Polish Microarray GSEA example

jaclyn-taroni commented 3 years ago

Purpose

Polishing microarray GSEA example.

Issue addressed

For the microarray GSEA example, the following are being addressed:

Enforcing comment character length limit (#406)
Updating the section that said it was about clusterProfiler but was really about msigdbr (#415)
Stopping row names from being printed for paged tables (#428)
Adding the introductory paragraphs that are in every pathway analysis notebook (#354)

There is also a good amount of editing happening in this pull request in the spirit of #290.

Directions for the reviewers

I would recommend that the reviewers look at the whole document when reviewing, rather that just the diff, to assess the level of detail and description of methods in the writing.

One concern I have is that the "main" description of how GSEA works is under Purpose of this analysis. Ideally it would be closer to the GSEA() business itself. However, I think we need some explanation of the method before we get down to removing duplicate identifiers. An idea: We could move the description of GSEA that's under Purpose to under the Perform gene set enrichment analysis (GSEA) header and then move the removal of duplicates (and the explanation) to under the Determine our pre-ranked genes list section.

Specific questions

@cbethell - We set the seed in the RNA-seq example, but we didn't here. I added a set.seed() step here, right before we "need" it should someone be viewing this example and have jumped to the analysis code. Is this the correct thing to do?
@jashapiro - you filed #410 and have looked at more examples than me recently! Is this an appropriate level of detail/description in your opinion?

jaclyn-taroni commented 3 years ago

When I've run snakemake, I've gotten:

Error in rule render_citations:
    jobid: 9
    output: 02-microarray/pathway-analysis_microarray_01_ora.html
    shell:
        Rscript scripts/render-notebooks.R --rmd 02-microarray/pathway-analysis_microarray_01_ora.Rmd --bib_file components/references.bib --cite_style components/genetics.csl --include_file components/include.R --html 02-microarray/pathway-analysis_microarray_01_ora.html --style
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

But running

Rscript scripts/render-notebooks.R --rmd 03-rnaseq/pathway-analysis_rnaseq_01_ora.Rmd --bib_file components/references.bib --cite_style components/genetics.csl --include_file components/include.R --html 03-rnaseq/pathway-analysis_rnaseq_01_ora.html --style

works fine / no visible error. We should probably figure this out before this get merged, but for the moment I'm going to work on polishing the RNA-seq GSEA notebook.

jashapiro commented 3 years ago

I just checked out this branch and ran through everything with

docker run --mount type=bind,target=/home/rstudio,source=$PWD ccdl/refinebio-examples:latest snakemake  --cores 4

I got no errors, so I anticipate that it will work on the server. Should I push the rendered files?

jaclyn-taroni commented 3 years ago

These should be up to date rendering wise because I ran the Rscript scripts/render-notebooks.R step but maybe not so sure.

AlexsLemonade / refinebio-examples