add raincloud plots from Beacon Biosignals #1725

SimonDanisch · 2022-03-04T14:27:54Z

We decided to open source @kimlaberinto amazing raincloud plots and add them to base Makie.
This is a direct port of the docs & the latest implementation.
@kimlaberinto wanted to spent some more time to make the recipe even more usable/pretty before we merge.
We also need to add some tests to the reference image tests.

cc: @haberdashPI @ericphanson @mich11 @palday @jrevels

kimlaberinto · 2022-03-04T17:32:46Z

@haberdashPI mentioned this in a previous discussion that we've had. I wanted to repost it here so others can see and so that we potentially make this change as well.

I want to advocate for the API that is made public to be compatible with AlgebraOfGraphics. I think it's a simple change and it would be nice if it worked straightforwardly in that case: basically the interface needs to use a flat array (like columns of a DataFrame) to denote the category labels along x, rather than using nested arrays by default. I was thinking of making a little PR myself to do this...

MakieBot · 2022-03-06T09:12:38Z

Compile Times benchmark

Note, that these numbers may fluctuate on the CI servers, so take them with a grain of salt.

using time

master:  9.11 < 9.12 > 9.18, 0.02+-
pr:      9.10 < 9.14 > 9.24, 0.04+-
speedup: 0.99 < 1.00 > 1.00, 0.01+-
median:  +0.24% => invariant

This PR does not change the using time.

ttfp time

master   25.53 < 25.61 > 25.73, 0.07+-
pr       25.47 < 25.57 > 25.91, 0.14+-
speedup: 0.99 < 1.00 > 1.01, 0.01+-
median:  -0.16% => invariant

This PR does not change the ttfp time.

haberdashPI · 2022-04-25T15:09:05Z

I've added some proposed changes in #1839. See that PR for details. I've tested this with a PR of AoG which supports the latest version of Makie (by just updated the [compat] entries), and that seems to be working well for calling visual(RainClouds).

* support flat array style for raincloud plot * hacky fix * revise category labels * fix labels * fix x labels again * working dodge / color * update docs * update news/docs * moved news item * fix `rainclouds` news item

haberdashPI · 2022-05-03T14:44:41Z

Sorry about that, it looks like my use of some newer keyword syntax is leading to the failures on 1.3: (;show_median) instead of (;show_median=show_median)

src/basic_recipes/raincloud.jl

Co-authored-by: David Little <david.frank.little@gmail.com>

NEWS.md

SimonDanisch · 2022-05-04T11:18:16Z

Ok, this should build now...
I removed dodge here: ba50702, since group_labels didn't seem to have the ability to deal with dodge...Not sure if zipping dodge in there was just an oversight, or if group_labels should be able to deal with that.
Also, it's all gray now, I think before, it was cycling the color?

haberdashPI · 2022-05-04T12:42:45Z

It should probably be cycling color; I can investigate/debug today or tomorrow. Is there anything special I should know to setup the doc build on my machine?

SimonDanisch · 2022-05-04T13:06:42Z

add raincloud plots from Beacon Biosignals by SimonDanisch · Pull Request #1725 · JuliaPlots/Makie.jl

I think it was doing that before, if I'm not mistaken.. So think something got removed ;)

Is there anything special I should know to setup the doc build on my machine?

I usually just copy out the code blocks, since the setup is a bit annoying and you can't just build a single page 😅

haberdashPI · 2022-05-13T14:36:30Z

I've made some updates to the docs in #1936 .

This also fixes a few bugs I found in the process.

* improve raincloud examples * improve docs * fix hist coloring * remove redundant computations

SimonDanisch · 2022-05-13T15:30:07Z

Test failures due to: #1937

NEWS.md

hannahilea · 2022-05-18T18:54:46Z

docs/examples/plotting_functions/rainclouds.md

+####
+
+function mockup_distribution(N)
+    all_possible_labels = ["Single Mode", "Double Mode", "Single Mode", "Double Mode", 


is it intentional that single mode and double mode show up twice here?

hannahilea · 2022-05-18T18:55:23Z

docs/examples/plotting_functions/rainclouds.md

+        random_mean = rand_localized(0, 8)
+        random_spread_coef = rand_localized(0.3, 1)
+        data_points = random_spread_coef*randn(Int(round(N/2.0))) .+ random_mean
+


Suggested change

random_mean = rand_localized(0, 8)

random_spread_coef = rand_localized(0.3, 1)

data_points = random_spread_coef*randn(Int(round(N/2.0))) .+ random_mean

potential duplication? otherwise these variables get overridden immediately

This looks right to me. (Note the vcat on line 33).

Co-authored-by: Hannah Robertson <hannahilea@users.noreply.github.com>

haberdashPI · 2022-06-02T15:39:55Z

What's left to have this merge? I thought small docs fixes addressed @hannahilea's comments based on the name, but it looks like that's actually fixing something else. Happy to address those unresolved issues in a new PR to merge here.

SimonDanisch · 2022-06-03T10:46:10Z

Yes, I think that's what's mostly left.
Would also be nice to bring back the color cycling. Let me know if you need help with that.

haberdashPI · 2022-06-03T12:01:36Z

Would also be nice to bring back the color cycling. Let me know if you need help with that.

I think this is addressed? At least when I ran the help examples on my machine they are colored now. (#1936)

I'll set up a PR to fix @hannahilea's comments.

SimonDanisch · 2022-06-03T12:12:22Z

Ah you're right, great :) Somehow the last time I checked the docs build, it was still all black

haberdashPI · 2022-06-03T15:09:10Z

#2019 makes a small fix to address @hannahilea's comments.

* small fix to raincloud docs * fix modes

SimonDanisch · 2022-06-03T16:38:34Z

Yay, thanks everyone :)

haberdashPI · 2022-06-07T20:34:06Z

src/basic_recipes/raincloud.jl

@@ -249,7 +249,7 @@ function plot!(plot::RainClouds)
                    show_median=show_median, side=side, width=width_ratio*cloud_width, plot.cycle,
                    plot.color, gap=0)
        elseif clouds === hist
-            for (_, ixs) in group_labels(zip(category_labels, plot.dodge[]), data_array)


Just realize that this was actually intentional. Without this, the histogram doesn't group by dodge, and so you get one histogram for all of the dodge groups. 😢

I'm submitting a small PR soon to implement orientation=:horizontal for rainclouds. I'll add a fix for this in that PR.

add raincloud plots from Beacon

9aaf611

Merge branch 'master' into sd/rainclouds

bc99a9f

haberdashPI mentioned this pull request Apr 25, 2022

Update compat bounds for Makie MakieOrg/AlgebraOfGraphics.jl#383

Closed

haberdashPI and others added 2 commits May 2, 2022 18:54

Improved Rainclouds API (#1839)

4ac8072

* support flat array style for raincloud plot * hacky fix * revise category labels * fix labels * fix x labels again * working dodge / color * update docs * update news/docs * moved news item * fix `rainclouds` news item

Merge branch 'master' into sd/rainclouds

54cb12d

SimonDanisch added 2 commits May 3, 2022 16:48

Merge branch 'master' into sd/rainclouds

3d9aab9

fixes for 1.3

3d04828

haberdashPI reviewed May 3, 2022

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haberdashPI reviewed May 3, 2022

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SimonDanisch and others added 2 commits May 3, 2022 19:54

Update src/basic_recipes/raincloud.jl

bd7471b

Co-authored-by: David Little <david.frank.little@gmail.com>

Update src/basic_recipes/raincloud.jl

46d8595

Co-authored-by: David Little <david.frank.little@gmail.com>

jrevels reviewed May 3, 2022

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SimonDanisch added 3 commits May 4, 2022 13:06

Merge branch 'master' into sd/rainclouds

74c9cd4

dodge doesn't seem to belong here

ba50702

fix spelling

95a67f8

Merge branch 'master' into sd/rainclouds

a1ee4cc

haberdashPI mentioned this pull request May 13, 2022

Small raincloud fixes #1936

Merged

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haberdashPI and others added 2 commits May 13, 2022 16:43

Small raincloud fixes (#1936)

388075f

* improve raincloud examples * improve docs * fix hist coloring * remove redundant computations

Merge branch 'master' into sd/rainclouds

a6a55bd

Merge branch 'master' into sd/rainclouds

a494d03

hannahilea reviewed May 18, 2022

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SimonDanisch and others added 4 commits May 19, 2022 11:50

Update NEWS.md

a047de2

Co-authored-by: Hannah Robertson <hannahilea@users.noreply.github.com>

Merge branch 'master' into sd/rainclouds

1450903

small docs fixes

fa21fb4

Merge branch 'master' into sd/rainclouds

d244162

Merge branch 'master' into sd/rainclouds

b6afc8a

haberdashPI and others added 2 commits June 3, 2022 17:47

Small fix to raincloud docs (#2019)

16d0305

* small fix to raincloud docs * fix modes

Update rainclouds.md

4d06fa5

SimonDanisch merged commit 0022960 into master Jun 3, 2022

SimonDanisch deleted the sd/rainclouds branch June 3, 2022 16:38

haberdashPI reviewed Jun 7, 2022

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haberdashPI mentioned this pull request Jun 7, 2022

Rainclouds: support orientation = :horizontal #2030

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add raincloud plots from Beacon Biosignals #1725

add raincloud plots from Beacon Biosignals #1725

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add raincloud plots from Beacon Biosignals #1725

add raincloud plots from Beacon Biosignals #1725

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Compile Times benchmark

using time

ttfp time

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