Update cheatsheet links for intro-R and scRNAseq #521

sjspielman · 2022-02-28T14:24:06Z

This PR addresses Issue #515 for the most immediate cheatsheet needs (with other cheatsheet updates coming in future PRs):

intro-to-R-tidyverse-cheatsheet.md
scRNA-seq-cheatsheet.md

Links have been moved from rdocumentation --> rdrr and otherwise updated when appropriate.

Feedback I know is needed:

Agree on updated links?
There is one item in the scRNA-seq cheatsheet which I could not update. The cheatsheet references a {scater} function normalize() which does not appear in any {scater} docs, but maybe {scuttle}?
It seems these cheatsheets are not rendered at build time, but I'm not clear which pandoc command is used to match the existing format, so there are no PDFs yet.

…or a scater link which I can't find. Future commits will figure out how to knit these into the right PDF format

jashapiro · 2022-02-28T15:51:20Z

There is one item in the scRNA-seq cheatsheet which I could not update. The cheatsheet references a {scater} function normalize() which does not appear in any {scater} docs, but maybe {scuttle}?

Yes, that is the correct function; it is reexported by scater. I think we can keep it listed as a scater function for now, to reduce cognitive load, but the link can go to the docs in scuttle

jashapiro · 2022-02-28T15:54:50Z

I assume that these were just rendered from an rstudio

It seems these cheatsheets are not rendered at build time, but I'm not clear which pandoc command is used to match the existing format, so there are no PDFs yet.

Going by the appearance, I would guess these were not rendered by pandoc, but were rendered as html followed by conversion "print to pdf" or equivilent. I would be 100% fine with the rendered versions being replaced by html.

jashapiro · 2022-02-28T15:57:01Z

I assume that these were just rendered from an rstudio

It seems these cheatsheets are not rendered at build time, but I'm not clear which pandoc command is used to match the existing format, so there are no PDFs yet.

Going by the appearance, I would guess these were not rendered by pandoc, but were rendered as html followed by conversion "print to pdf" or equivilent. I would be 100% fine with the rendered versions being replaced by html.

I take that back: changing to html would require link updates... Not sure we want to do that right now as it will take some time to track those down. Adding html would be fine though!

jashapiro

Looks good overall. I made some formatting and content suggestions in my comments below, and we will definitely want the PDFs in this PR to preserve current links to those files. As per my previous comment, adding html versions will not hurt.

module-cheatsheets/intro-to-R-tidyverse-cheatsheet.md

jashapiro · 2022-02-28T16:07:23Z

module-cheatsheets/intro-to-R-tidyverse-cheatsheet.md

-| Base `R`          | [`c()`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/c)                     | Combine           | Combines values into a vector or list.                                                                                                                                                             |
+| Base `R`          | [`library()`](https://rdrr.io/r/base/library.html)                    | Library   | Loads and attaches additional packages to the R environment.                                                                                                                                                  |
+| Base `R`          | [`<-`](https://rdrr.io/r/base/assignOps.html)                    | Assignment operator   | Assigns a name to something in the R environment.                                                                                                                                                  |
+| Base `R`          | [`c()`](https://rdrr.io/r/base/c.html)                     | Combine           | Combines values into a vector or list.                                                                                                                                                             |
 | Base `R`          | [`%in%`](http://www.datasciencemadesimple.com/in-operator-in-r/)                                  | "in" logical operator           | Checks if the given value(s) on the left side of the operator are in the vector or other R object defined on the right side of the operator. It returns a logical `TRUE` or `FALSE` statement.                                                                                                                                                              |


Suggested change

| Base `R` | [`%in%`](http://www.datasciencemadesimple.com/in-operator-in-r/) | "in" logical operator | Checks if the given value(s) on the left side of the operator are in the vector or other R object defined on the right side of the operator. It returns a logical `TRUE` or `FALSE` statement. |

| Base `R` | [`%in%`](http://www.datasciencemadesimple.com/in-operator-in-r/) | "in" logical operator | Checks if the given value(s) on the left side of the operator are in the vector or other R object defined on the right side of the operator. It returns a logical `TRUE` or `FALSE` statement. |

Do we want to link to https://rdrr.io/r/base/match.html for uniformity? We could link to both...

I actually went back and forth on this one. I liked the datasciencemadesimple more because it was just about the operator, but point taken about consistency. I think both is a good call for this one. I can change the link to rdrr, and add into description [This](datsciencemadesimple) is also useful or similar.

jashapiro · 2022-02-28T16:10:19Z

module-cheatsheets/scRNA-seq-cheatsheet.md



 ### `ggplot2`

-Read the `ggplot2` documentation [**here**](https://ggplot2.tidyverse.org/reference/).
+Read the `ggplot2` documentation [**here**](https://ggplot2.tidyverse.org/).


Curious about this change. I think the link to the list of all functions may be more useful than the homepage for this use case. This may also apply to the earlier ggplot2 link in the intro cheatsheet (we should be consistent either way).

First, this is a general thing to come back to for consistency.

I much prefer presenting the overall landing page for the documentation, sans reference, because it allows them to hop anywhere in the ggplot2 docs without being strictly presented with an overwhelming list of functions, most of which will be unfamiliar to them. Maybe we need a third opinion on this one..

Middle ground: we can have it all!

Read the ggplot2 package documentation here, as well as an overall reference for ggplot2 functions here.

Just noting here that you didn't implement the same changes as in the intro here, but I think that is fine. I also noticed that we only apparently add one new ggplot command here, which makes me wonder if we need it at all. Maybe just add geom_vline to the geom_hline section from the intro and remove it from the single cell doc?

Just noting here that you didn't implement the same changes as in the intro here, but I think that is fine.

Can't hurt, will do.

Maybe just add geom_vline to the geom_hline section from the intro and remove it from the single cell doc?

Makes sense to me!

I've decided to also delete the final description bit that suggests geom_vline() and friends can only be used on top of another geom.

module-cheatsheets/intro-to-R-tidyverse-cheatsheet.md

jashapiro · 2022-02-28T16:18:55Z

module-cheatsheets/scRNA-seq-cheatsheet.md

+| `SingleCellExperiment`| [`counts()`](https://bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html#4_Convenient_access_to_named_assays)| Counts| Stores or extracts raw single-cell experiment count data as an assay of the `SingleCellExperiment` object|
+| `scran` | [`quickCluster()`](https://rdrr.io/bioc/scran/man/quickCluster.html) | Quick Clustering     | Groups similar cells into clusters which are stored in the `SingleCellExperiment` object and are used for the calculation of size factors by `scran::computeSumFactors`|
+| `scran` | [`computeSumFactors()`](https://rdrr.io/bioc/scran/man/computeSumFactors.html)  | Compute Sum Factors| Returns a numeric vector of computed sum factors for each cell cluster stored in the `SingleCellExperiment` object. The cluster-based size factors are deconvolved into cell-based size factors that are stored in the `SingleCellExperiment` object and used by the `scran::normalize` function for the normalization of each cell's gene expression profile|
+| `scater`| [`TODO!!!!! normalize()`](https://www.rdocumentation.org/packages/scater/versions/1.0.4/topics/normalize)| Normalize | Returns the `SingleCellExperiment` object with normalized expression values for each cell, using the size factors stored in the object 


When you update this, consider moving it with the other scater functions.

module-cheatsheets/scRNA-seq-cheatsheet.md

jaclyn-taroni · 2022-02-28T16:33:03Z

Commenting on the PDF, HTML bit only from the context in my email (what could go wrong!) - a concern I have about having both files is that they'll get out of date with each other. So can we add a docs change with how to render via pandoc to a module-cheatsheets/README? A future enhancement could have this rendering as part of the other rendering workflow?

sjspielman · 2022-02-28T16:40:24Z

Going by the appearance, I would guess these were not rendered by pandoc, but were rendered as html followed by conversion "print to pdf" or equivalent.

They are definitely not rendered with pagedown::chrome_print() from what I can tell, because links don't come out blue anymore...and markdown links are wrecked. Attached is an example of a chrome-printed version.
intro-to-R-tidyverse-cheatsheet_chrome_print.pdf

@jaclyn-taroni Yes, this definitely needs to be added to README, once we know where they came from in the first place 🙃

jaclyn-taroni · 2022-02-28T16:41:25Z

You're not going to like this answer, but almost certain it's MacDown. It doesn't need to stay that way though.

Co-authored-by: Joshua Shapiro <[email protected]>

sjspielman · 2022-02-28T19:52:50Z

The plot thickens! It's been a bit hard to find concise docs for normalize() and unfortunately I found it here - https://rdrr.io/bioc/scater/man/defunct.html 🤔

jashapiro · 2022-02-28T20:03:14Z

The plot thickens! It's been a bit hard to find concise docs for normalize() and unfortunately I found it here - https://rdrr.io/bioc/scater/man/defunct.html 🤔

Looks like we followed that warning and removed it some time ago. So we should change that to logNormCounts, which we do use!

sjspielman · 2022-02-28T22:06:05Z

You're not going to like this answer, but almost certain it's MacDown.

Womp. Confirmed, it was definitely MacDown. And excitingly, it will remain MacDown!

sjspielman · 2022-03-01T18:56:11Z

Since we're probably going to stick with MacDown PDF export (they look nice!), I'd like to get the final PDFs for these two cheatsheets into this PR too. Once we feel the md's are ready to go, I will commit updated PDFs, and also add a README about this.. "rendering workflow."

jashapiro · 2022-03-01T19:01:26Z

Since we're probably going to stick with MacDown PDF export (they look nice!), I'd like to get the final PDFs for these two cheatsheets into this PR too. Once we feel the md's are ready to go, I will commit updated PDFs, and also add a README about this.. "rendering workflow."

Go ahead and commit the PDFs alongside any md changes. No need to wait for multiple rounds of review.

…eq FYI about package versions

jashapiro · 2022-03-01T19:28:27Z

module-cheatsheets/README.md

@@ -0,0 +1,8 @@
+### Cheatsheets Module


I think this content makes more sense as part of CONTRIBUTING.md than living here.

components/dictionary.txt

Co-authored-by: Joshua Shapiro <[email protected]>

sjspielman · 2022-03-01T19:57:49Z

Looks like a few subheaders had either not previously made in into the TOC, or they had been manually removed.

sjspielman · 2022-03-01T19:58:09Z

And the dictionary is sad again :/

jashapiro

This looks good; Thanks for the update to the contributing docs as well!

I had one remaining comment about the lonely ggplot section in the single-cell cheatsheet. I'd be fine with merging it into the intro, but it is up to you. If you do make that update, make sure to rerender both PDFs.

I don't think I need to rereview.

jashapiro · 2022-03-01T20:54:09Z

module-cheatsheets/scRNA-seq-cheatsheet.md



 ### `ggplot2`

-Read the `ggplot2` documentation [**here**](https://ggplot2.tidyverse.org/reference/).
+Read the `ggplot2` documentation [**here**](https://ggplot2.tidyverse.org/).


Just noting here that you didn't implement the same changes as in the intro here, but I think that is fine. I also noticed that we only apparently add one new ggplot command here, which makes me wonder if we need it at all. Maybe just add geom_vline to the geom_hline section from the intro and remove it from the single cell doc?

jashapiro · 2022-03-01T21:05:23Z

And the dictionary is sad again :/

Surprised it checked the contributing doc, but ah well. My only other comment would have been to change "md" to "`.md`" to avoid making "md" a dictionary word (the spellchecker skips code and I think it knows that backticks denote code.)

jashapiro · 2022-03-01T21:06:55Z

CONTRIBUTING.md

+ Open a md cheatsheet in MacDown, and go to `File` -> `Export` -> `PDF`
+ Save appropriately and voila!
+
+When choosing documentation links to incorporate in cheatsheets, we prefer to use [https://rdrr.io/](https://rdrr.io/) when possible for Base R and Bioconductor, and we prefer to use [https://www.tidyverse.org/](https://www.tidyverse.org/) for `tidyverse` functions. 


Get past spellcheck

Suggested change

When choosing documentation links to incorporate in cheatsheets, we prefer to use [https://rdrr.io/](https://rdrr.io/) when possible for Base R and Bioconductor, and we prefer to use [https://www.tidyverse.org/](https://www.tidyverse.org/) for `tidyverse` functions.

When choosing documentation links to incorporate in cheatsheets, we prefer to use [`https://rdrr.io/`](https://rdrr.io/) when possible for Base R and Bioconductor, and we prefer to use [https://www.tidyverse.org/](`https://www.tidyverse.org/`) for `tidyverse` functions.

Oh boy those latter tickmarks are wrong anyways, huh. Good catch.

No, my suggestion was wrong with one of them!

components/dictionary.txt

Co-authored-by: Joshua Shapiro <[email protected]>

CONTRIBUTING.md

…tsheet. Re-render PDF

Co-authored-by: Joshua Shapiro <[email protected]>

sjspielman added 3 commits February 25, 2022 17:08

Links updated for intro-to-R-tidyverse-cheatsheet

1cd02ca

Removed HTMLs which we do not save. Updated scRNA cheatsheet EXCEPT f…

d8a5a3d

…or a scater link which I can't find. Future commits will figure out how to knit these into the right PDF format

Removed yaml

f62abe7

sjspielman requested a review from jashapiro February 28, 2022 14:24

Add function to ggplot section of cheatsheet, as discussed in Issue #520

53b41de

sjspielman mentioned this pull request Feb 28, 2022

Replace xlab() and ylab() with labs() in intro and scRNA-seq modules #522

Merged

jashapiro reviewed Feb 28, 2022

View reviewed changes

jaclyn-taroni mentioned this pull request Feb 28, 2022

Add rendering of module cheatsheets to make-live workflow #523

Open

sjspielman and others added 4 commits February 28, 2022 13:12

Update module-cheatsheets/intro-to-R-tidyverse-cheatsheet.md

978b566

Co-authored-by: Joshua Shapiro <[email protected]>

Update module-cheatsheets/intro-to-R-tidyverse-cheatsheet.md

d201194

Co-authored-by: Joshua Shapiro <[email protected]>

Update module-cheatsheets/scRNA-seq-cheatsheet.md

77eb6fb

Co-authored-by: Joshua Shapiro <[email protected]>

Update module-cheatsheets/scRNA-seq-cheatsheet.md

f303167

Co-authored-by: Joshua Shapiro <[email protected]>

sjspielman added 2 commits February 28, 2022 17:07

Fixed normalize link

f19c4ae

Updates to intro cheatsheet

cc40f7b

sjspielman added 3 commits March 1, 2022 14:12

PDFs of updated cheatsheets with MacDown. Also added blurb to scRNA-s…

14a9e53

…eq FYI about package versions

we use macdown for pdfs

9c15f26

Dictionary updates for cheatsheet README

c444097

jashapiro reviewed Mar 1, 2022

View reviewed changes

Removed cheatsheet readme and fleshed out section in CONTRIBUTING

f7ca9c1

jashapiro reviewed Mar 1, 2022

View reviewed changes

components/dictionary.txt Outdated Show resolved Hide resolved

sjspielman and others added 2 commits March 1, 2022 14:53

Update components/dictionary.txt

1beccc7

Co-authored-by: Joshua Shapiro <[email protected]>

doctoc'd CONTRIBUTING

88d78d7

markdown words back into the dictionary

3535f53

jashapiro approved these changes Mar 1, 2022

View reviewed changes

jashapiro reviewed Mar 1, 2022

View reviewed changes

components/dictionary.txt Outdated Show resolved Hide resolved

sjspielman and others added 2 commits March 1, 2022 18:04

Update components/dictionary.txt

163bf0f

Co-authored-by: Joshua Shapiro <[email protected]>

Update CONTRIBUTING.md

0431341

Co-authored-by: Joshua Shapiro <[email protected]>

jashapiro reviewed Mar 1, 2022

View reviewed changes

CONTRIBUTING.md Outdated Show resolved Hide resolved

sjspielman and others added 4 commits March 1, 2022 18:15

rm ggplot from scRNA-seq, include hline and vline geoms in intro chea…

8ba3de6

…tsheet. Re-render PDF

Update CONTRIBUTING.md

5f1175b

Co-authored-by: Joshua Shapiro <[email protected]>

go away md

31ee52a

PDF formatting fixed

0c883d4

sjspielman merged commit 747a2bd into master Mar 1, 2022

jashapiro mentioned this pull request Mar 3, 2022

Update cheatsheet links #515

Closed

jaclyn-taroni mentioned this pull request Mar 3, 2022

Update links in RNA-seq, pathway-analysis, and machine-learning cheatsheets #528

Open

3 tasks

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update cheatsheet links for intro-R and scRNAseq #521

Update cheatsheet links for intro-R and scRNAseq #521

sjspielman commented Feb 28, 2022 •

edited

Loading

jashapiro commented Feb 28, 2022

jashapiro commented Feb 28, 2022

jashapiro commented Feb 28, 2022

jashapiro left a comment

jashapiro Feb 28, 2022

sjspielman Feb 28, 2022

jashapiro Feb 28, 2022

sjspielman Feb 28, 2022

sjspielman Feb 28, 2022

jashapiro Mar 1, 2022

sjspielman Mar 1, 2022

sjspielman Mar 1, 2022

jashapiro Feb 28, 2022

jaclyn-taroni commented Feb 28, 2022

sjspielman commented Feb 28, 2022 •

edited

Loading

jaclyn-taroni commented Feb 28, 2022

sjspielman commented Feb 28, 2022

jashapiro commented Feb 28, 2022

sjspielman commented Feb 28, 2022 •

edited

Loading

sjspielman commented Mar 1, 2022

jashapiro commented Mar 1, 2022

jashapiro Mar 1, 2022

sjspielman commented Mar 1, 2022

sjspielman commented Mar 1, 2022

jashapiro left a comment

jashapiro Mar 1, 2022

jashapiro commented Mar 1, 2022

jashapiro Mar 1, 2022

sjspielman Mar 1, 2022

jashapiro Mar 1, 2022

	\| Base `R` \| [`%in%`](http://www.datasciencemadesimple.com/in-operator-in-r/) \| "in" logical operator \| Checks if the given value(s) on the left side of the operator are in the vector or other R object defined on the right side of the operator. It returns a logical `TRUE` or `FALSE` statement. \|
	\| Base `R` \| [`%in%`](http://www.datasciencemadesimple.com/in-operator-in-r/) \| "in" logical operator \| Checks if the given value(s) on the left side of the operator are in the vector or other R object defined on the right side of the operator. It returns a logical `TRUE` or `FALSE` statement. \|

	When choosing documentation links to incorporate in cheatsheets, we prefer to use [https://rdrr.io/](https://rdrr.io/) when possible for Base R and Bioconductor, and we prefer to use [https://www.tidyverse.org/](https://www.tidyverse.org/) for `tidyverse` functions.
	When choosing documentation links to incorporate in cheatsheets, we prefer to use [`https://rdrr.io/`](https://rdrr.io/) when possible for Base R and Bioconductor, and we prefer to use [https://www.tidyverse.org/](`https://www.tidyverse.org/`) for `tidyverse` functions.

Update cheatsheet links for intro-R and scRNAseq #521

Update cheatsheet links for intro-R and scRNAseq #521

Conversation

sjspielman commented Feb 28, 2022 • edited Loading

jashapiro commented Feb 28, 2022

jashapiro commented Feb 28, 2022

jashapiro commented Feb 28, 2022

jashapiro left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

jaclyn-taroni commented Feb 28, 2022

sjspielman commented Feb 28, 2022 • edited Loading

jaclyn-taroni commented Feb 28, 2022

sjspielman commented Feb 28, 2022

jashapiro commented Feb 28, 2022

sjspielman commented Feb 28, 2022 • edited Loading

sjspielman commented Mar 1, 2022

jashapiro commented Mar 1, 2022

Choose a reason for hiding this comment

sjspielman commented Mar 1, 2022

sjspielman commented Mar 1, 2022

jashapiro left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

jashapiro commented Mar 1, 2022

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

sjspielman commented Feb 28, 2022 •

edited

Loading

sjspielman commented Feb 28, 2022 •

edited

Loading

sjspielman commented Feb 28, 2022 •

edited

Loading