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2
cheatsheets/julia.qmd
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@ -11,7 +11,7 @@
| What is ...? | `typeof(obj)` | `type(obj)` | `class(obj)` |
| Is it really a ...? | `isa(obj, SomeType)` | `isinstance(obj, SomeType)` | `is(obj, SomeType)` |
## debugging
## debugging {#debugging}
| | |
|------------------------------------|------------------------------------|

14
material/1_mon/firststeps/firststeps_handout.qmd
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@ -428,6 +428,18 @@ Macros allow to programmers to edit the actual code **before** it is run. We wil
@show a
```
## Debugging
XXX
### Debug messages
```julia
@debug "my debug message"
ENV["JULIA_DEBUG"] = Main
ENV["JULIA_DEBUG"] = MyPackage
```
### Debugger proper:
[Cheatsheet for debugging](../../../cheatsheets/julia.qmd#debugging)
In most cases, `@run myFunction(1,2,3)` is sufficient.

199
material/3_wed/vis/handout.ipynb
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@ -6,10 +6,13 @@
"source": [
"---\n",
"\n",
"\n",
"\n",
"\n",
"jupyter: julia-1.9\n",
"---"
],
"id": "d0dd3b54"
"id": "18cb9530"
},
{
"cell_type": "markdown",
@ -26,6 +29,32 @@
"\n",
"I will use `GLMakie` or `CairoMakie`. To switch use `CairoMakie.activate!()`\n",
"\n",
"## Standard plotting commands\n"
],
"id": "d83f21c4"
},
{
"cell_type": "code",
"metadata": {},
"source": [
"f = Figure()\n",
"x = rand(100)\n",
"y = rand(100)\n",
"\n",
"scatter(f[1,1],x,y)\n",
"lines(f[1,2],x,y)\n",
"hist(f[2,1],x)\n",
"density!(f[2,1],x) # inplace -> add to current plot\n",
"stem(f[2,2],x)"
],
"id": "811907e9",
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Layouts for scientific figures\n",
"\n",
"# Pluto.jl for easy interactivity\n",
@ -46,7 +75,7 @@
"\n",
"### Loading data"
],
"id": "0ca52ae6"
"id": "69dda8de"
},
{
"cell_type": "code",
@ -59,7 +88,7 @@
"penguins = dropmissing(DataFrame(PalmerPenguins.load()))\n",
"first(penguins, 6)"
],
"id": "56b4e637",
"id": "334f10aa",
"execution_count": null,
"outputs": []
},
@ -82,42 +111,150 @@
"### AoG basics\n",
"\n",
"\n",
"`data * mapping * visual`\n",
"\n",
"```julia\n",
"`data * mapping * visual`\n"
],
"id": "0bfbe711"
},
{
"cell_type": "code",
"metadata": {},
"source": [
" vis_pen = data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * visual(Scatter) \n",
" draw(vis_pen)\n",
"```\n",
"\n",
"### Adding color\n",
"\n",
"```julia\n",
" draw(vis_pen)"
],
"id": "cc740038",
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Adding color\n"
],
"id": "3fd4693f"
},
{
"cell_type": "code",
"metadata": {},
"source": [
"vis_pencolor = data(penguins) * mapping(:bill_length_mm, :bill_depth_mm, color = :species) * visual(Scatter)\n",
"draw(vis_pencolor)\n",
"\n",
"```\n",
"But that is a bit redundant, you can shortcut this, by reusing existing mappings / inputs:\n",
"```julia\n",
"draw(vis_pencolor)"
],
"id": "b8e715a3",
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"But that is a bit redundant, you can shortcut this, by reusing existing mappings / inputs:"
],
"id": "ca61723b"
},
{
"cell_type": "code",
"metadata": {},
"source": [
"vis_pencolor2 = vis_pen * mapping(color=:species)\n",
"draw(vis_pencolor2)\n",
"\n",
"```\n",
"\n",
"draw(vis_pencolor2)"
],
"id": "84f60a09",
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Why `Algebra`OfGraphics?\n",
"\n",
"Follows some algebraic rules of multiplying out sums\n",
"\n",
"`data * mapping * visual(Scatter+Lines)`\n",
"\n",
"```julia\n",
"\n",
" vis_pen = data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * visual(Scatter+Lines) \n",
"```\n",
"\n",
"### Faceting\n",
"jl plt = penguin_bill * layers * mapping(color = :species, col = :sex)"
"`data * mapping * (visual(Scatter)+visual(Lines))`\n"
],
"id": "3ead8444"
"id": "cad8ff41"
},
{
"cell_type": "code",
"metadata": {},
"source": [
"data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * (visual(Scatter)+visual(Lines)) |> draw"
],
"id": "84fc3a4e",
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Faceting"
],
"id": "1b7f38f7"
},
{
"cell_type": "code",
"metadata": {},
"source": [
"data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * mapping(color = :species, col = :sex) |> draw"
],
"id": "90ba7bee",
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"metadata": {},
"source": [
"data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * mapping(color = :species, col = :sex,row=:body_mass_g => x-> x>3500) |> draw"
],
"id": "84d76ff4",
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Linear & Non-linear summaries"
],
"id": "ed061ded"
},
{
"cell_type": "code",
"metadata": {},
"source": [
"data(penguins) * mapping(:bill_length_mm, :bill_depth_mm, color=:species) * (linear() + visual(Scatter)) |> draw"
],
"id": "bfaf33f5",
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"metadata": {},
"source": [
"data(penguins) * mapping(:bill_length_mm, :bill_depth_mm, color=:species) * (smooth() + visual(Scatter)) |> draw"
],
"id": "00aaa0bd",
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Interactivity\n",
"\n",
"With Makie.jl, two ways of interactivity:\n",
"\n",
"**Observables** - very general way, a little bit more verbose\n",
"\n",
"**Pluto.jl Sliders** - very simple, need to redraw plot everytime^[it is technically possible t combine Pluto with Observables, but it is a bit buggy] \n"
],
"id": "fb64ae39"
}
],
"metadata": {

161
material/3_wed/vis/handout.qmd
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@ -1,7 +1,4 @@
---
jupyter: julia-1.9
---
# Makie.jl
## Backends
@ -13,9 +10,135 @@ Four backends:
I will use `GLMakie` or `CairoMakie`. To switch use `CairoMakie.activate!()`
## Standard plotting
```julia
f = Figure()
x = rand(100)
y = rand(100)
scatter(f[1,1],x,y)
lines(f[1,2],x,y)
hist(f[2,1],x)
density!(f[2,1],x) # inplace -> add to current plot
stem(f[2,2],x)
```
## Layouts for scientific figures
# Pluto.jl for easy interactivity
Makie has the best layouting tool I have ever used. [full tutorial here](https://docs.makie.org/stable/tutorials/layout-tutorial/)
```julia
f = Figure()
# we plan to generate two subfigures (with subplots each) - better to generate two "separate" layouts
ga = f[1, 1] = GridLayout()
gb = f[2, 1] = GridLayout()
axtop = Axis(ga[1,1])
axmain = Axis(ga[2, 1], xlabel = "before", ylabel = "after")
axright = Axis(ga[2, 2])
labels = ["treatment", "placebo", "control"]
d = randn(3, 100, 2) .+ [1, 3, 5]
for (label, col) in zip(labels, eachslice(d, dims = 1))
scatter!(axmain, col, label = label)
density!(axtop, col[:, 1])
density!(axright, col[:, 2], direction = :y)
end
linkyaxes!(axmain, axright)
linkxaxes!(axmain, axtop)
hidedecorations!(axtop, grid = false)
hidedecorations!(axright, grid = false)
#--- add a legend
leg = Legend(ga[1, 2], axmain)
# absolute size for now :shrug:
leg.width =100
leg.height =100
leg.tellwidth = true
leg.tellheight = true
#----
# second plot
ax,h = heatmap(gb[1,1],rand(100,10),colorrange = [0,1])
ax2,h2 = heatmap(gb[1,2],rand(100,10),colorrange = [0,1])
cb = Colorbar(gb[1,3],h)
cb.alignmode = Mixed(right=0)
#----
# Labels
Label(ga[1, 1, TopLeft()], "A1", font = :bold, padding = (0, 0, 5, 0))
Label(ga[2, 1, TopLeft()], "A2", font = :bold, padding = (0, 0, 5, 0))
Label(ga[2, 2, TopLeft()], "A3", font = :bold, padding = (0, 0, 5, 0))
Label(gb[1, 1, TopLeft()], "B", font = :bold, padding = (0, 0, 5, 0))
#---
# top plot needs more space
rowsize!(f.layout,2,Relative(0.3))
#---
f
```
# Interactivity
With Makie.jl, two ways of interactivity:
**Observables** - very general way, a little bit more verbose
**Pluto.jl Sliders** - very simple, need to redraw plot everytime^[it is technically possible to combine Pluto with Observables, but it is a bit buggy]
## Pluto.jl
### Installation / Start
```julia
]add Pluto
Pluto.run()
```
::: {.callout-tip}
If you need remote access, run it via `Pluto.run(host="0.0.0.0")`
:::
### Sliders
A slider is defined like this:
```julia
@bind yourVarName PlutoUI.Slider(from:to) # from:step:to is optional, step by def 1
```
if you move the slider, `yourVarName` + all cells that depend on that variable are automatically recalculated. Quick & dirty way to generate an interactive plot
## Bonus: Makie Interactivity
There is another way to get to interactivity. Using `Observables.jl`
To provide a simple example of the logic:
```julia
using GLMakie
x = rand(10_000)
obs_ix = Observable(1) # index to plot until
scatter(@lift(x[1:obs_ix])) # non-interactive example # <1>
f = Figure()
obs_sl = GLMakie.Slider(f[2,1],range=1:length(x))
y = @lift(x[1:$(obs_sl.value)])
ax,s = scatter(f[1,1],y)
xlims!(ax,0,length(x))
```
1. `@lift` does the heavy lifting (hrhr) here. It adds a listener to `obs_ix`, whenever that value is changed, the value of the output of `@lift` is changed as well
## Task 2: Interactivity
[Click here for the next task](tasks.qmd#2)
# Grammar of Graphics
@ -24,15 +147,15 @@ The grammar of graphics is a convenient way to build common explorative plots.
For example:
#### For ggplot enthusiasts:
## For ggplot enthusiasts
You could use [TidierPlots.jl - a ggplot clone](https://github.com/TidierOrg/TidierPlots.jl)
Check out the [../../../../cheatsheets/ggplotAOG.qmd]:
Check out the [AoG/GGplot cheatsheet](../../../../cheatsheets/ggplotAOG.qmd):
## AlgebraOfGraphics.jl
### Loading data
```{julia}
```julia
using GLMakie # backend
using AlgebraOfGraphics
using PalmerPenguins, DataFrames # example dataset
@ -58,20 +181,20 @@ Tidy data make your visualization life much easier as you will see!
`data * mapping * visual`
```{julia}
```julia
vis_pen = data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * visual(Scatter)
draw(vis_pen)
```
### Adding color
```{julia}
```julia
vis_pencolor = data(penguins) * mapping(:bill_length_mm, :bill_depth_mm, color = :species) * visual(Scatter)
draw(vis_pencolor)
```
But that is a bit redundant, you can shortcut this, by reusing existing mappings / inputs:
```{julia}
```julia
vis_pencolor2 = vis_pen * mapping(color=:species)
draw(vis_pencolor2)
@ -83,34 +206,30 @@ Follows some algebraic rules of multiplying out sums
`data * mapping * (visual(Scatter)+visual(Lines))`
```{julia}
```julia
data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * (visual(Scatter)+visual(Lines)) |> draw
```
### Faceting
```{julia}
```julia
data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * mapping(color = :species, col = :sex) |> draw
```
```{julia}
```julia
data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * mapping(color = :species, col = :sex,row=:body_mass_g => x-> x>3500) |> draw
```
### Linear & Non-linear summaries
```{julia}
```julia
data(penguins) * mapping(:bill_length_mm, :bill_depth_mm, color=:species) * (linear() + visual(Scatter)) |> draw
```
```{julia}
```julia
data(penguins) * mapping(:bill_length_mm, :bill_depth_mm, color=:species) * (smooth() + visual(Scatter)) |> draw
```
# Interactivity
## Task 3
With Makie.jl, two ways of interactivity:
**Observables** - very general way, a little bit more verbose
**Pluto.jl Sliders** - very simple, need to redraw plot everytime^[it is technically possible t combine Pluto with Observables, but it is a bit buggy]
[Click here for the next task](tasks.qmd#3)

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material/3_wed/vis/tasks.qmd
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@ -0,0 +1,161 @@
# Setting up Pluto.jl
Pluto is nice as you can prototype pretty fast.
::: callout-important
Pluto.jl has its own dependency management included!
If you want to add packages that are not registered, you have to activate your own environment. For example
```julia
using Pkg
Pkg.activate(mktempdir())
Pkg.add("/path/to/your/package/CoolPackage")
Pkg.add(url="https://github.com/username/MyPackage.jl")
using CoolPackage,MyPackage
```
:::
To run pluto in the first place use:
``` julia
]add Pluto
Pluto.run()
```
# Task 1: Visualize some statistic properties {#1}
## 1. Data
### Generate 500 normally distributed samples
::: callout-tip
You might want to make your results reproducible by fixing some seeds for the random generators. The two most common random generators used in julia are `Random.MersenneTwister` and `StableRNGs.StableRNG` - For this execrise I would recommend the latter (even though MersenneTwister is much more common to be used), thus run:
``` julia
using StableRNGs
randn(StableRNG(1),100)
```
to get 100 random numbers.
:::
Scale the random numbers to fullfill `std(x) ≈ 10`
### functionize it
Next wrap that code in a function `simulate` which takes two arguments, a random seed and the number of samples
## 2. cumulative mean
Calculate the cumulative mean of a single simulation. save it to a variable
Note that there is no `cummean` function, but clever element-wise division in combination with `cumsum` should lead you there - or you just use a loop :shrug:
::: {.callout-tip collapse="true"}
## click to show solution
`cumsum(x) ./ 1:length(x)`
:::
## 3. Plotting!
Now for your first plot. Use a `scatter` plot to visualize the cummulative mean output, if you do not generate a `Figure()` + `ax = f[1,1] = Axis(f)` manually, you can get it back by the scatter call. `f,ax,s = scatter()`. This is helpful as we later want to extend the `Axis` and `Figure` with other plot elements
Use `hlines!` to add a horizontal line at your "true" value
## 4. Subplot
### simulate repeatedly
Let's simulate 1000x datasets, each with a different seed, and take the mean over all simulated values
::: {.callout-tip collapse="true"}
## click to show tip
An easy way to call a function many times is to broadcast it on an array e.g. `1:1000` - you could also use `map` to do it, but I don't think it is as clear :)
:::
::: {.callout-tip collapse="true"}
## click to show solution
`simulate.(1:1000,nmax)`
:::
### Mean it
calculate the mean of each simulation
::: {.callout-tip collapse="true"}
## click to show solution
```julia
using Statistics
mean.(simulate.(1:1000,nmax))
# or
sum.(...) ./ nmax
```
:::
### Add it as a subplot
We want to add a histogram of the 1000 means to the plot.
1. Add a new Axis to `f[1,2]`
2. use it to plot the histogram of the means via `hist!` - don't forget to change the `direction=:x` to flip the histogram
3. link the axes using `linkaxes`
## 5. Prettify it
There are some simple tricks to make a plot look nicer:
- remove the "box" using `hidespines!(ax,:r,:t)
- resize the right sub-plot to be smaller `colsize!` and `Relative(X)`
- hide the x-grid (type `ax.`+ `TAB` to find all possible attributes)
- hide the `xlabels` + `xticks` + `bottomspine` from the right subplot
- add two Labels `(A)` and `(B)` to the plot
- Bonus: use `color` to color the cummulative sum samples according to how many samples went into that sum. `colormap=:Reds` looks good to me!
::: {.callout-tip collapse="true"}
## Bonus: Click for more fancy labels
You can create a slightly fancier label by adding a circle around it :)
```julia
Label(f[1,2,TopLeft()],"B",padding=[0,0,5,0])
Label(f[1,2,TopLeft()],"⭕",padding=[0,0,8,0],fontsize=30)
```
:::
# Task 2: Interactivity! {#2}
Using the `Pluto.jl` reactive backend, changing a value in some cell will automatically update all other cells - including plots.
We can use Sliders instead of fixing the parameters of the simulation
A slider is defined like this:
```julia
@bind yourVarName PlutoUI.Slider(from:to) # from:step:to is optional, step by def 1
```
## Adding interactivity via sliders
1. Define a slider that controls the number of samples from 1:500
2. Define a second slider that adds a constant offset to all values of the simulation simulation
3. make sure to fix the x/y-limits to get a nice looking plot :-)
:::{.callout-tip collapse="true"}
## Bonus: Advanced slider management
After understanding the slightly awkward syntax, the following gives a nice collection of Sliders, Checkboxes, Widgets etc. with at the same time being drag-and-dropable and in a sidebar. Neat!
```julia
using PlutoExtras
PlutoExtras.BondTable([
PlutoExtras.@BondsList "Sliders" let
"name A" = @bind(varA,PlutoUI.Slider(1:500))
"name B" = @bind(varB, PlutoUI.Slider(-5:5))
end
])
```
:::
# Task 3: AlgebraOfGraphics