GeneTonic does not load

[Rafaelsoler13]

Hi!

I was using GeneTonic, and now I get this message in R:

> library("GeneTonic")

Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio
Error: package or namespace load failed for ‘GeneTonic’:
 object ‘bs4TabPanel’ is not exported by 'namespace:bs4Dash'

And in the bs4Dash I cannot see any package called bs4TabPanel

... bs4SidebarUserPanel Create a Boostrap 4 dashboard main sidebar bs4SocialCard AdminLTE3 social card bs4Sortable BS4 sortable section bs4Stars AdminLTE3 stars bs4TabCard Create a Boostrap 4 tabCard bs4TabItem Boostrap 4 dashboard body bs4TabItems Boostrap 4 dashboard body bs4Timeline AdminLTE3 timeline block bs4TimelineEnd AdminLTE3 timeline block bs4TimelineItem AdminLTE3 timeline block bs4TimelineItemMedia AdminLTE3 timeline block ...

Could the package have been renamed?

[Rafaelsoler13]

They seem to have removed the function:

https://rinterface.github.io/bs4Dash/news/index.html#bs4dash-2-0-0-unreleased

[federicomarini]

Good catch, the release of bs4Dash is indeed fresh news. Hopefully the developers are providing a drop-in replacement for that? I'll investigate 😉

[federicomarini]

BTW: for the time being, @Rafaelsoler13 - you can get it up and running

devtools::install_version("bs4Dash", "0.5.0")

[Rafaelsoler13]

Thanks Federico! And great tool 👌😊

[federicomarini]

I put together a quick fix - available here: https://github.com/federicomarini/GeneTonic/tree/newbs4dash

You can install it via

devtools::install_github("federicomarini/GeneTonic@newbs4dash")

Could you give it a try on your machine please?

[Rafaelsoler13]

Yes! This is the output

√  checking for file 'C:\Users\Usuario\AppData\Local\Temp\Rtmpa6TiCH\remotes44a03ab34e17\federicomarini-GeneTonic-6bb9772/DESCRIPTION' ... 
-  preparing 'GeneTonic': (361ms)
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
-  building 'GeneTonic_1.5.2.tar.gz'

Installing package into ‘C:/Users/Usuario/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
* installing *source* package 'GeneTonic' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace 'bs4Dash' 0.5.0 is being loaded, but >= 2.0.0 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Ejecución interrumpida
ERROR: lazy loading failed for package 'GeneTonic'
* removing 'C:/Users/Usuario/Documents/R/win-library/4.1/GeneTonic'
* restoring previous 'C:/Users/Usuario/Documents/R/win-library/4.1/GeneTonic'
Warning message:
In i.p(...) :
  installation of package ‘C:/Users/Usuario/AppData/Local/Temp/Rtmpa6TiCH/file44a04c816758/GeneTonic_1.5.2.tar.gz’ had non-zero exit status

[federicomarini]

Oh, could you try that in a fresh R session? It seems the older bs4Dash was still loaded.

[Rafaelsoler13]

Yes! Now it works! :)

Could I suggest a couple of changes? It would be very interesting if it were also included with the KEGG or REACTOME pathways option, I think that the volcano plots and the heatmaps of the GO terms are too small (or maybe I don't know how to enlarge them), and finally I'm working with 5000 DEGs, for what the map of GO terms and its interactions is very crowded and does not turn out well.

Greetings and congratulations! :)

[federicomarini]

Thanks for the report!

Could I suggest a couple of changes? It would be very interesting if it were also included with the KEGG or REACTOME pathways option

Well, you can use these sets anyway, it mostly depends on your upstream tool.

, I think that the volcano plots and the heatmaps of the GO terms are too small (or maybe I don't know how to enlarge them),

Probably best if you use the functions offline to have most control on the appearance. Say, in a RMarkdown report and then tweak fig.height and fig.width.

and finally I'm working with 5000 DEGs, for what the map of GO terms and its interactions is very crowded and does not turn out well.

Oh, that is a huge bunch. Probably you can obtain similar or better polished results if you select DE with a higher degree of stringency. Say, a smaller FDR, or testing against a different null hypothesis (not subsetting for logFC post hoc, but rather using a TREAT-like approach if using edgeR, or the lfcThreshold parameter in DESeq2 - an example for that can be found in the vignettes, or is also what I did for the demo dataset)

Enjoy it, and thanks for the input!

[federicomarini]

FYI, https://github.com/federicomarini/GeneTonic/pull/19 is in now, so it should be available to all in the master branch, and soon in the version propagated in the Bioc build system

[lucius81]

I put together a quick fix - available here: https://github.com/federicomarini/GeneTonic/tree/newbs4dash

You can install it via

devtools::install_github("federicomarini/GeneTonic@newbs4dash")

Could you give it a try on your machine please?

This worked for me !

[federicomarini]

Awesome, thanks @lucius81 for stepping in 😄 I'll leave this one open for some time to give @Rafaelsoler13 time to check, and while not everyone might have updated both packages it could help as a reference (if one goes from scratch now, I am enforcing bs4Dash as >= 2.0.0 so it should not even bother)

[Rafaelsoler13]

Yes, it also worked for me :)