 | annotation_custom(rasterGrob(image = img1, 80 | x=0.27, 81 | y=0.49, 82 | width = unit(0.45,"npc"), 83 | height = unit(0.87,"npc")), 84 | -Inf, Inf, -Inf, Inf) + 85 | annotation_custom(rasterGrob(image = img2, 86 | x=0.73, 87 | y=0.49, 88 | width = unit(0.45,"npc"), 89 | height = unit(0.87,"npc")), 90 | -Inf, Inf, -Inf, Inf) + 91 | 92 | geom_ellipse(aes(x0 = 0.25, 93 | y0 = 0.3, 94 | a = 0.1, 95 | b = 0.04, 96 | angle = 0), 97 | color="yellow", 98 | size=1)+ 99 | scale_x_continuous(limits = c(0,1))+ 100 | scale_y_continuous(limits=c(0,1)) + 101 | geom_segment(aes(x=0.15, 102 | xend=0.2, 103 | y=0.75, 104 | yend=0.7), 105 | arrow = arrow(length=unit(0.30,"cm"), 106 | ends="last", 107 | type = "closed"), 108 | size = 1, 109 | color="white") + 110 | geom_segment(aes(x=0.3, 111 | xend=0.9, 112 | y=0.7, 113 | yend=0.7), 114 | arrow = arrow(length=unit(0.30,"cm"), 115 | ends="both", 116 | type = "closed"), 117 | size = 1, 118 | color="red") + 119 | 120 | 121 | annotate("text", x = 0.25, y = 0.5, label = "PNG",color="white") + 122 | annotate("text", x = 0.75, y = 0.5, label = "JPEG",color="white") + 123 | annotate("text", x = 0.25, y = 1, label = "image 1",color="black") + 124 | annotate("text", x = 0.75, y = 1, label = "image 2",color="black") + 125 | annotate("text", x = 0.39, y = 0.07, label = "20~mu*m",color="white",parse=T) + 126 | annotate("text", x = 0.89, y = 0.07, label = "20~mu*m",color="white",parse=T) + 127 | geom_segment(aes(x=0.33,xend=0.45,y=0.03,yend=0.03), size = 2,color="white") + 128 | geom_segment(aes(x=0.83,xend=0.95,y=0.03,yend=0.03),size = 2,color="white") + 129 | theme_void() +# blank plot w/o axes etc. 130 | theme(plot.margin = unit(c(0,0,1,0), "cm"), 131 | aspect.ratio = 1) 132 | 133 | 134 | # Panel B ---- 135 | 136 | data_B = read.csv("./data_B.csv") 137 | 138 | # format data to ggplot's liking 139 | data_B = data.frame("n"=c(data_B$n,data_B$n), 140 | "sample"=c(rep("apical side",nrow(data_B)), 141 | rep("basal side",nrow(data_B))), 142 | "fraction"=c(data_B$fraction1,data_B$fraction2), 143 | "err"=c(data_B$err1,data_B$err2) 144 | ) 145 | 146 | # define lognormal distribution to be called via ggplot2::stat_function 147 | sigma = 0.14 148 | n = seq(3,10,1) 149 | logn_dist <- function(n) exp(-(log(n)-log(6))^2/(2*sigma^2))/(sqrt(2*pi)*sigma*n) 150 | 151 | 152 | 153 | panel_B <- 154 | ggplot(data=data_B,(aes(x=n, # aes: aesthetics 155 | y=fraction, 156 | fill=sample)))+ 157 | geom_bar(stat = "identity", 158 | position=position_dodge()) + # dodge overlapping objects side-to-side 159 | stat_function(fun=logn_dist, 160 | geom="line", 161 | linetype="solid", 162 | aes(x=n, 163 | y=logn_dist(n))) + 164 | geom_errorbar(aes(ymin=fraction-err, 165 | ymax=fraction+err), 166 | width=.2, 167 | position=position_dodge(.9)) + 168 | scale_fill_manual(values=c('#f2a340','#998fc2'))+ 169 | scale_x_continuous(expand = c(0, 0), # prevent gap between origin and first tick 170 | breaks=c(seq(from = min(data_B$n), 171 | to = max(data_B$n), 172 | by = 1)), 173 | limits = c(min(data_B$n),max(data_B$n))) + 174 | scale_y_continuous(expand = c(0, 0), 175 | breaks=c(seq(0,0.6,0.1)), 176 | limits = c(0,0.6) 177 | )+ 178 | my_theme() + 179 | # some extra theme tweaking 180 | theme(legend.position = c(0.18,0.95), 181 | legend.title = element_blank(), 182 | axis.ticks.x=element_blank(), 183 | axis.text.x = element_text(vjust=-0.5), 184 | axis.title.x = element_text(vjust=-0.5), 185 | legend.key.size = unit(0.4, "lines"), 186 | plot.margin = unit(c(0,1,0,0), "cm"), 187 | aspect.ratio = 1 188 | ) + 189 | xlab(expression(paste("number of neighbors ",italic("n")))) + 190 | ylab("fraction of cells (%)") 191 | 192 | 193 | inset_curve <- function(n) 180*(n-2)/n 194 | 195 | # now comes the inset plot 196 | 197 | inset <- 198 | ggplot() + geom_line(aes(n,inset_curve(n))) + 199 | annotate("text", 200 | x=6.5,y=160, 201 | label=TeX("$180^\\circ(\\textit{n}-2)/\\textit{n}$"), 202 | parse=TRUE,size=2) + 203 | scale_x_continuous(expand = c(0, 0), 204 | breaks=c(seq(3,10,1)), 205 | limits = c(3,10)) + 206 | scale_y_continuous(expand = c(0, 0), 207 | breaks=c(seq(60,180,20)), 208 | limits = c(60,180) 209 | ) + 210 | my_theme() + 211 | xlab(expression(italic(n)))+ 212 | # expression doc: https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/plotmath.html 213 | ylab(expression(interior~angle~italic(theta[n])(degree))) + 214 | # some extra theme tweaking 215 | theme( 216 | panel.background = element_blank(), 217 | plot.background = element_blank(), 218 | axis.ticks.length = unit(-0.1, "lines"), # make ticks a bit shorter 219 | axis.title.x = element_text(size = 0.5*base_size, 220 | color = "black", 221 | margin = margin(t = -4)), 222 | # top (t), right (r), bottom (b), left (l) 223 | axis.title.y = element_text(size = 0.5*base_size, 224 | color = "black", angle = 90, 225 | margin = margin(r = -4)), 226 | axis.text.x = element_text(size = base_size*0.5, 227 | color = "black", 228 | lineheight = 0.9, 229 | margin=unit(c(0.1,0.1,0.1,0.1), "cm")), 230 | axis.text.y = element_text(size = base_size*0.5, color = "black", 231 | lineheight = 0.9, 232 | margin=unit(c(0.1,0.1,0.1,0.1), "cm")) 233 | ) 234 | 235 | 236 | # create grob (grid graphical object) from the inset plot 237 | panel_B_inset <- ggplotGrob(x = inset) 238 | 239 | 240 | # now for some regular polygon drawing 241 | polygons <- 242 | ggplot() + 243 | ggforce::geom_regon(aes(x0=c(seq(3,10,1)), 244 | y0=rep(-0.3,8), 245 | sides = c(seq(3,10,1)), 246 | angle=0, r=0.3), 247 | fill=NA, 248 | color="black") + 249 | theme_void() + coord_fixed() 250 | 251 | # finally, we can combine everything to plot panel B 252 | 253 | panel_B <- 254 | panel_B + 255 | annotation_custom(grob = panel_B_inset, 256 | xmin=6.6, xmax=10.1, ymin=0.1, ymax=0.6) + 257 | annotation_custom(grob = ggplotGrob(polygons), 258 | xmin = 2.36, xmax = 10.68, ymin = -0.192, ymax = 0.085) 259 | 260 | 261 | # Panel C ---- 262 | 263 | data_Cwt_E8.5 = read.csv( "./data_Cwt_E8.5.csv") 264 | data_Cwt_E9.5 = read.csv( "./data_Cwt_E9.5.csv") 265 | data_Cwt_E10.5 = read.csv("./data_Cwt_E10.5.csv") 266 | data_Cwt_E11.5 = read.csv("./data_Cwt_E11.5.csv") 267 | data_Cmu_E8.5 = read.csv( "./data_Cmu_E8.5.csv") 268 | data_Cmu_E9.5 = read.csv( "./data_Cmu_E9.5.csv") 269 | data_Cmu_E10.5 = read.csv("./data_Cmu_E10.5.csv") 270 | data_Cmu_E11.5 = read.csv("./data_Cmu_E11.5.csv") 271 | 272 | # format data to ggplot's liking 273 | data_C = data.frame( 274 | "type" = c( 275 | rep( 276 | "wildtype", 277 | nrow(data_Cwt_E8.5) + 278 | nrow(data_Cwt_E9.5) + 279 | nrow(data_Cwt_E10.5) + 280 | nrow(data_Cwt_E11.5) 281 | ), 282 | rep( 283 | "mutant", 284 | nrow(data_Cmu_E8.5) + 285 | nrow(data_Cmu_E9.5) + 286 | nrow(data_Cmu_E10.5) + 287 | nrow(data_Cmu_E11.5) 288 | ) 289 | ), 290 | "dev_stage" = c( 291 | rep("E8.5", nrow(data_Cwt_E8.5)), 292 | rep("E9.5", nrow(data_Cwt_E9.5)), 293 | rep("E10.5", nrow(data_Cwt_E10.5)), 294 | rep("E11.5", nrow(data_Cwt_E11.5)), 295 | rep("E8.5", nrow(data_Cmu_E8.5)), 296 | rep("E9.5", nrow(data_Cmu_E9.5)), 297 | rep("E10.5", nrow(data_Cmu_E10.5)), 298 | rep("E11.5", nrow(data_Cmu_E11.5)) 299 | ), 300 | "trachea_length" = c( 301 | data_Cwt_E8.5[, 1] , 302 | data_Cwt_E9.5[, 1] , 303 | data_Cwt_E10.5[, 1] , 304 | data_Cwt_E11.5[, 1] , 305 | data_Cmu_E8.5[, 1] , 306 | data_Cmu_E9.5[, 1] , 307 | data_Cmu_E10.5[, 1] , 308 | data_Cmu_E11.5[, 1] 309 | ) 310 | ) 311 | 312 | panel_C <- 313 | ggplot(data=data_C, 314 | aes(x=dev_stage, 315 | y=trachea_length, 316 | fill=type))+ 317 | geom_boxplot() + 318 | geom_point(position=position_jitterdodge(), # jitter for h-dist, dodge for grouped dists 319 | pch=21, 320 | alpha=0.4) + # transparency 321 | scale_x_discrete(limits=c("E8.5","E9.5","E10.5","E11.5")) + 322 | scale_fill_manual(values=c('#f2a340','#998fc2'))+ # custom colors in hex code 323 | my_theme() + 324 | theme(legend.position = c(0.18,0.95), 325 | legend.title = element_blank(), 326 | legend.key = element_blank() 327 | ) + 328 | scale_y_continuous(expand = c(0, 0), 329 | breaks=c(seq(20,120,by=20)), 330 | limits = c(20,120) 331 | )+ 332 | xlab("developmental stage (days)") + 333 | ylab(TeX("tracheal length ($\\mu$m)")) 334 | 335 | # Panel D ---- 336 | 337 | data_D1 = read.csv("./data_D1.csv") 338 | data_D2 = read.csv("./data_D2.csv") 339 | # format data to ggplot's liking 340 | data_D = data.frame("width"=c(data_D1$width,data_D2$width), 341 | "unit"=c(rep("shear_stress",nrow(data_D1)), 342 | rep("velocity",nrow(data_D2))), 343 | "value"=c(data_D1$shear_stress,data_D2$velocity) 344 | ) 345 | 346 | curve_D1 = data.frame(width=data_D1$width, 347 | shear_stress=33.28/(pi*18*data_D1$width^2)) 348 | 349 | 350 | panel_D1 <- ggplot(data=data_D1, 351 | aes(x=width, 352 | y=shear_stress)) + 353 | geom_point(fill="red", 354 | size=3, 355 | pch=22) + 356 | geom_line(data=curve_D1) + 357 | theme_void()+ 358 | scale_x_log10(expand=c(0,0), # prevent gap between origin and first tick 359 | breaks=c(0.5,1,2,5,10,20,50), 360 | labels=c(0.5,1,2,5,10,20,50), 361 | limits=c(0.5,50)) + 362 | scale_y_log10( expand = c(0, 0), 363 | # using trans_format from the scales package, but one can also use expressions 364 | labels = trans_format('log10', math_format(10^.x)), 365 | breaks=c(0.001,0.01,0.1,1), 366 | limits = c(0.001,1) 367 | ) + 368 | annotation_logticks(sides = "l") + 369 | theme( 370 | line = element_blank(), 371 | # exclude everything outside axes bc it messes with positioning of grob in panel_D 372 | text = element_blank(), 373 | title = element_blank(), 374 | axis.line.y = element_line(colour = "black"), 375 | aspect.ratio = 1 376 | ) + 377 | ylab("shear stress (Pa)") 378 | 379 | 380 | 381 | panel_D <- 382 | ggplot(data=data_D2, 383 | aes(x=width, 384 | y=velocity))+ 385 | # add plot of first dataset as grob as a trick to introduce two y-axes with different scalings 386 | annotation_custom(ggplotGrob(panel_D1)) + 387 | geom_point(fill="blue", 388 | size=3, 389 | pch=21) + 390 | my_theme() + 391 | geom_line(color="blue") + 392 | geom_vline(xintercept = 1.1, 393 | linetype="dashed") + 394 | geom_hline(yintercept = 0.9, 395 | linetype="dashed") + 396 | scale_x_log10(expand=c(0,0), 397 | breaks=c(0.5,1,2,5,10,20,50), 398 | labels=c(0.5,1,2,5,10,20,50), 399 | limits=c(0.5,50)) + 400 | annotation_logticks(sides = "b") + 401 | scale_y_continuous(expand = c(0,0), 402 | breaks = seq(0,1,0.1), 403 | limits = c(0,1), 404 | # putting the y axis of the second plot to the right 405 | position = "right", 406 | # now the secondary axis becomes the left axis 407 | # we need the axis text+title for panel_D1 408 | # They were excluded in panel_D1 bc they were messing with the positioning 409 | sec.axis = sec_axis(~., 410 | name = "shear stress (Pa)", 411 | # rescale breaks bc sec_axis inherits scale from primary y axis 412 | breaks=rescale(c(-3,-2,-1,0), 413 | to = c(0,1)), 414 | labels = c(expression("10"^"-3", 415 | "10"^"-2", 416 | "10"^"-1", 417 | "10"^"0"))) 418 | 419 | ) + 420 | # some extra theme tweaking 421 | theme( 422 | aspect.ratio = 1, 423 | plot.margin = unit(c(0.1,0,0,0.5), "cm"), # to match other panels 424 | axis.title.y = element_text(margin = margin(r=1)), 425 | axis.text.y = element_text(margin = margin(r=6)), 426 | axis.text.y.right = element_text(margin = margin(l=7)), 427 | axis.title.y.right = element_text(angle = 90) 428 | ) + 429 | #xlab(expression(lumen~width~(mu*m))) + 430 | xlab(TeX("lumen width ($\\mu$m)")) + 431 | ylab("relative flow velocity") + 432 | annotate(geom = "text",x =6 ,y =0.85 ,label = "italic(tau) == 0.5~Pa",parse=T) + 433 | annotate(geom = "text",x =1.4 ,y =0.4 ,label = "italic(b) == 1.1*mu*m",parse=T,angle=90) + 434 | annotate(geom = "text",x =6.5 ,y =0.6 ,label = "italic(tau) == frac(4*italic(mu*Q),pi*italic(a*b)^2)",parse=T) 435 | 436 | 437 | 438 | # Panel E ---- 439 | 440 | data_Ea = read.csv("./data_Ea.csv") 441 | data_Eb = read.csv("./data_Eb.csv") 442 | data_Ec = read.csv("./data_Ec.csv") 443 | data_E = data.frame("gene"=c(rep("gene a",nrow(data_Ea)), 444 | rep("gene b",nrow(data_Eb)), 445 | rep("gene c",nrow(data_Ec))), 446 | "t"=c(data_Ea$t,data_Eb$t,data_Ec$t), 447 | "C"=c(data_Ea$C,data_Eb$C,data_Ec$C), 448 | "pos_err"=c(data_Ea$err,data_Eb$pos_err,data_Ec$pos_err_C), 449 | "neg_err"=c(data_Ea$err,data_Eb$neg_err,data_Ec$neg_err_C), 450 | "pos_err_t"=c(rep(NA, nrow(data_Ea)),rep(NA, nrow(data_Eb)),data_Ec$pos_err_t), 451 | "neg_err_t"=c(rep(NA, nrow(data_Ea)),rep(NA, nrow(data_Eb)),data_Ec$neg_err_t) 452 | ) 453 | 454 | f1 = function(t) 0.2*exp(-t/48) 455 | f2 = function(t) 0.3*exp(-t/60) 456 | f3 = function(t) 0.4*exp(-t/72) 457 | t = seq(0,96,1) 458 | 459 | ribbon = data.frame( 460 | "f2" = 0.3*exp(-t/60), 461 | "t" = t 462 | ) 463 | 464 | manual_pch =c(15,16,17) # available pch: type ?pch 465 | 466 | panel_E <- ggplot(data=data_E) + 467 | geom_point(aes(x=t,y=C,pch=factor(gene)),size=2) + 468 | geom_ribbon(data=ribbon, aes(x=t,ymin=0.85*f2,ymax=1.15*f2), 469 | fill="black",alpha=0.1) + 470 | stat_function(fun=f1, geom="line",linetype="dashed") + 471 | stat_function(fun=f2, geom="line") + 472 | stat_function(fun=f3, geom="line",linetype="dotted") + 473 | geom_errorbar(aes(x=t,ymin=C-neg_err, ymax=C+pos_err), 474 | width=2) + 475 | geom_errorbarh(aes(y=C,xmin=t-neg_err_t,xmax=t+pos_err_t))+ 476 | scale_shape_manual(values=manual_pch) + 477 | my_theme() + theme(legend.title=element_blank())+ 478 | theme(legend.position = c(0.9,0.95)) + 479 | scale_x_continuous(expand = c(0, 0), 480 | breaks = c(seq(0,96,12)), 481 | limits = c(0,96) 482 | ) + 483 | scale_y_continuous(expand = c(0, 0), 484 | breaks = c(seq(0,0.4,0.05)), 485 | limits = c(0,0.4) 486 | ) + 487 | theme( 488 | panel.grid.major = element_line("gray95", size = 0.1), 489 | # putting label closer to axis bc exponent makes it bigger 490 | axis.title.y = element_text(margin = margin(r = -9)) 491 | ) + 492 | xlab("time (h)") + 493 | ylab(expression(paste("concentration (mmol",~cm^-3,")"))) + 494 | coord_cartesian(clip = "off") # to allow for plotting outside axes 495 | 496 | 497 | # Panel F ---- 498 | 499 | data_F = read.csv("./data_F.csv") 500 | 501 | panel_F <- ggplot(data=data_F, 502 | aes(x=K,y=n, 503 | size=amplitude, 504 | fill=duration))+ 505 | geom_point(pch=21) + 506 | my_theme() + 507 | 508 | scale_x_continuous(expand = c(0, 0), 509 | trans = 'log10', 510 | labels=c(1,10,100), 511 | breaks=c(1,10,100), 512 | limits = c(1,100)) + 513 | scale_y_continuous(expand = c(0, 0), 514 | breaks=c(seq(0,4,by=0.5)), 515 | limits = c(0,4)) + 516 | annotation_logticks(sides='b') + 517 | scale_size(range = c(1, 3)) + 518 | scale_fill_viridis(option="D") + # a color palette from the viridis package 519 | theme( legend.position = c(0.9,0.35)) + 520 | coord_cartesian(clip = "off") + 521 | xlab(expression(paste("dissociation constant",~~italic("K")," (M)"))) + 522 | ylab("Hill coefficient n") 523 | 524 | 525 | 526 | # Plotting ---- 527 | 528 | wrap_plots(panel_A,panel_B,panel_C,panel_D,panel_E,panel_F) + 529 | plot_annotation(tag_levels = 'A') 530 | 531 | # RStudio instructions for saving the final plot: 532 | # Whenever you resize the 'Plots' window, click 'refresh current plot' 533 | # For best results save as SVG with a resolution of 1148 x 686 534 | # open SVG in inkscape, (do some optional post-processing) and 'save as' PDF 535 | 536 | -------------------------------------------------------------------------------- /figure_example.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/macromeer/scifig_plot_examples_R/08ea31cb7ccab53de315275b3807360617abedd4/figure_example.pdf -------------------------------------------------------------------------------- /figure_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/macromeer/scifig_plot_examples_R/08ea31cb7ccab53de315275b3807360617abedd4/figure_example.png 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