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Initiate scAdvanced cheatsheet #663
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…monade/training-modules into sjspielman/scAdvanced-cheatsheet
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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...
Co-authored-by: Joshua Shapiro <[email protected]>
@jashapiro this should be ready for another look! I've implemented the in-line reviews, and I also went ahead and purged all the |
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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?
@@ -24,12 +24,16 @@ Read the Base `R` documentation [**here**](https://rdrr.io/r/). | |||
| Base `R`| [`<-function(x) { <code> }`](https://adv-r.hadley.nz/functions.html) | Function | Creates a function that would take the defined parameters as input and execute the commands within the curly braces | |
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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
Co-authored-by: Joshua Shapiro <[email protected]>
…a CSS comment style and that's a thing i made up
This has been updated in a couple ways:
I also decided to think a little bit about PDF export, whose current status quo (please enjoy the |
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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.
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 |
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. |
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A couple more suggestions for rendering
Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: Joshua Shapiro <[email protected]>
@jashapiro I had missed the TOC and PDF re-render for the |
👍🏼 |
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:
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 committedmd
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:
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 lightpurrr
in intro, too!!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 thescater
functions into the advanced, since they're important for advanced and come up a lot (plotReducedDim
andplotUMAP
). Eventually this will get solidified with "cheatsheets by topic," so I thought this duplication would be ok for now.miQC
explanations, any thoughts? Somehow "Plot the miQC model" forplotModel()
didn't seem enough, but actually explaining what gets plotted makes for a LONG table row...!HarmonyMatrix()
is "Main Harmony interface". Feeling like I just ignore that and write "harmony matrix"...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 justggplot2
?)