Initiate scAdvanced cheatsheet

[sjspielman]

Towards #646

This PR begins the process of establishing a scAdvanced cheatsheet. I am going to split this up into 2 PRs, since there's a decent amount to review here.
This PR accomplishes two goals:

• Add functions to the intro cheatsheet that should have been in the intro cheatsheet all along
• Establish the scAdvanced cheatsheet, including all tables of functions

There will be one additional PR to add in Seurat <-> SCE conversions (stubbed out but not filled out in the cheatsheet!). Right now, I have only committed md files since I expect changes! At the end of this PR, I'd like for the intro PDF to make it into the repo, but the advanced PDF will be part of the next PR.

Some specific notes for reviewers:

• Enjoy link clicking and finding all the links I didn't get right 🥴! That's it for this bullet.
• Turns out map_df() is in the intro r cheatsheet, but it's only used in setup code for the intro workshop. It didn't seem like a big deal to me to leave in. I had forgotten there was some very light purrr in intro, too!!
• Any overall thoughts on order of the topics in the cheatsheet? I tried to loosely structure in order of when items appear (though this isn't possible to do fully linearly), with all tidyverse at the end. The conversion is stubbed out at the top as this is a common question.
• plotExpression() is really the only "new" scater function in scAdvanced. But, I went ahead and added some of intro the scater functions into the advanced, since they're important for advanced and come up a lot (plotReducedDim and plotUMAP). Eventually this will get solidified with "cheatsheets by topic," so I thought this duplication would be ok for now.
• I couldn't quite land on the right level of detail for miQC explanations, any thoughts? Somehow "Plot the miQC model" for plotModel() didn't seem enough, but actually explaining what gets plotted makes for a LONG table row...!
• I'm not a fan, but the title for HarmonyMatrix() is "Main Harmony interface". Feeling like I just ignore that and write "harmony matrix"...
• Currently all tidyverse is in one table, and I both feel like that's reasonable and it's excessive! Therefore, how many tables this is can be up to reviewers! (Maybe a separate table for just ggplot2?)

[jashapiro]

This looks good to start!

I think I addressed most of your bullet points with line comments, but for some of the more overall comments, I think the order is fine, though I might move the seurat conversion to the end. But I can probably go either way on that.

I checked many links, but probably not all of them...

[sjspielman]

@jashapiro this should be ready for another look! I've implemented the in-line reviews, and I also went ahead and purged all the here links from the 3 cheatsheets (intro r, intro sc, advanced sc) since it was moving brackets around. The only TBD is this comment which I wasn't quite sure what you meant? #663 (comment)

[jashapiro]

Looks good! But since we are apparently moving the links, I made them bigger and more specific.

I also realized we don't have syntax \(x){} anywhere, which we should. Somewhere. I don't care too much about where, but made a suggestion.

Also, maybe TOCs?

[jashapiro]

I realized that we don't have a link to the \() anywhere... I don't know if this is the right place, but we should put it somewhere... Maybe with purrr? Docs here: https://rdrr.io/r/base/function.html

[sjspielman]

This has been updated in a couple ways:

• I added cheatsheet links to the advanced cheatsheet, but not to the intro, under the assumption that we'll do a cheatsheet overall organizing by topic in the not distant future and can update all around at that time
• For all PDF links, I added language that they are downloads
• Added TOCs via doctoc and copy/pasting
• Added a code chunk showing anonymous function syntax, feedback appreciated there! The example I chose is inspired by things we do in the integration instruction notebook

I also decided to think a little bit about PDF export, whose current status quo (please enjoy the blame view here and the most recent commit 🥴) is not my favorite - a little too manual, and MacDown is no longer being maintained if this issue is any indication. I ended up settling on the markdown-pdf VS Code extension, with some css to override mediocre font colors in module-cheatsheets/assets/markdown-pdf.css. I quite like the look of these cheatsheets, and they are at least more reproducible than what we've been doing! If reviewers are on board, I'll file a subsequent PR to update instructions for PDF export. For fun, reviewers may also appreciate this commit 3ff00fd and infer the silly journey I had along the way 😄

[jashapiro]

This looks good, with a few minor comments below.

On the subject of conversion; I agree that moving away from MacDown is a good goal, but I don't think moving to another interactive tool is necessarily the way we should go about this. I might rather have a little script that renders to html with rmarkdown then converts that to pdf via pandoc or some other scriptable tool. I don't think this PR is the place to spend our time on it.

[sjspielman]

then converts that to pdf via pandoc or some other scriptable tool.

I'll just note that if this involves a custom LaTeX template, that's all you.... I will revert to Macdown-exported PDFs, but will state for the record I find those versions way less attractive than what markdown-pdf gives.

[jashapiro]

then converts that to pdf via pandoc or some other scriptable tool.

I'll just note that if this involves a custom LaTeX template, that's all you.... I will revert to Macdown-exported PDFs, but will state for the record I find those versions way less attractive than what markdown-pdf gives.

No latex! I was thinking whatever is being used under the hood here, maybe with a conda environment to install it.

I'm fine with leaving these as they are here. I just don't want to get into encoding & documenting a new method that may be similarly brittle.

[jashapiro]

A couple more suggestions for rendering

[sjspielman]

@jashapiro I had missed the TOC and PDF re-render for the intro cheatsheet. Can I get a thumbs here for changes made in f103eb5 and 4795e88 ?

[jashapiro]

@jashapiro I had missed the TOC and PDF re-render for the intro cheatsheet. Can I get a thumbs here for changes made in f103eb5 and 4795e88 ?

👍🏼