Fix tidyr::separate_rows issue with plots

[toniecrumley]

Summary

The updated version of CoSIA introduced an issue for a deprecated tidyr function. The function was changed to the newer function that replaces it.

Author Checklist

• This repository has a Lasseigne Lab ruleset configured.
  See instructions here.
• A singularity container has been created with all dependancies and the
  cap_container command has been included in each script using a container.
• All of the necessary scripts, dependencies, and inputs have been included
  in this pull request.
• Only files relevant to this change are included; no temporary, generated,
  or unrelated files are part of this pull request. Use .gitignore to prevent
  irrelevant files from accidentally being included.
• Results have been reproduced and verified with lasseignelab and
  default environments by running the job until two consecutive runs produce
  the same results. Code comments (per script) have been added for
  non-reproducible scripts. Include information about why the script is not
  reproducible.
• All automated code checks have passed. The "All checks have passed"
  message should show in the GitHub pull request status box above the
  "Merge pull request" button.
• No merge conflicts exist. Merge conflicts are indicated by the "This
  branch has conflicts that must be resolved" message in the GitHub pull
  request status box above the "Merge pull request" button.
• Setup instructions have been provided.
• Reproducing results instructions have been provided.
• Verification instructions have been provided.
• Setup, reproduce results, and verification instructions have been tested in a clean scratch environment.
• Primary and secondary reviewers have been requested to review this
  pull request.

Self/Peer Review Checklist (Coding Guidelines)

• Meaningful variable and function names
• File header comments
• Function comments
• In-line comments summarize logical sections of code by concisely explaining
  why, not what the code is doing. Avoid excessive or redundant commenting.
• Random seed is set
• Reasonable processing time for each job or script is specified
• All outputs have been saved
• Session info included in the scripts
• Cross-reference the working draft of the paper
• Confirm the code performs the intended analysis
• Confirm the code reproduces the reported results

Setup

cd $USER_SCRATCH
git clone git@github.com:lasseignelab/CoSIA.git
cd CoSIA
git checkout fix-tidyr

Test

Run the testthat unit test suite:

./tests/test.sh

Validate that the plot has been fixed:

./validation/gene_expression.sh

This image is the broken plot.

This image is the fixed plot.

View the plot with the Research Computing Files interface and also run the following md5 command.

md5sum validation/output/gex_plot.png

The md5 output should be.

af0c76b79af4349930686c203e09e432  validation/output/gex_plot.png

Cleanup

cd $USER_SCRATCH
rm -rf CoSIA

[tsoelter]

I get the plot to verify both with the md5 as well as visually. 🎉

I get an error when running the test suite, though. See screenshot below:

[tchowton]

I had the same error as Tabea above and this one when running ./validation/gene_expression.sh

CoSIA version : 1.11.2
CoSIA path : /scratch/tchowton/CoSIA

--- DS_Gene multi-species ---
Joining with by = join_by(h_sapiens_ensembl_id)
Joining with by = join_by(h_sapiens_ensembl_id)
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Joining with by = join_by(h_sapiens_ensembl_id)
Joining with by = join_by(h_sapiens_ensembl_id)

see ?CoSIAdata and browseVignettes('CoSIAdata') for documentation
downloading 1 resources
retrieving 1 resource
Error loading resource.
attempting to re-download
downloading 1 resources
retrieving 1 resource
ERROR: failed to load resource
name: EH7858
title: VST normalized RNA-Sequencing data with annotations for 362,533,125 Homo sapiens samples from Bgee
reason: 1 resources failed to download
Warning messages:
1: download failed
web resource path: ‘https://experimenthub.bioconductor.org/fetch/7908’
local file path: ‘/data/user/tchowton/bioconductor/bioc-cache/experimenthub/d1bc70aaf_7908’
reason: HTTP 403 Forbidden.
2: bfcadd() failed; resource removed
rid: BFC3
fpath: ‘https://experimenthub.bioconductor.org/fetch/7908’
reason: download failed
3: download failed
hub path: ‘https://experimenthub.bioconductor.org/fetch/7908’
cache resource: ‘EH7858 : 7908’
reason: bfcadd() failed; see warnings()
4: download failed
web resource path: ‘https://experimenthub.bioconductor.org/fetch/7908’
local file path: ‘/data/user/tchowton/bioconductor/bioc-cache/experimenthub/d5fa8643d_7908’
reason: HTTP 403 Forbidden.
5: bfcadd() failed; resource removed
rid: BFC4
fpath: ‘https://experimenthub.bioconductor.org/fetch/7908’
reason: download failed
6: download failed
hub path: ‘https://experimenthub.bioconductor.org/fetch/7908’
cache resource: ‘EH7858 : 7908’
reason: bfcadd() failed; see warnings()
Error: unable to find an inherited method for function ‘plotSpeciesGEx’ for signature ‘object = "NULL"’
Execution halted

[toniecrumley]

@tsoelter @tchowton A fix for the test suite failing has been pushed. It should work for Tabea since she probably has the ExperimentHub data cached. The download issue TC is getting seems to be a problem with Bioconductor and ExperimentHub, even though ExperimentHub shows as operational on the Bioconductor status website. After removing my cache, I get the same error on Cheaha and locally trying to access CoSIA data and other data in RStudio.

Our data:

library(ExperimentHub)

eh <- ExperimentHub()
eh["EH7858"]
eh[["EH7858"]]

Other data:

library(ExperimentHub)

eh <- ExperimentHub()
eh["EH5419"]
eh[["EH5419"]]

[tsoelter]

You were right, @toniecrumley, I still had the cache, so everything worked, including the test suite!

[toniecrumley]

@tchowton ExperimentHub is working this morning, so I was able to run the tests and validation. Please give it another try. Thanks!!

[tchowton]

The tests validate now and the image reproduces.