Generating colorblind-friendly scatter plots for single-cell data
- Department of Electrical and Computer Engineering, A. James Clark School of Engineering, The University of Maryland, United States
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, United States
- Convergence Institute, Johns Hopkins University, United States
- Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine, United States
- Department of Applied Mathematics and Statistics, Johns Hopkins University, United States
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, United States
Decision letter
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Jungmin ChoiReviewing Editor; Korea University College of Medicine, Republic of Korea
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Mone ZaidiSenior Editor; Icahn School of Medicine at Mount Sinai, United States
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Daniel G BunisReviewer; University of California, San Francisco, United States
Our editorial process produces two outputs: i) public reviews designed to be posted alongside the preprint for the benefit of readers; ii) feedback on the manuscript for the authors, including requests for revisions, shown below. We also include an acceptance summary that explains what the editors found interesting or important about the work.
Decision letter after peer review:
Thank you for submitting your article "scatterHatch: an R/Bioconductor package for generating colorblind-friendly scatter plots for single-cell data" for consideration by eLife. Your article has been reviewed by 2 peer reviewers, one of whom is a member of our Board of Reviewing Editors, and the evaluation has been overseen by Mone Zaidi as the Senior Editor. The following individual involved in the review of your submission has agreed to reveal their identity: Daniel G Bunis (Reviewer #2).
The reviewers have discussed their reviews with one another, and the Reviewing Editor has drafted this to help you prepare a revised submission.
Essential revisions:
1) In Figure 1, it is a little hard to see the yellow-colored points in the sparse points demonstration. Perhaps the colors could be cycled, or one of the other regions could be used, in order for a darker color to be used for this demonstration.
2) The manuscript appears well written and where there are shortcomings would be in helping inexperienced r users navigate the add-on package. I would recommend a supplementary guide that helps novice users install and use the package--this would help strive for greater inclusiveness of individuals with varying levels of skill in r.
3) The pattern-overlay framework could be expanded and applied to other plots such as alluvial plots, violin plots, etc in addition to dim plots.
Reviewer #2 (Recommendations for the authors):
scatterHatch seems a well-constructed R package, and the manuscript is well-written. I believe this manuscript will be a very valuable addition to the field, especially because scatterHatch's system provides aid to viewers with monochromatic vision, an aid that even other common CVD-aware visualization tools fail to provide.
https://doi.org/10.7554/eLife.82128.sa1Author response
Essential revisions:
1) In Figure 1, it is a little hard to see the yellow-colored points in the sparse points demonstration. Perhaps the colors could be cycled, or one of the other regions could be used, in order for a darker color to be used for this demonstration.
We have revised the illustration in Figure 1 to show a different cell group with darker colors for the demonstration of the scatterHatch workflow.
2) The manuscript appears well written and where there are shortcomings would be in helping inexperienced r users navigate the add-on package. I would recommend a supplementary guide that helps novice users install and use the package--this would help strive for greater inclusiveness of individuals with varying levels of skill in r.
We agree that a user guide will be really helpful! We are including a supplementary guide based on the scatterHatch package vignette in the revised submission.
3) The pattern-overlay framework could be expanded and applied to other plots such as alluvial plots, violin plots, etc in addition to dim plots.
Such pattern overlays can be obtained using existing packages like the ggpattern package available on github. However, we agree with the reviewer’s suggestion that future work could include creating a multi-purpose colorblind friendly visualization software, which include CVD-friendly strategies such as scatterHatch, ggpattern, etc.
https://doi.org/10.7554/eLife.82128.sa2Download links
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Generating colorblind-friendly scatter plots for single-cell data
eLife 11:e82128.
https://doi.org/10.7554/eLife.82128
