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.mor...@roswellpark.org>
*Sent: *Saturday, September 9, 2017 01:17
*To: *Arman Shahrisa <mailto:shahrisa.ar...@hotmail.com>; bioc-devel
<mailto:bioc-devel@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.mor...@roswellpark.org>
*Sent: *Saturday, September 9, 2017 00:34
*To: *Arman Shahrisa <mailto:shahrisa.ar...@hotmail.com>; bioc-devel
<mailto:bioc-devel@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.mor...@roswellpark.org>
*Sent: *Friday, September 8, 2017 23:48
*To: *Arman Shahrisa <mailto:shahrisa.ar...@hotmail.com>; bioc-devel
<mailto:bioc-devel@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
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