Interactive RShiny Reports – Independence and Autonomy in Medical Data Visualization


Abstract

The article discusses the use of the R language, especially the RShiny tool, to create interactive reports in the field of medical data analysis. The authors emphasize the need for an interdisciplinary approach to teaching statistics among medical students. An alternative to traditional static reports was presented, proposing the creation of interactive web applications that enable exploration, analysis and visualization of medical data changing in real time. The use of the R language as an open source tool allows for the development of medical students' competences in the field of data analysis and the adaptation of research tools to individual needs. A draft lesson plan using sample medical data on cervical cancer was also presented, along with a proposal for specific analyzes of these data and their visualization using interactive RShiny reports. The article ends with a discussion on the role of learning the R language in the education of students of Polish medical universities and the need to expand the educational offer for them with courses in data analysis in an open source environment.


Keywords

RShiny; R; data visualization; interactive report; statistics; medical teaching

ABM, Creation and development of Regional Digital Medicine Centers–2023–Medical Research Agency, konkurs ABM. https://www.abm.gov.pl/pl/konkursy/archiwalne-nabory-1/2023/1918, Tworzenie-i-rozwoj-Regionalnych-Centrow-Medycyny-Cyfrowej.html.

Biecek, P. (2013). Data analysis with R program. https://ksiegarnia.pwn.pl/Analiza-dani-z-programem-R,68467550,p.html.

Biecek, P. (2017). Guide to the R package – Publishing House of the Warsaw University of Technology.

http://www.wydawnictwopw.pl/index.php?s=karta&id=3217.

Central Statistical Office / Thematic areas / Health. (n.d.). Retrieved 7 January 2024, from https://stat.gov.pl/obszary-tematyczne/zdrowie/.

CRAN:Manuals. (n.d.). Retrieved December 28, 2023, from https://cran.r-project.org/manuals.html

Daniel Adrian | IntroStat Shiny Apps. (n.d.). Retrieved 28 December 2023, from https://facweb.gvsu.edu/adriand1/215apps.html.

Farrel, A., Li, P., Veenbergen, S., Patel, K., Maris, J. M., & Leonard, W. J. (2023). ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery. BMC Bioinformatics, 24 (1), 303. https://doi.org/10.1186/s12859-023-05420-y.

Fawcett, L. (2018). Using Interactive Shiny Applications to Facilitate Research-Informed Learning and Teaching. Journal of Statistics Education, 26 (1), 2–16. https://doi.org/10.1080/10691898.2018.1436999.

Fernandes, Kelwin, Cardoso, Jaime, & Fernandes, J. (2017). Cervical cancer (Risk Factors).

Published: UCI Machine Learning Repository. https://archive.ics.uci.edu/dataset/383/cervical+cancer+risk+factors.

Garfield, J. & Ben-Zvi, D. (2007). How Students Learn Statistics Revisited: A Current Review of Research on Teaching and Learning Statistics. International Statistical Review, 75 (3), 372–396. https://doi.org/10.1111/j.1751-5823.2007.00029.x.

Gov.pl: How to get access to SRP - Ministry of Digitization–Gov.pl portal. (n.d.). Retrieved 7 January 2024, from https://www.gov.pl/web/cyfryzacji/jak-uzyskac-dostep-do-srp.

Grześkowiak, M., Chudzicka-Strugała, I., Zwoździak, B., Swora-Cwynar, E., Nijakowski, K., Jokiel, M., & Roszak, M. (2020). E-learning During the Coronavirus Pandemic – Creating Educational Resources for Teaching Medical Students. Studies in Logic, Grammar and Rhetoric, 64 (1), 77–97. https://doi.org/doi:10.2478/slgr-2020-0041.

Guzik, P. & Więckowska, B. (2023). Data distribution analysis – a preliminary approach to quantitative data in biomedical research. Journal of Medical Science, 92(2):e869. https://doi.org/10.20883/medical.e869.

Hegarty, M. (2004). Dynamic visualizations and learning: Getting to the difficult questions. Learn Instr, 14. https://doi.org/10.1016/j.learninstruc.2004.06.007.

Discover! Disclose! Explain! A collection of essays on the art of presenting data – PDF, (2014). https://www.wuw.pl/product-pol-6322-Odkryc-Ujawniac-Objasniac-Zbior-esejow-o-sztuce-prezentowania-anych-PDF.html.

Jamie, D. M. (2002). Using Computer Simulation Methods to Teach Statistics: A Review of the Literature. Journal of Statistics Education, 10 (1), null-null. https://doi.org/10.1080/10691898.2002.11910548.

Jiang, Z., Cao, W., Chu, H., Bazerbachi, F., & Siegel, L. (2023). RIMeta: An R shiny tool for estimating the reference interval from a meta-analysis. Research Synthesis Methods, 14 (3), 468–478. https://doi.org/10.1002/jrsm.1626.

Kumar, A., Kumar, P., Palvia, S. C. J., & Verma, S. (2017). Online education worldwide: Current status and emerging trends. Journal of Information Technology Case and Application Research, 19. https://doi.org/10.1080/15228053.2017.1294867.

Laureaci_szp_2023_2.pdf. (n.d.). Retrieved 22 December 2023, from https://www.umb.edu.pl/photo/pliki/aktualnosci/2023/laureaci_szp_2023_2.pdf.

Liebig, P., Pröhl, H., Sudhaus-Jörn, N., Hankel, J., Visscher, C., & Jung, K. (2022). Interactive, Browser-Based Graphics to Visualize Complex Data in Education of Biomedical Sciences for Veterinary Students. Medical Science Educator, 32 (6), 1323–1335. https://doi.org/10.1007/s40670-022-01613-x.

Liu, L., Xie, Y., Yang, H., Lin, A., Dong, M., Wang, H., Zhang, C., Liu, Z., Cheng, Q., Zhang, J., Yuan, S., & Luo, P. (2023). HPVTIMER: A shiny web application for tumor immune estimation in human papillomavirus-associated cancers. IMeta, 2 (3), e130. https://doi.org/10.1002/imt2.130.

Milewski, R. & Roszak, M. (2023). The Issue of Selection of Appropriate Methodology and Methods of Graphical Representation of Data in Biomedical Research. Studies in Logic, Grammar and Rhetoric, 68 (1), 123–131. https://doi.org/10.2478/slgr-2023-0006.

Murray, S. (2014). Interactive data visualization (1–1 online resource). Helion; WorldCat. http://www.myilibrary.com?id=610946.

Pfannkuch, M. (2011). The Role of Context in Developing Informal Statistical Inferential Reasoning: A Classroom Study. Mathematical Thinking and Learning, 13 (1–2), 27–46. https://doi.org/10.1080/10986065.2011.538302.

The Polish Mbaza AI application is one of the best in the world according to UNESCO. (2023, December 28). MamStartup. https://mamstartup.pl/polska-aplikacja-mbaza-ai-chodzi-z-najlepszych-na-swiecie-wg-unesco/.

Roszak, M., Leszczyński, P., Starowicz, K., Wiktorzak, P., Torres, K., Świniarski, P., & Kononowicz, A. (2020). E-learning in medical education. Warsaw: Warsaw University of Technology. https://ruj.uj.edu.pl/xmlui/handle/item/266266.

Jagiellonian University Medical College syllabus. Retrieved 28 December 2023, from https://sylabus.cm-uj.krakow.pl/pl/6/1/7/1/1?masterElement.

Wang, C., Govindarajan, H., Katsonis, P., & Lichtarge, O. (2023). ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis. Bioinformatics, 39 (8), btad467. https://doi.org/10.1093/bioinformatics/btad467.

Wang, S. L., Zhang, A. Y., Messer, S., Wiesner, A., & Pearl, D. K. (2021). Student-Developed Shiny Applications for Teaching Statistics. Journal of Statistics and Data Science Education, 29 (3), 218–227. https://doi.org/10.1080/26939169.2021.1995545.

Wickham, H. (2021). Welcome | Mastering Shiny (2021st ed.). https://mastering-shiny.org/.

Wickham, H. (2023). R for Data Science, 2nd Edition [Book]. https://www.oreilly.com/library/view/r-for-data/9781492097396/.

Download

Published : 2024-04-10


MarcinkowskaJ., & RoszakM. (2024). Interactive RShiny Reports – Independence and Autonomy in Medical Data Visualization. International Journal of Research in E-Learning, 1-24. https://doi.org/10.31261/IJREL.2024.10.1.03

Justyna Marcinkowska  justyna@ump.edu.pl
Poznan University of Medical Sciences  Poland
https://orcid.org/0000-0002-6510-5538
Magdalena Roszak 
Poznan University of Medical Sciences  Poland
https://orcid.org/0000-0001-6495-6771




Creative Commons License

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

The Copyright Owners of the submitted texts grant the Reader the right to use the pdf documents under the provisions of the Creative Commons 4.0 International License: Attribution-Share-Alike (CC BY SA). The user can copy and redistribute the material in any medium or format and remix, transform, and build upon the material for any purpose.

1. License

The University of Silesia Press provides immediate open access to journal’s content under the Creative Commons BY-SA 4.0 license (http://creativecommons.org/licenses/by-sa/4.0/). Authors who publish with this journal retain all copyrights and agree to the terms of the above-mentioned CC BY-SA 4.0 license.

2. Author’s Warranties

The author warrants that the article is original, written by stated author/s, has not been published before, contains no unlawful statements, does not infringe the rights of others, is subject to copyright that is vested exclusively in the author and free of any third party rights, and that any necessary written permissions to quote from other sources have been obtained by the author/s.

If the article contains illustrative material (drawings, photos, graphs, maps), the author declares that the said works are of his authorship, they do not infringe the rights of the third party (including personal rights, i.a. the authorization to reproduce physical likeness) and the author holds exclusive proprietary copyrights. The author publishes the above works as part of the article under the licence "Creative Commons Attribution-ShareAlike 4.0 International".

ATTENTION! When the legal situation of the illustrative material has not been determined and the necessary consent has not been granted by the proprietary copyrights holders, the submitted material will not be accepted for editorial process. At the same time the author takes full responsibility for providing false data (this also regards covering the costs incurred by the University of Silesia Press and financial claims of the third party).

3. User Rights

Under the CC BY-SA 4.0 license, the users are free to share (copy, distribute and transmit the contribution) and adapt (remix, transform, and build upon the material) the article for any purpose, provided they attribute the contribution in the manner specified by the author or licensor.

4. Co-Authorship

If the article was prepared jointly with other authors, the signatory of this form warrants that he/she has been authorized by all co-authors to sign this agreement on their behalf, and agrees to inform his/her co-authors of the terms of this agreement.

I hereby declare that in the event of withdrawal of the text from the publishing process or submitting it to another publisher without agreement from the editorial office, I agree to cover all costs incurred by the University of Silesia in connection with my application.