rOpenSci | Data Visualization

Data Visualization

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Preliminary Visualisation of Data

Nicholas Tierney
Description

Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using ggplot2.

Scientific use cases
  1. Tierney, N. (2017). visdat: Visualising Whole Data Frames. The Journal of Open Source Software, 2(16), 355. https://doi.org/10.21105/joss.00355
  2. Tierney, N. J., & Cook, D. H. (2018). Expanding tidy data principles to facilitate missing data exploration, visualization and assessment of imputations. arXiv preprint arXiv:1809.02264. https://arxiv.org/abs/1809.02264
  3. Stuijfzand, S., Garthus-Niegel, S., & Horsch, A. (2020). Parental Birth-Related PTSD Symptoms and Bonding in the Early Postpartum Period: A Prospective Population-Based Cohort Study. Frontiers in Psychiatry, 11. https://doi.org/10.3389/fpsyt.2020.570727
  4. Borg, D. N., Nguyen, R., & Tierney, N. J. (2020). Missing Data: Current Practice in Football Research and Recommendations for Improvement. https://doi.org/10.31236/osf.io/fhwcu
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Interactive, Complex Heatmaps

Alicia Schep
Description

Make complex, interactive heatmaps. iheatmapr includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap() function for making relatively standard heatmaps.

Scientific use cases
  1. Gershanov, S., Toledano, H., Michowiz, S., Barinfeld, O., Pinhasov, A., Goldenberg-Cohen, N., & Salmon-Divon, M. (2018). MicroRNA&ndash,mRNA expression profiles associated with medulloblastoma subgroup 4. Cancer Management and Research, Volume 10, 339–352. https://doi.org/10.2147/cmar.s156709
  2. Ruiz, J. L., Tena, J. J., Bancells, C., Cortés, A., Gómez-Skarmeta, J. L., & Gómez-Díaz, E. (2018). Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum. Nucleic Acids Research. https://doi.org/10.1093/nar/gky643
  3. Ott, C. J., Federation, A. J., Schwartz, L. S., Kasar, S., Klitgaard, J. L., Lenci, R., … Bradner, J. E. (2018). Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia. Cancer Cell. https://doi.org/10.1016/j.ccell.2018.11.001
  4. Kim, K. W., Allen, D. W., Briese, T., Couper, J. J., Barry, S. C., … Colman, P. G. (2019). Distinct gut virome profile of pregnant women with type 1 diabetes in the ENDIA study. Open Forum Infectious Diseases. https://doi.org/10.1093/ofid/ofz025
  5. Reyes, A. L. P., Silva, T. C., Coetzee, S. G., Plummer, J. T., Davis, B. D., Chen, S., … Jones, M. R. (2019). GENAVi: a shiny web application for gene expression normalization, analysis and visualization. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-019-6073-7
  6. Kim, K. W., Allen, D. W., Briese, T., Couper, J. J., Barry, S. C., … Colman, P. G. (2020). Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes. Pediatric Diabetes, 21(2), 271–279. https://doi.org/10.1111/pedi.12952
  7. Meng, S., Zhan, S., Dou, W., & Ge, W. (2019). The interactome and proteomic responses of ALKBH7 in cell lines by in-depth proteomics analysis. Proteome Science, 17(1). https://doi.org/10.1186/s12953-019-0156-x
  8. Shi, L., Tian, H., Wang, P., Li, L., Zhang, Z., Zhang, J., & Zhao, Y. (2020). Spaceflight and simulated microgravity suppresses macrophage development via altered RAS/ERK/NFκB and metabolic pathways. Cellular & Molecular Immunology. https://doi.org/10.1038/s41423-019-0346-6
  9. Caseys, C., Gongjun Shi, Nicole Soltis, Raoni Gwinner, Jason Corwin, Susanna Atwell, Daniel Kliebenstein. 2020. Quantitative interactions drive Botrytis cinerea disease outcome across the plant kingdom. bioRxiv preprint 507491; https://doi.org/10.1101/507491
  10. Wang, Y., Zhang, X., Song, Q., Hou, Y., Liu, J., Sun, Y., & Wang, P. (2020). Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model. Alzheimer’s Research & Therapy, 12(1). https://doi.org/10.1186/s13195-020-00598-2
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