[Bioc-devel] How can I remove limit of row numbers that can be printed on console?
Martin Morgan
martin.morgan at roswellpark.org
Fri Sep 8 23:40:49 CEST 2017
On 09/08/2017 04:55 PM, Arman Shahrisa wrote:
> I mean is it correct approach to use put View(x) inside my function
> code, so that upon finishing, the results be shown automatically by
> View() and also stored as an excel file simultaneously? I can add a
> function argument for activating/deactivating the View() so that it
> won’t affect the vignette.
no, you would not want to put View() inside your function, or to print
10k lines of output to the console in your function.
Rethink what you are doing and how you are interacting with the user.
Maybe you want to do what cdgsr does, allowing the user to navigate
through some kind of work flow that involves selection of options
through a series of function calls.
Martin
>
> Sincerely,
>
> Arman
>
> *From: *Martin Morgan <mailto:martin.morgan at roswellpark.org>
> *Sent: *Saturday, September 9, 2017 01:17
> *To: *Arman Shahrisa <mailto:shahrisa.arman at hotmail.com>; bioc-devel
> <mailto:bioc-devel at r-project.org>
> *Subject: *Re: [Bioc-devel] How can I remove limit of row numbers that
> can be printed on console?
>
> (Keeping the devel mailing list in the loop, so that others with
> similar questions / answers can benefit / contribute)
>
> On 09/08/2017 04:41 PM, Arman Shahrisa wrote:
>> I tested your first solution (View(studies)). I added it to the end of
>> my code and everything worked perfectly. Do think I can use it this way
>> or I have to write instruction for the users (vignette) to run it themself?
>
> in the vignette you could give the user a taste for what they'll see
> with `head()` in an evaluated chunk, and mention that they could use
> `View()` in a non-evaluated chunk, something like
>
>
> ```{r}
> x = ...
> head(x)
> ```
>
> To explore this object interactively, try
>
> ```{r, eval=FALSE}
> View(x)
> ```
>
> Martin
>>
>> Best regards,
>>
>> Arman
>>
>> *From: *Martin Morgan <mailto:martin.morgan at roswellpark.org>
>> *Sent: *Saturday, September 9, 2017 00:34
>> *To: *Arman Shahrisa <mailto:shahrisa.arman at hotmail.com>; bioc-devel
>> <mailto:bioc-devel at r-project.org>
>> *Subject: *Re: [Bioc-devel] How can I remove limit of row numbers that
>> can be printed on console?
>>
>> On 09/08/2017 03:50 PM, Arman Shahrisa wrote:
>>> Thank you very much for helping. I have a package in Bioconductor
>>> submission procedure.
>>>
>>> One of package functions shows the available cancer studies, allowing
>>> the user to choose
>>>
>>> from them. I have two options: Saving the output to the package
>>> directory or printing it
>>>
>>> on the console. Apparently, assigning the output to environment is not
>>> allowed,
>>>
>>> unless user does it by arrow sign him/her self (To me, both look like
>>> the same!).
>>>
>>> Therefore, I have to print the output on console. I’ve seen such
>>> approach in *cgdsr *package
>>>
>>> without any truncation. I took a look through its R code and couldn’t
>>> figure it out. I thought
>>>
>>> maybe somebody knows what to do?
>>>
>>> My function also stores an excel file with the same output (to shre it
>>> with others ). There is no
>>>
>>> logics behind saving the excel file and then opening it with R. So, I
>>> think at the same time results
>>>
>>> should be stored as a variable or printed on console.
>>
>> One way of using cgdsr is like
>>
>> library("cgdsr")
>> cbiop <- CGDS("http://www.cbioportal.org/public-portal/")
>> studies = getCancerStudies(cbiop)
>> View(studies)
>>
>> does that fit your needs?
>>
>> Another approach is to provide a simple way for the user to get more
>> relevant data, for instance
>>
>> queryStudies <- function(url, query) {
>> stopifnot(
>> is.character(url), length(url) == 1L, nzchar(url),
>> !is.na(url),
>> is.character(query), length(query) == 1L, nzchar(query),
>> !is.na(query)
>> )
>> cbiop <- CGDS(url)
>> studies = getCancerStudies(cbiop)
>> idx = Reduce(`|`, lapply(studies, grepl, pattern=query))
>> if (sum(idx) > 1000)
>> stop("'query' returned > 1000 matches; be more specific")
>> studies[idx, , drop=FALSE]
>> }
>>
>> used as
>>
>> > mystudies = queryStudies(url, "brca"))
>> > dim(mystudies)
>> [1] 9 3
>>
>> which is very easy to work with, e.g., View()
>>
>> Martin
>>
>>
>>>
>>> Best wishes,
>>>
>>> Arman
>>>
>>> *From: *Martin Morgan <mailto:martin.morgan at roswellpark.org>
>>> *Sent: *Friday, September 8, 2017 23:48
>>> *To: *Arman Shahrisa <mailto:shahrisa.arman at hotmail.com>; bioc-devel
>>> <mailto:bioc-devel at r-project.org>
>>> *Subject: *Re: [Bioc-devel] How can I remove limit of row numbers that
>>> can be printed on console?
>>>
>>> On 09/08/2017 02:11 PM, Arman Shahrisa wrote:
>>>>
>>>> Hi everyone,
>>>>
>>>> How can I prevent the R from truncating the printed result on console? I have to
>>>> print the output on console and I can�t use options(max.print = 10000) in my
>>>> function. What else I can do?
>>>
>>> this isn't really the right forum for base R questions (the r-help
>>> mailing list or StackOverflow might be more appropriate), but since you
>>> ask on the wrong forum ;), maybe I'll ask about why you'd want to print
>>> that much information to the console? you're not really going to read
>>> through it, are you?
>>>
>>> Martin
>>>
>>>>
>>>> Sincerely
>>>> Arman
>>>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
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