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david-barnett / microViz

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
https://david-barnett.github.io/microViz/
GNU General Public License v3.0
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girafe_html #28

Closed atgustin closed 3 years ago

atgustin commented 3 years ago

Hello - can't wait to get to work using this package. Thank you for offering it!

I'm able to initiate a new browser window (in firefox or safari) but when the new window comes up, clicking the edit menu produces no options. My meta data are available in drop down boxes, but there are no images in the view window.

When I stop running the command in Rstudio it provides an error with traceback as follows:

Listening on http://127... object 'girafe_html' not found

  1. | execCallbacks(timeoutSecs, all, loop$id)

  2. | run_now(timeoutMs/1000, all = FALSE)

  3. | service(timeout)

  4. | serviceApp()

  5. | ..stacktracefloor..(serviceApp())

  6. | withCallingHandlers(expr, error = doCaptureStack)

  7. | domain$wrapSync(expr)

  8. | promises::with_promise_domain(createStackTracePromiseDomain(), expr)

  9. | captureStackTraces({ while (!.globals$stopped) { ..stacktracefloor..(serviceApp()) } ...

  10. | ..stacktraceoff..(captureStackTraces({ while (!.globals$stopped) { ..stacktracefloor..(serviceApp()) } ...

  11. | runApp(x)

  12. | print.shiny.appobj(x)

  13. | (function (x, ...) UseMethod("print"))(x)

Thank you for any insights you may be able to provide!

Andrew Gustin

david-barnett commented 3 years ago

Hi Andrew, thanks for the report. To help me understand what might be going on here, it would help if you can do three things:

  1. create the error again and then run devtools::session_info() and paste the code and the output here
  2. check if you are able to run (any of) the examples for ord_explore https://david-barnett.github.io/microViz/reference/ord_explore.html (e.g. the code below) or if this gives the same error
  3. If it only occurs with your phyloseq, could you just print(your_phyloseq) and paste the output here?
library(microViz)
corncob::ibd_phylo %>%
   tax_fix() %>%
   ord_explore()

cheers, David

david-barnett commented 3 years ago

@atgustin I assume you resolved this problem, feel free to reopen if not :)