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10.4 years ago
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Hello folks,
I dont know if it is the place to ask this. I have developed a script in R to analyses small sequences and display some results.
My question is, I don't want that R display the braces with the elements number like this simple example:
> 1+1
[1] 2
I would like to have only 2, not [1] 2
Is it possible to change it any place inside display settings ?
Thanks
Update: I have a pipeline from bash that uses python that reads small sequences in a file and sends them to R and then waits for a response. But the response comes with braces. I would like to remove braces. I would do that in another ways, regex for example, but there's probably a better way.
Hello igoralves1!
We believe that this post is does not fit the main topic of this site.
Try an R forum. Having said that, print methods often give row names, try
cat().For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!
Hello Devon,
Well, I am a bioinformatician, maybe like you. And you know, in the bioinformatics field, we deal every moment with all kind of software and issues. And I am noting asking something about photoshop. I am asking something about R, the software that we as bioinformaticians use every day is it not? Otherwise you should close a lot of or almost all questions about R for example this one that ask something about displaying results in R, like mine... Highlight specific bars depending of a factor. That question ask how to highlight some specifics bars. Me I ask how not display something.... I can not see the difference.... Could you explain me? And thanks.. you solved my issue!
The post that you linked to probably should have been closed too :P
The general idea is that if a question is purely about programming then it's considered off-topic. The typical way around that is to just rephrase the question to use a bioinformatics example. So, say you have a bash pipeline to do some data processing and it needs to output some computations from R to the terminal (for some reason or another). Then, it's considered on-topic. This is pretty much the only way to keep the site from being over-run with R/perl/python question, since realistically the people on this site can typically give good advice there.
Anyway, best of luck with your project!
It is exactly what I have. I pipeline from bash that use python that reads small seqs in a file and send to R and wait a response. But the response comes with braces. I would like to remove braces. I would do that in another ways, regex for example.
I don't think I need to explain that, otherwise the message would be exhaustive. But if you do not consider that as a bioinformatics question, where is exactly the bioinformatics examples in the post a have mentioned before? The title of each bar? "sam_760"? Why don't you close these topic, so? I don't believe I am losing my time to discuss something like that. Thanks
Please note that it is the poster's responsibility to describe the connection to bioinformatics in the first place. Please note that many simple programming questions even if related to bioinformatics do better get answered elsewhere, because they are generic enough. Please note further that we moderators and all users of BioStar are working for free to maintain a high level of quality in response to questions and answers. To achieve this goal, we have to moderate posts that might not fit the scope of this site and to make difficult decisions which might not be shared by everyone. While this process sometimes might get to the limits, I think that we have quite good and fair judgement in most cases.
As the first comments state, we are willing to discuss and very liberal with reopening any post with even the faintest relation to bioinformatics, an objection is part of the standard work-flow of question moderation. Should you however still think you are wasting your time here, feel free to just leave.
I would also add that anyone in the community has the responsibility to make an explicit connection to bioinformatics, in case the original poster has neglected to do so, and should reach for this option first if possible, before reaching to close the question. I often see questions closed out of some kind of gleeful formality, when the connection to bioinformatics is surrounded by implication, but simply not explicitly stated. It's annoying when people ask dry programming questions without bioinformatics context, but it can be instructive to add the context in the answer: "I sometimes write bed (or other) files using R, where I have to form the output explicitly, and I can use the cat() statement for this..." I much prefer this approach to closing the question, or being told to go to stack exchange, where I know I often won't be able to understand the answer. Questions like these provide an opportunity to instruct how programming can be used for a bioinformatics task that many people might not have considered. Of course, if one can not see a connection at all, close the question, but at least try to engage your imagination first (if you can).
Hello Michael Dondrup, the matter of this discussion is beyond put my post on hold or not. It is about the way people like you (certain privileges) use to make judgment about topics in this community (put on hold) for example . What I was discussing with Devon is not about exclusively my post. It seems that the parameters used to judge my post was not the same used to judge another one with the same idea, BEHAVIOR of something displayed on a screen. In another words, programming question too. But programming question in a pipeline of bioinformatics environment using R as part of pipeline, form me and for him. it was not photoshop. The authors of the other post did not explain all the pipeline too as you mentioned ("Please note that it is the poster's responsibility to describe the connection to bioinformatics in the first place".). He went directly to the question too, like me.. I know it is difficult to judge even when the used parameters are no so clear or when you are in a borderline. But, once you assumed to make a judgement, be fair. You know - With Great Power Comes Great Responsibility. If you have the power to put on hold, your responsibility is spend your time to search good parameters to do what you are about to do and to be fair. Otherwise we gonna have situations like that. Is is only a matter to choose what are bioinformatics issues or not. Only to remember you, bioinformatics field goes from a way to represent a chemical reaction inside a cell and can pass through a statistic model to validate that until a software development to manage the process. So the parameters to say what is bioinformatics or not is very huge. Not so easy to classify. So if you think I am not correct, please put the post on hold again.
Maybe you should hold your breath for a second and look at the answer you have gotten. The post was moderated and re-opened on your note and your edit. It is impossible to apply perfectly objective and identical standards at all times and to treat every post exactly the same way, even though we try our best. Take into account we are many and the topics are very variable at times.
I do not want to discuss the moderation issue any further at this point because it is futile imo.
I've updated your question with that info and reopened it. BTW, you might also consider using rpy2. It's a bit quirky, but it allows direct access to R from within python without the parsing issues.