How should irrelevant comment(s) from a peer reviewer be handled?

This is simple.
A) If the Editor was writing to you that rejections was due to the argument that "why the apple is red" is not discussed: Then you are free to approach the Editorial Board i.e. the Editor and the EiC for reassessment (and this usually works very well if done polite and convincing). There you need to argue scientifically why red apples are not related to lily flowers, and ask for reevaluation of your (revised) submission (including revision addressing all purposeful comments and an accompanying letter). 
B) If the editor named other arguments of rejection (while the referees was dabating also the red apple): Often this does cause angriness; and you will understand better once calming down from the initial frustration. Then think about these concerns and accept the rejection. Next is to substantiate the manuscript against the concerning issues (if you can). Usually you have to send it somewhere else (after rejection) unless the "previous" Editor was allowing an extensively reworked manuscript as new submission (i.e. new peer-review, usually different referees).
C) The Editor did reject your submission without giving an argument other then forwarding the referee comments: That is a badly managed Journal. Bad luck for you. Seek for a more professional one that has useful SOPs to support scientific publishing.

With kindness and diplomacy. If irrelevant, gently note that the scope of the work is directed elsewhere. Maintaining a professional and courteous tone is essential. 

Once a decision has been on publication, the author should take a critical review of the comments issued on their paper then consider resubmission or submitting else. Also, the author may need to have constructive exchange with the editor incase of any mistakes or oversights. Eye is to man.

Based on many criteria like the methodology, the transparence, the novelty many things and the most imoprtant to be neutral 

If the author(s) believe a reviewer's comments are invalid, they should be highlighted and brought to the editor's attention. If the editor has already rejected a manuscript based on such feedback, it is still worth bringing to their attention, as they should consider this feedback and may suggest a resubmission. The reviewer may also be marked as problematic if it was felt that this was a deliberate attempt to reject a paper incorrectly.

 Игнорировать и делать по своему если уверен в своих данных. Но учесть замечания 
в последующей работе.

This issue should be discussed with the editor.

Best

What you mention is quite common, especially when a manuscript goes to reviewers who do not have the background to understand your research work. If your paper is rejected, I think the most practical thing to do is submit it to another journal whose aims and scope are within your manuscript. 

In my oppinion, the author can politely write the editor proving his case with strong justification(s) and calling the attention of the editor about such comment. Sometimes, the editors are too busy with many papers, they might not notice such misleading comment from the reviewer. Authors should know that they can always challenge or rebut some review comments if they have strong justification.

I think the best decision is to resubmit your manuscript to another Journal considering comments of reviewer(s). There are many possibilities for this and author(s) will certainly find suitable Journal. Although I had to review manuscripts which hardly could be published in any Journal.

 In any case, rejections are to be based on proper explanations and simplifications. The author should know what were the main reasons for being rejected.
      Each one of us, including people from all professions, should take rejection as a natural part of life and career  advancement.