By Víctor Quesada https://orcid.org/0000-0002-8398-3457

Review Details

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Reviewer has chosen not to be Anonymous

Summary of paper in a few sentences:

The manuscript describes the port of BioVenn to R and Python, which allows users to easily automate their operations with the algorithm.
The work describes an update of a tool for proportional Venn diagrams, which has been widely used. The manuscript reviews existing tools for similar uses with fairness, showing strengths and weaknesses. I only have two small observations in this regard.
• First, even though it is not properly a Venn diagram generator, the manuscript should mention UpSetR. I see no need to change the tables or figures, but a small description would improve the manuscript.
• Second, nVenn has both an R interface (nVennR) and a web interface.

Regarding the technical merits of the manuscript:
• One feature I consider unique and useful in BioVenn is the automatic mapping of Affymetrix and EntrezGene IDs to Ensembl IDs. However, I have not found this option while using the R interface, and it is not mentioned in the vignette. If this is not available, the author should delete the last sentence of the first paragraph of Results. If it is available, the author should add the procedure to the manuscript and the documentation.
• The manuscript should make it clear that exact proportionality for more than two sets is not achievable with circles. This is not a limitation of the program. In the example provided, if we delete the "1007_s_at" element in “list_z”, the “list_x intersect list_z” overlap should be zero. However, the overlap in the result is nonzero (the region is not labeled, which informs the user of this discrepancy). For the sake of completeness, this limitation should be pointed out in the manuscript.

Regarding presentation:
• The text, figures, and tables of the work are accessible, pleasant to read, clearly structured, and free of major errors in grammar or style. I would point one small error at page 9: “This also makes sure that the user cannot mathematically impossible numbers…” should be “This also ensures that the user cannot input mathematically impossible numbers…”

Reasons to accept:

The tool described is widely used and has some unique features that may be interesting to scientists.

Reasons to reject:

I do not find any issues important enough to reject the manuscript.

Nanopublication comments:

Further comments:

I have left five points with potential improvements to the manuscript. They are all minor and easily verifiable.

By Michael Hinterberg https://orcid.org/0000-0003-0693-7075

Review Details

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Reviewer has chosen not to be Anonymous

Summary of paper in a few sentences:

Tim Hulsen provides an updated, straightforward R and Python package to support drawing of area-proportional Venn diagrams of up to 3 overlapping lists. Biological lists can be mapped from Entrez/Affy to Enembl before calculating overlaps. The functions are parameterized so layout elements such as labels, font, colour, etc. can be adjusted. Additionally, the functions return the overlapping list permutations.

Reasons to accept:

When working directly within R or Python, BioVenn appears to provide a quick and easy option for creating presentation and manuscript-worthy images. This is especially true within the specific use case of working with and between supported EntrezGene, Affymetrix, and Ensembl IDs. In those use cases, it is easier than using a web-based option, and the area-proportional output can be helpful for rapid visual insight.

Reasons to reject:

The novelty of this tool is the biggest drawback. It appears to be an API change to an existing tool more than a truly novel approach. The "Bio" part is of limited use (or not properly explained), as a user with R, for example, could pre-process ID translations if desired, and a biological use-case is not strongly described in this paper. For general use, it is unclear if there are substantial differences between this and 'eulerr' for visual output in R. There are a few formatting parameters that appear to be supported in this tool (BioVenn), and of course it works natively in R and Python, but eulerr has a similar interface and allows for >3 sets. While the cross-platform support in R and Python may be helpful for some, a natural R improvement would be a tidy data/ggplot API that supported additional overlapping sets, as well as an easier layered graphical interface such that layout elements can easily be 'themed' instead of a lengthy and specific argument list. Additionally, while the area-proportional plots seem intuitive and visually attractive, the paper could benefit for an insight-driven/workflow use case that showed the utility of area-proportionality; for example, real-world cases where equal-sized circles could be misleading, or where proportionality instead improved cognition.

In summary, this is an easy and potentially useful tool for specific use cases, with limited additional support compared to alternatives (although the alternatives are nicely shown). A scientific paper, as opposed to a Vignette/application note, would benefit more strongly from a specific use-case example or literature examples showing, or at least suggesting, the insight gained by presenting proportional Venn diagrams, which would be more compelling material for a paper than a description of all of the functional arguments.

Nanopublication comments:

Further comments:

By Emma Beauxis-Aussalet https://orcid.org/0000-0002-4657-892X

Review Details

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Reviewer has chosen not to be Anonymous

Summary of paper in a few sentences:

The paper introduces R and python libraries for drawing Venn diagram, with areas proportional to the size of each set and subset.
Compared to existing libraries, the new libraries include: automatic mapping of IDs into sets/subsets, choice of displaying set size as number or percentage, full adjustment of color and text aesthetics (incl. interactive label positioning, with SVG option). They also include a mapping of "Affymetrix and EntrezGene IDs to Ensembl IDs." which is not clearly specified.

Reasons to accept:

The novelty of the new libraries is clear, the new functionalities seem relevant for the bioinformatics community, and beyond. The review of existing libraries is clear and comprehensive. The paper is clear and well-written.

Reasons to reject:

The mapping of mapping of "Affymetrix and EntrezGene IDs to Ensembl IDs" remains unspecified, and a few other points need clarification (see below).

it is important to briefly specify the mapping of "Affymetrix and EntrezGene IDs to Ensembl IDs" or else readers are not provided with all information needed to understand what the libraries does. If it is unclear what this special mapping does, then it is unclear how to reuse the libraries, especially for users who do not display bioinformatics data (and would not read citation [15] to fully understand the mapping). The potential reuse for use cases other than bioinformatics needs to be clarified (e.g., need to disable the "special" mapping? or just avoid ID labels in the typical bioinformatics format?).

Nanopublication comments:

Further comments:

Direct links to the reference manuals should be added (e.g., for R https://cran.r-project.org/web/packages/BioVenn/BioVenn.pdf).

Introduction:
- It ends with " the following paragraphs" but describes only the next section. Having on overview of all sections would be clearer.
- The "ID mapping" functionality should also be specified in the introduction, both the "basic mapping" into the "13 sets" and the mapping of "Affymetrix and EntrezGene IDs to Ensembl IDs" (e.g., described with a brief sentence).

- Section 3.1: "‘drag-and-drop’ functionality of text and numbers" -> "‘drag-and-drop’ functionality for repositioning labels"
- Section 4: "Generate lists of the thirteen possible sets, and count them" -> "and count the number of elements per set"
- Section 4: "Calculate the angles of the XYZ triangle" -> specify what is the XYZ triangle (I understand that it's the centre of the 3 circles, but the reader is left to interpret what the "XYZ triangle" is).
- Section 5.3: "Xenopus" -> "frog" for consistency with other labels of animals.
- Table 2: Improve the layout
- Page 9: recap why areas in other libraries are "inaccurate". Also fix the syntax of "the user cannot mathematically impossible numbers" -> "the user cannot [input] impossible numbers