downstream analyses - shiny?

[antoine4ucsd]

Hello I am trying to perform downstream analyses but it looks like shiny app is not working. when clicking on downstream analyses, R studio is opening the downstream.R is showing up but nothing happen. I wonder if there could be a conflict between Rstudios? I tried to install shiny via conda and in Rstudio again but nothing changes. any thoughts?

[gnanibioinfo]

Hi, on right top corner of R studio source panel, click on runapp and wait.. the required r libraries will install and then EzMap window will pop up...

[antoine4ucsd]

it generates

and then some kind of path issue when trying to install shiny /Users/myname/anaconda2/lib/R/bin/R: line 142: /Users/myname/anaconda2/lib/R/etc/ldpaths: No such file or directory

[gnanibioinfo]

Try to install shiny via BiocManager

[antoine4ucsd]

ok

-- a

From: gnanibioinfo @.> Date: Tuesday, August 10, 2021 at 5:04 PM To: gnanibioinfo/EzMAP @.> Cc: antoine @.>, Author @.> Subject: Re: [gnanibioinfo/EzMAP] downstream analyses - shiny? (#4)

Try to install shiny via BiocManager

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[antoine4ucsd]

no more success... I tried to install interactiveDisplay but still same issue

[gnanibioinfo]

Can u screen shot your R studio?

[antoine4ucsd]

it keeps aking to reinstall shiny

but installing from Rstudio failed

[gnanibioinfo]

what happens when you click on install on the yellow alert message?

[antoine4ucsd]

it fails - see attached Rlog.txt

[gnanibioinfo]

After looking into Rlog, i feel like this is an issue with Conda. Please install R from CRAN and try again.

[gnanibioinfo]

I mean to say that conda-installed version of R is an issue here. so i suggest you to uninstall R and re-install R from CRAN and try again.

[antoine4ucsd]

you mean uninstalling R from the qiime conda env and reinstall it from CRAN? thank you again for all the advices

[gnanibioinfo]

Yes

[gnanibioinfo]

you are welcome

[antoine4ucsd]

Hello What I did: I reinstalled the qiime2 env without the R packages (using the attached xml) this is still unclear because when I list the env , it indicates a lot of R script (see conda list attached) Once done, I run the downstream analyses with the jar function. R studio is showing up with no error and shiny seems installed BUT I get the error below when clicking on the green arrow (top right)?

really sorry about that. Maybe you have a R script that can be run separately and generate ALL intermediate and outputs from downstream analyses?

qiime2-2021.4-py38-osx-conda_noR.yml.txt conda list.txt

[antoine4ucsd]

one way to overcome this issue although not very elegant From my terminal within the qiime2 env, I ran directly Rstudio downstream analyses: open -na /Applications/RStudio.app ~/Desktop/EzMAP/Downstream/downstream.R

then I installed shiny as requested --> it makes a shiny deployment specific to this conda env (my understanding) it took a while to install but no error.

shiny is opening and I have to manually indicate the biom file and tree input. is there a way to automatically save all outputs at once?

thank you!

[gnanibioinfo]

Hi thank you for your update. It is not mandatory to run R Studio within the qiime2 environment. EzMAP makes use of R Studio installed via CRAN. Anyhow, you have figured it to run. Yes, one should manually indicate the biom and tree files. EzMAP is designed in such as way, that if one wish to use EzMAP for the purpose of downstream analyses alone. All the qiime2 analysis files (qza and qzv) will be stored in the respective folders within the EzMAP_Analysis folder. We are working on EzMAP update (will be available from October), to provide the users with download options for all the output files and graphs. Thank you for using EzMAP. Comments and Suggestion are welcome, which might be very helpful and can be considered in future release of EzMAP.

[antoine4ucsd]

thank you! I would be happy to be one of your (bad) beta-tester if the need arises.