As a young scholar I frequently struggle with knowing the extent to which I should be critical of particular components of papers I am reviewing. I can formulate a rough hierarchy between major concerns (things that need to be changed or this shouldn't be published) and relatively minor concerns (things I think would improve the manuscript, but aren't substantive enough to affect whether the paper is publishable or not).The question here concerns the latter, in essence I don't know where the cut-off in reasonableness should be for minor concerns.
For one example, being curmudgeonly I would say bad graphics are the norm rather than the exception in my field, although they aren't frequently so bad I can't figure out what the author is trying to say. Are minor critques of graphs appropriate (e.g. your gridlines are very obtrusive, the aspect ratio of your chart isn't appropriate, your colors/patterns are hard to distinguish, you should use a dot plot instead of a stacked bar graph, etc.) Frequently my suggested improvements would be somewhat arbitrary though, so I frequently hesitate to give such advice.
Is there any advice to guide the role of the peer-reviewer? Another side question too, does the scope change if I'm doing this for a colleague versus as an anonymous reviewer for a journal?
PLoS Computational Biology editor P.E. Bourne has written a series of very decent “Ten simples rules to …” articles. There is no detailed guide to being a good reviewer, but Ten Simple Rules for Reviewers sure is a good starting point. Summing it up:
Do Not Accept a Review Assignment unless You Can Accomplish the Task in the Requested Timeframe—Learn to Say No
Avoid Conflict of Interest
Write Reviews You Would Be Satisfied with as an Author
As a Reviewer You Are Part of the Authoring Process
Be Sure to Enjoy and to Learn from the Reviewing Process
Develop a Method of Reviewing That Works for You
Spend Your Precious Time on Papers Worthy of a Good Review
Maintain the Anonymity of the Review Process if the Journal Requires It
Write Clearly, Succinctly, and in a Neutral Tone, but Be Decisive
Make Use of the “Comments to Editors”
I would add: carefully read both the “instructions for authors” and “instructions for reviewers” of the journal you are reviewing for, if you are not already very familiar with them.