starting visualization journey

_quarto.yml

@@ -61,7 +61,7 @@ website:
             contents:
               - href: material/3_wed/docs/handout.qmd
                 text: "📝 1 - Docs"
-              - href: material/3_wed/vis/slides.jl
+              - href: material/3_wed/vis/handout.qmd
                 text: "📝 2 - Visualizations"
               - href: material/3_wed/linalg/slides.qmd
                 text: "📝 3 - LinearAlgebra"

cheatsheets/ggplotAOG.qmd

@@ -0,0 +1,21 @@
+# AlgebraOfGraphics.jl vs. GGPlot.jl
+[CC-by-SA Pumas.ai](https://tutorials.pumas.ai/html/PlottingInJulia/01-AoG-intro.html)
+|---|---|---|
+||ggplot2	|AoG.jl
+|Input data	|ggplot(df)	| data(df)
+|Map aesthetics	|aes(...)	|mapping(...)
+|Add geometries	|geom_*(...)	|visual(...)
+|Combine layers	| +	|*
+|Facetting	|facet_[wrap|grid](~ column)	|mapping(...; [row|col|layout]=:column)
+|Customize scales	|scale_*_manual()	| renamer(...)
+|Themes	theme_*(...)	|set_theme!(theme_*()); |draw(plt)
+|Customize axes labels	|[x|y]lab("...")	|draw(plt, axis=(; [x|y]label="..."))
+|Customize color	|scale_[fill|color]_*(...)	|draw(plt, palettes=(; color=...)) or visual(..., colormap=...")
+|Save plot	|ggsave("file.[png|svg]")	|save("file.[png|svg]", draw(plt))
+|Frequency	|geom_bar() or stat_count()	|frequency()
+|Histogram	|geom_histogram or stat_bin()	|histogram()
+|Density	|geom_density or stat_density()	|density()
+|Expectation/Mean|	stat_summary(fun = "mean")	|expectation()
+|Smooth trend	|stat_smooth or geom_smooth()	|(visual(...) + smooth())
+|Linear trend	|stat_smooth(method = "lm") or geom_smooth(method = "lm")|	(visual(...) + linear())
+|Log scale	|scale_[x|y]_log10()	|draw(plt; axis=(; [x|y]scale=log10))

material/3_wed/vis/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+PalmerPenguins = "8b842266-38fa-440a-9b57-31493939ab85"

material/3_wed/vis/handout.ipynb

@@ -0,0 +1,132 @@
+{
+  "cells": [
+    {
+      "cell_type": "raw",
+      "metadata": {},
+      "source": [
+        "---\n",
+        "\n",
+        "jupyter: julia-1.9\n",
+        "---"
+      ],
+      "id": "d0dd3b54"
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "# Makie.jl\n",
+        "\n",
+        "## Backends\n",
+        "Four backends:\n",
+        "1. `CairoMakie` - SVG\n",
+        "2. `GLMakie` - 2D/3D/fast interactivity\n",
+        "3. `WGLMakie` - Same as GLMakie, but in browser\n",
+        "4. `RPRMakie` - experimental raytracing\n",
+        "\n",
+        "I will use `GLMakie` or `CairoMakie`. To switch use `CairoMakie.activate!()`\n",
+        "\n",
+        "## Layouts for scientific figures\n",
+        "\n",
+        "# Pluto.jl for easy interactivity\n",
+        "\n",
+        "# Grammar of Graphics\n",
+        "\n",
+        "The grammar of graphics is a convenient way to build common explorative plots.\n",
+        "\n",
+        "For example:\n",
+        "\n",
+        "\n",
+        "#### For ggplot enthusiasts:\n",
+        "You could use [TidierPlots.jl - a ggplot clone](https://github.com/TidierOrg/TidierPlots.jl)\n",
+        "\n",
+        "Check out the [../../../../cheatsheets/ggplotAOG.qmd]:\n",
+        "\n",
+        "## AlgebraOfGraphics.jl\n",
+        "\n",
+        "### Loading data"
+      ],
+      "id": "0ca52ae6"
+    },
+    {
+      "cell_type": "code",
+      "metadata": {},
+      "source": [
+        "using GLMakie # backend\n",
+        "using AlgebraOfGraphics\n",
+        "using PalmerPenguins, DataFrames  # example dataset\n",
+        "\n",
+        "penguins = dropmissing(DataFrame(PalmerPenguins.load()))\n",
+        "first(penguins, 6)"
+      ],
+      "id": "56b4e637",
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "::: callout-note\n",
+        "A `tidy dataframe` is a dataframe that follows these three rules:\n",
+        "\n",
+        "\n",
+        "1. Every column is a variable.\n",
+        "2. Every row is an observation.\n",
+        "3. Every cell is a single value.\n",
+        "\n",
+        "Tidy data make your visualization life much easier as you will see!\n",
+        ":::\n",
+        "\n",
+        "\n",
+        "### AoG basics\n",
+        "\n",
+        "\n",
+        "`data * mapping * visual`\n",
+        "\n",
+        "```julia\n",
+        "  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",
+        "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",
+        "vis_pencolor2 = vis_pen * mapping(color=:species)\n",
+        "draw(vis_pencolor2)\n",
+        "\n",
+        "```\n",
+        "\n",
+        "### 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)"
+      ],
+      "id": "3ead8444"
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "name": "julia-1.8",
+      "language": "julia",
+      "display_name": "Julia 1.8.3"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 5
+}

material/3_wed/vis/handout.qmd

@@ -0,0 +1,116 @@
+---
+
+jupyter: julia-1.9
+---
+# Makie.jl
+
+## Backends
+Four backends:
+1. `CairoMakie` - SVG
+2. `GLMakie` - 2D/3D/fast interactivity
+3. `WGLMakie` - Same as GLMakie, but in browser
+4. `RPRMakie` - experimental raytracing
+
+I will use `GLMakie` or `CairoMakie`. To switch use `CairoMakie.activate!()`
+
+## Layouts for scientific figures
+
+# Pluto.jl for easy interactivity
+
+# Grammar of Graphics
+
+The grammar of graphics is a convenient way to build common explorative plots.
+
+For example:
+
+
+#### For ggplot enthusiasts:
+You could use [TidierPlots.jl - a ggplot clone](https://github.com/TidierOrg/TidierPlots.jl)
+
+Check out the [../../../../cheatsheets/ggplotAOG.qmd]:
+
+## AlgebraOfGraphics.jl
+
+### Loading data
+```{julia}
+using GLMakie # backend
+using AlgebraOfGraphics
+using PalmerPenguins, DataFrames  # example dataset
+
+penguins = dropmissing(DataFrame(PalmerPenguins.load()))
+first(penguins, 6)
+``` 
+
+::: callout-note
+A `tidy dataframe` is a dataframe that follows these three rules:
+
+
+1. Every column is a variable.
+2. Every row is an observation.
+3. Every cell is a single value.
+
+Tidy data make your visualization life much easier as you will see!
+:::
+
+
+### AoG basics
+
+
+`data * mapping * visual`
+
+```{julia}
+  vis_pen = data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * visual(Scatter) 
+  draw(vis_pen)
+```
+
+### Adding color
+
+```{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}
+vis_pencolor2 = vis_pen * mapping(color=:species)
+draw(vis_pencolor2)
+
+```
+
+### Why `Algebra`OfGraphics?
+
+Follows some algebraic rules of multiplying out sums
+
+`data * mapping * (visual(Scatter)+visual(Lines))`
+
+```{julia}
+
+data(penguins) * mapping(:bill_length_mm, :bill_depth_mm) * (visual(Scatter)+visual(Lines)) |> draw
+```
+
+### Faceting
+```{julia}
+data(penguins) * mapping(:bill_length_mm, :bill_depth_mm)  * mapping(color = :species, col = :sex) |> draw
+
+```
+```{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}
+data(penguins) * mapping(:bill_length_mm, :bill_depth_mm, color=:species) * (linear() + visual(Scatter)) |> draw
+```
+```{julia}
+data(penguins) * mapping(:bill_length_mm, :bill_depth_mm, color=:species) * (smooth() + visual(Scatter)) |> draw
+```
+
+
+# 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 t combine Pluto with Observables, but it is a bit buggy]