Implement an autostop mode for gruffi

[heylf]

Dear @vertesy,
I took the liberty from my previous question and implemented an automatic mode for gruffi. Please check if that is to your liking. I took a route which does not require too much reformatting and simply implemented an argument (atuostop) to trigger a button click after the app is initialized.

I also updated the manual for the Shiny.GO.thresh function to include the autostop option.

The code was tested it on my machine (Ubunut 22.04) and it works with R 4.3.0.

It requires the package shinyjs !! First I wanted to let you check the code before I also include the package in the installation.

Cheers,
Florian

[vertesy]

Thank you & sorry, been very busy, but I try to get back on this soon!

[heylf]

The autostop is not completly automatic yet because you still have to run a browser in order to stop the application. Thus, if you execute the program on a cluster (e.g., IBM) the script freezes. Consequently, I tried a few things, but an implementation without the execution of a browser is not trivial.

[heylf]

Do not merge the PR I will work on this!

[heylf]

So. I have added a total new function for an automatic setting. Took code parts from the server.R and gruffi.R. This will not run the Shiny.app anymore, but has the same functionality. Yet, @vertesy please check if I have not made any mistakes.

[liezeltamon]

Hi!

The added function Auto.GO.thresh() is super useful and just wondering when you are planning to merge this? Thank you!

[vertesy]

Hey,

I am very sorry, for the late follow up. I now checked the code and will pull. Will test and probably further modify.

Of note, I did a major update of the package (bf, cleanup).

[vertesy]

I went over the new function from this PR, and will commit the changes soon.

• I massively cleaned up the Auto.GO.thresh() the code. The code was very verbose (largely inherited from Shiny.GO.thresh(), that is cleaned up as well.)
• The original PR was missing the threshold assignments to @misc
• Variable names were often misleading (again, inherited and fixed in both places).
• Removed parts that were not used
• Code restructuring / organization
• Some code annotation

I will now add a new feature for visualization of intermediate results.
One reason for not implementing originally an Auto.GO.thresh() is to force people to look at the results and understand what happens, instead of blindly taking a T/F column.
I understand that for automated workflows this is a problem. Therefore with some more feedback Auto.GO.thresh() is now part of the package.

Thank you for the contribution, much appreciated!

Remaining issues

Shiny.GO.thresh() seems to round up threshold values, wheread Auto.GO.thresh() does not. I added a signif() but it's still not the same.
Note that rounding may lead, in very rare cases, suboptimal results. Will remove from both.

Auto.GO.thresh()

$thresh.stress.ident1
[1] 0.690027

$thresh.stress.ident2
[1] 0.71495

$thresh.notstress.ident3
[1] 0.672001

Shiny.GO.thresh()

$thresh.stress.ident1
[1] 0.69

$thresh.stress.ident2
[1] 0.715

$thresh.notstress.ident3
[1] 0.672

[liezeltamon]

thank you both! hope to try this soon