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Hackout2 / incidence

The incidence package for computation and visualization of incidence from outbreak linelists
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shiny feature needs to be implemented as a function #3

Open thibautjombart opened 9 years ago

thibautjombart commented 9 years ago

Current shiny stuff has been moved to /inst/shiny. Some changes are needed for users to be able to access the shiny features.

We would need:

One way to do this is:

There is an example of that with the function adegenetServer() in adegenet:

rolinavg commented 9 years ago

Hi Thibaut,

I've divided the script file into ui.R and server.R files, but now I'm not sure what to do with the system.files() command and how to pass variables to these files without calling them as source code. Can you work your magic? How am I supposed to commit my changes now? I tried to git pull origin shinyFeatures, but it said the following:

git pull origin shinyFeatures From https://github.com/Hackout2/incidence

  • branch shinyFeatures -> FETCH_HEAD Updating d851b54..8d83195 error: Your local changes to the following files would be overwritten by merge: R/clickableTimeSeries.R Please, commit your changes or stash them before you can merge. Aborting <<<<<<<<<<<

I think it would be cool to add maps to the interactive time series. Any other thoughts on improving this code are naturally welcome!

Rolina

thibautjombart commented 9 years ago

Hi Rolina, Cool! Did you check the links to adegenet's stuff I posted? This one shows how to refer to the installed files when calling runApp: https://sourceforge.net/p/adegenet/code/ci/master/tree/pkg/R/servers.R

thibautjombart commented 9 years ago

As for the git error, this is because you probably haven't committed your changes in your local branch. You have to commit first, then pull, then push. Otherwise pulling would erase the changes you haven't committed. Makes sense?

rolinavg commented 9 years ago

Hi Thibaut,

That last comment makes sense, yes. As for the example files you posted, I did indeed look at those, but it wasn't clear to me how user-defined variables are passed to ui.R and server.R. Would you put them in the brackets at line 6 or at line 20 (line references refer to your example code)? And how about code that is neither in the ui.R file nor server.R file and is necessary to modify the user-defined variables? Where does this go? Finally, presumably the server.R location should be inst\shiny and I should reference the incidence package at line 21. Correct?

Thanks! Rolina

thibautjombart commented 9 years ago

Hi Rolina, I'm not sure about the passing of variables, I guess it depends which ones. Passing the dataset directly when calling shiny should be possible, but I haven't done this yet. As for referring incidence, it should not be the case: the code will be run, by definition, when the package is attached. If you want to push what you have so far, I'll have a look later. Cheers Thibaut

On Thu, Feb 19, 2015 at 1:52 PM, rolinavg notifications@github.com wrote:

Hi Thibaut,

That last comment makes sense, yes. As for the example files you posted, I did indeed look at those, but it wasn't clear to me how user-defined variables are passed to ui.R and server.R. Would you put them in the brackets at line 6 or at line 20 (line references refer to your example code)? And how about code that is neither in the ui.R file nor server.R file and is necessary to modify the user-defined variables? Where does this go? Finally, presumably the server.R location should be inst\shiny and I should reference the incidence package at line 21. Correct?

Thanks! Rolina

— Reply to this email directly or view it on GitHub https://github.com/Hackout2/incidence/issues/3#issuecomment-75054680.

rolinavg commented 9 years ago

I see. Ok. Perhaps I'll revert to the one-file function-friendly format that I had developed and just push that for now. In this one file, shiny is called within a normal R function, allowing me to pass whichever user-defined variables I want. I'll push it later this evening when I get home or tomorrow.

Rolina

rolinavg commented 9 years ago

Hi Thibaut, I've committed / pulled / pushed my code onto the shinyFeatures branch. I hope I did it correctly. Had some error messages pop up, but google seemed to provide a useful solution. I still need to edit and modify a few things. Feel free to have a look when you have the chance. Rolina

thibautjombart commented 9 years ago

Hi Rolina, cool, I can see the commit now, thanks! Cheers Thibaut

On Thu, Feb 19, 2015 at 10:23 PM, rolinavg notifications@github.com wrote:

Hi Thibaut, I've committed / pulled / pushed my code onto the shinyFeatures branch. I hope I did it correctly. Had some error messages pop up, but google seemed to provide a useful solution. I still need to edit and modify a few things. Feel free to have a look when you have the chance. Rolina

— Reply to this email directly or view it on GitHub https://github.com/Hackout2/incidence/issues/3#issuecomment-75151408.

thibautjombart commented 9 years ago

Sorry I have left this hanging for a while. @rolinavg I probably won't have time to work on the shiny app over the days to come. What do you think? Shall we make the first release without this functionality? Or would you rather sort it out first?

rolinavg commented 9 years ago

Hi Thibaut,

Sorry for the late reply! I thought that I might have time to work on it on Friday or during the weekend, but it turns out that those days were more fully booked than I anticipated. I may have some time to look at it this weekend, but am rather swamped until then. Will this be okay?

Rolina

On Thu, Mar 26, 2015 at 1:18 PM, Thibaut Jombart notifications@github.com wrote:

Sorry I have left this hanging for a while. @rolinavg https://github.com/rolinavg I probably won't have time to work on the shiny app over the days to come. What do you think? Shall we make the first release without this functionality? Or would you rather sort it out first?

— Reply to this email directly or view it on GitHub https://github.com/Hackout2/incidence/issues/3#issuecomment-86486948.

thibautjombart commented 9 years ago

Hi Rolina, sure! Best Thibaut