unfoldtoolbox · behinger · Nov 30, 2023 · Nov 25, 2023 · Nov 25, 2023 · Nov 25, 2023
diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,7 @@
 .vscode/
 /test/Manifest.toml
 /docs/Manifest.toml
-
+/docs/.CondaPkg
 /Manifest.toml
 /docs/build/
 /docs/src/generated
diff --git a/Project.toml b/Project.toml
@@ -16,6 +16,7 @@ DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 GridLayoutBase = "3955a311-db13-416c-9275-1d80ed98e5e9"
 ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
+Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

diff --git a/docs/literate/plot_results_styling.jl b/docs/literate/plot_results_styling.jl
@@ -8,29 +8,29 @@
 using CairoMakie
 
 
-include(joinpath(dirname(pathof(Unfold)), "../test/test_utilities.jl") ) # to load data
+include(joinpath(dirname(pathof(Unfold)), "../test/test_utilities.jl")) # to load data
 data, evts = loadtestdata("test_case_3b");
-basisfunction = firbasis(τ=(-0.4,.8),sfreq=50,name="stimulus")
-f  = @formula 0~1+conditionA+continuousA
+basisfunction = firbasis(τ=(-0.4,.8), sfreq=50, name="stimulus")
+f  = @formula 0 ~ 1 + conditionA + continuousA
 
-bfDict = Dict(Any=>(f,basisfunction))
+bfDict = Dict(Any=>(f, basisfunction))
 
-m = fit(UnfoldModel,bfDict,evts,data); 
+m = fit(UnfoldModel, bfDict, evts, data); 
 results = coeftable(m); nothing
 
 # # Styling your plot
 # ## Mapping's
 # everything you can put in a mapping(...) AoG group can be modified, for instance:
-plot_results(results,linestyle=:coefname)
+plot_results(results, mapping=(; linestyle=:coefname))
 
 # ## Adding P-values
 # You can provide a dataframe with columns (must): `:from`,`:to`,future versions might allow a `:pvalue` column
 pvals =  DataFrame( :from=>[0.1,0.,-0.1],
                    :to=>[0.5,0.3,0.6],
                     :pvalue=>[0.01,0.01,0.001], # optional
                     :coefname=>["(Intercept)","conditionA","continuousA"])
 
-plot_results(results,pvalue=pvals)
+plot_results(results, pvalue=pvals)
 
 # !!! note
 #   If you do not give the coefname, all lines will be the same color as the first color-grouping (typically coefname), and they might overlap!
-#   If you do not give the coefname, all lines will be the same color as the first color-grouping (typically coefname), and they might overlap!
+#   If you do not give the coefname, all lines will be the same color as the first color-grouping (typically coefname), and they might overlap!
-#   If you do not give the coefname, all lines will be the same color as the first color-grouping (typically coefname), and they might overlap!
+#   If you do not give the coefname, all lines will be the same color as the first color-grouping (typically coefname), and they might overlap!
diff --git a/docs/literate/reference/positions.md b/docs/literate/reference/positions.md
diff --git a/docs/literate/tutorials/erp.jl b/docs/literate/tutorials/erp.jl
@@ -62,7 +62,7 @@ plot_erp(
     res_effects;
     mapping = (; y = :yhat, color = :continuous, group = :continuous),
     legend = (; nbanks = 2),
-    layout = (; showLegend = true, legend_position = :right),
+    layout = (; show_legend = true, legend_position = :right),
     categorical_color = false, categorical_group = true,
 )
 

diff --git a/docs/make.jl b/docs/make.jl
@@ -49,10 +49,9 @@ makedocs(;
         ],
         "How To" => [
             "Butterfly Colormap" => "how_to/position2color.md",
-            "Fix Parallel Coordinates Plot" => "how_to/fix_pcp.md",
             "Hide Axis Spines and Decorations" => "how_to/hide_deco.md",
             "Include multiple Visualizations in one Figure" => "how_to/mult_vis_in_fig.md",
-            "Show out of Bounds Label" => "how_to/show_oob_labels.md",
+            "Designmatrix: Show out of Bounds Label" => "how_to/show_oob_labels.md",
         ],
         "Reference" => [
             "Convert 3D positions / montages to 2D layouts" => "generated/reference/positions.md",

diff --git a/docs/src/api.md b/docs/src/api.md
@@ -7,4 +7,5 @@ Internally, we use a `PlotConfig` struct to keep track of common plot options, i
 
 ```@docs
 PlotConfig
+UnfoldMakie.PCPTicks
 ```
diff --git a/docs/src/how_to/fix_pcp.md b/docs/src/how_to/fix_pcp.md
diff --git a/docs/src/how_to/mult_vis_in_fig.md b/docs/src/how_to/mult_vis_in_fig.md
@@ -77,7 +77,7 @@ plot_erp!(f[2, 4:5], res_effects; categorical_color=false, categorical_group=tru
     legend=(; nbanks=2),
     layout=(; show_legend=true, legend_position=:right))
 
-plot_parallelcoordinates!(f[3, 2:3], uf_5chan, [1, 2, 3, 4, 5]; mapping=(; color=:coefname), 
+plot_parallelcoordinates(f[3, 2:3], uf_5chan; mapping=(; color=:coefname), 
     layout=(; legend_position=:bottom))
 
 plot_erpimage!(f[1, 4:5], times, dat_e; sortvalues=evts.Δlatency)

diff --git a/docs/src/tutorials/parallelcoordinates.md b/docs/src/tutorials/parallelcoordinates.md
@@ -10,42 +10,130 @@ using DataFrames
 using CairoMakie
 ```
 
-## Data
-
-We use the test data of `erpcore-N170.jld2`.
-
+## Data generation
 ```@example main
 include("../../example_data.jl")
-results_plot, positions = example_data();
+r1, positions = example_data();
+r2 = deepcopy(r1)
+r2.coefname .= "B" # create a second category
+r2.estimate .+= rand(length(r2.estimate))*0.1
+results_plot = vcat(r1, r2);
+nothing #hide
 ```
 
 ## Plot PCPs
 
 ```@example main
-plot_parallelcoordinates(results_plot, [5,3,2]; # this selects channel 5,3 & 2 
-    mapping = (color = :coefname, y = :estimate))
+  plot_parallelcoordinates(
+        subset(results_plot, :channel => x -> x .<= 5);
+        mapping = (; color = :coefname),
+    )
 ```
 
 
+## Normalization
+On the first image, there is no normalization and the extremes of all axes are the same and equal to the max and min values across all chanells. 
+On the second image, there is a `minmax normalization``, so each axis has its own extremes based on the min and max of the data.
+
+Typically, parallelplots are normalized per axis. Whether this makes sense for estimating channel x, we do not know.
+
+```@example main
+    f = Figure()
+    plot_parallelcoordinates(
+        f[1, 1],
+        subset(results_plot, :channel => x -> x .< 10);
+        mapping = (; color = :coefname),
+    )
+    plot_parallelcoordinates(
+        f[2, 1],
+        subset(results_plot, :channel => x -> x .< 10);
+        mapping = (; color = :coefname),
+        normalize = :minmax,
+    )
+    f
 
-!!! important
-    the following is still outdated...
-
-## Column Mappings for PCPs
 
-Since PCPs use a `DataFrame` as an input, the library needs to know the names of the columns used for plotting.
+```
 
-While there are multiple default values that are checked in that order if they exist in the `DataFrame`, a custom name might need to be choosen for:
+## Labels
+Use `ax_labels` to specify labels for the axes.
 
-### y
-Default is `(:y, :estimate, :yhat)`.
+```@example main
+    plot_parallelcoordinates(
+        subset(results_plot, :channel => x -> x .< 5);
+        visual = (; color = :darkblue),
+        ax_labels = ["Fz", "Cz", "O1", "O2"],
+    )
 
-### channel
-Default is `:channel`.
+```
 
-### color
-XXX Default is `:coef`.
+## Tick labels
+Specify tick labels on axis. There are four different options for the tick labels.
 
-### time
-Default is `:time`.
+```@example main
+ f = Figure()
+    plot_parallelcoordinates(
+        f[1, 1],
+        subset(results_plot, :channel => x -> x .< 5);
+        ax_labels = ["Fz", "Cz", "O1", "O2"],
+        ax_ticklabels = :all,
+        normalize = :minmax,
+    ) # all tick labels on all axis
+    plot_parallelcoordinates(
+        f[2, 1],
+        subset(results_plot, :channel => x -> x .< 5);
+        ax_ticklabels = :left,
+        normalize = :minmax,
+    ) # tick labels on extremities + tickets on the left
+    plot_parallelcoordinates(
+        f[3, 1],
+        subset(results_plot, :channel => x -> x .< 5);
+        ax_ticklabels = :outmost,
+        normalize = :minmax,
+    ) # show tick labels on extremities of axis
+
+    plot_parallelcoordinates(
+        f[4, 1],
+        subset(results_plot, :channel => x -> x .< 5);
+        ax_ticklabels = :none,
+        normalize = :minmax,
+    ) #  disable tick labels
+    f 
+```
 
+
+## Bending the parallel plot
+Bending the linescan be helpful to make them more visible.
+
+```@example main
+    f = Figure()
+    plot_parallelcoordinates(f[1,1], 
+        subset(results_plot, :channel=>x->x.<10))
+    plot_parallelcoordinates(f[2,1], 
+        subset(results_plot, :channel=>x->x.<10), bend=true)
+    f
+
+```
+
+## Transparancy 
+```@example main
+    uf_5chan = example_data("UnfoldLinearModelMultiChannel")
+
+    f = Figure()
+    plot_parallelcoordinates(
+        f[1, 1],
+        uf_5chan;
+        mapping = (; color = :coefname),
+        layout = (; legend_position = :right),
+        visual=(; alpha=0.1)
+    )
+    plot_parallelcoordinates(
+        f[2, 1],
+        uf_5chan;
+        mapping = (; color = :coefname),
+        layout = (; legend_position = :right),
+        visual=(; alpha=0.9)
+    )
+    f
+
+```
diff --git a/src/UnfoldMakie.jl b/src/UnfoldMakie.jl
@@ -1,5 +1,6 @@
 module UnfoldMakie
 
+import Makie.get_ticks
 using Makie
 #using CairoMakie
 using AlgebraOfGraphics
@@ -17,6 +18,8 @@ using ColorTypes
 
 using DocStringExtensions # for $SIGNATURES
 
+using Interpolations # for parallelplot
+
 using DataStructures
 using DataFrames
 using SparseArrays
@@ -27,6 +30,7 @@ using CoordinateTransformations # for 3D positions to 2D
 
 import Makie.hidedecorations!
 import Makie.hidespines!
+
 import AlgebraOfGraphics.hidedecorations!
 #import AlgebraOfGraphics.hidespines!
 
@@ -62,7 +66,7 @@ export plot_erpimage!
 export plot_topoplot
 export plot_topoplot!
 export plot_parallelcoordinates
-export plot_parallelcoordinates!
+
 export plot_butterfly
 export plot_butterfly!
 export plot_circulareegtopoplot