This article is receiving a lot of attention on social media [1]. Almost all of the comments are negative. This indicates that the decision to publish was a major error on the part of the reviewers and editors. Indeed, it would seem to be in direct conflict with many of the PLoS ONE guidelines for software papers [2].

1. The tool must be of use to the community and must present a proven advantage over existing alternatives, where applicable. Recapitulation of existing methods, software, or databases is not useful and will not be considered for publication.

Clearly, this article is a recapitulation of existing methods and software. It is a method for drawing heat maps; a well-known methodology with many implementations. The figure presented in the article can be generated easily using numerous existing methods (e.g. [3]). The authors themselves allude to one such tool, the R package "fields" (first published 2001 [4]). This package even includes a function named "quilt.plot". Furthermore, heat maps with age and time axes date back to at least 1984, described as "Lexis surfaces" [5].

The arguments provided as to the utility of the software are extremely weak. We are told that "the novelty is to make these types of methodologies more accessible for researchers from different scientific backgrounds and without the need for strong computing skills." Yet:

- their own code is not provided in an accessible or usable form (see point 3, below).
- They state that "heat maps require the specification of 21 arguments". This is simply not true; many of the arguments are optional or may be set to "NA". See [6] for code to generate a plot not dissimilar to Figure 1 in this way.
- As any R user knows, using R requires some effort and self-education on the part of the user. Providing simpler versions of existing functions does not lower the barrier to users with less experience.
- in what way are the data presented "large", as implied by the title?

2. simpler instances (i.e. presenting a subset of an already existing database) may not be considered

The authors themselves state that their software is a simpler instance of existing tools:

“Quilt plots can be considered as a simple formulation of “heat maps”. They produce a similar graphical display to “heat maps” when the “clustering” and “dendrogram” options are turned off."

Rewriting an existing function with different arguments and calling it by a different name does not, in my opinion, represent an original research contribution.

3. Software should be open source, deposited in an appropriate archive, and conform to the Open Source Definition

The code associated with this article is provided as graphical screenshots embedded in a Word document. In this form, it cannot even be copy-pasted. This goes against every good principle of software availability and reproducibility. It certainly contradicts the stated aim of making the methodology more accessible to less-experienced users.



[1] http://www.plosone.org/ar...
[2] http://www.plosone.org/st...
[3] http://www.r-bloggers.com...
[4] http://cran.r-project.org...
[5] http://www.demogr.mpg.de/...
[6] http://pastebin.com/tUimR...