added AoG/Makie for references,fixed many small problems in documenta…

…tion building

docs/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"

docs/make.jl

@@ -3,7 +3,10 @@ using Documenter
 using DocStringExtensions
 
 # preload once
+
 using CairoMakie
+const Makie = CairoMakie # - for references
+using AlgebraOfGraphics
 using Unfold
 using DataFrames
 using DataFramesMeta
@@ -54,6 +57,7 @@ makedocs(;
 
         ],
         "API" => "api.md",
+        "Utilities" => "helper.md",
     ],
 
 )

docs/src/helper.md

@@ -5,15 +5,8 @@ UnfoldMakie.eeg_topoplot_series!
 UnfoldMakie.config_kwargs!
 UnfoldMakie.eeg_matrix_to_dataframe
 UnfoldMakie.rel_to_abs_bbox
-UnfoldMakie.plot_parallelcoordinates
-UnfoldMakie.plot_topoplot
 UnfoldMakie.to_positions
 UnfoldMakie.df_timebin
-UnfoldMakie.plot_erp
-UnfoldMakie.plot_circulareegtopoplot
-UnfoldMakie.plot_designmatrix
 UnfoldMakie.cart3d_to_spherical
-UnfoldMakie.plot_topoplotseries
-UnfoldMakie.plot_butterfly
 UnfoldMakie.valType_to_symbol
 ```

docs/src/how_to/fix_pcp.md

@@ -5,11 +5,6 @@ Since Makie doesn't have a native function to draw PCPs, our version is somewhat
 Under certain circumstances the PCP is not visualized correctly.
 This leads to truncated edges of the PCP and unused space.
 
-In particular, if the container size is changed by adjusting the figure resolution, or if multiple plots are added to a figure, the PCP may not fit.
-
-![PCP with cutoff and bad spacing](../images/broken_PCP.png)
-
-
 
 Since the plot could have more space above and below, we can change the aspect ratio of the plot with:
 ```
@@ -35,7 +30,4 @@ pc_tick_label_size = 25,
 ...
 ```
 
-By setting these manually through trial and error we can fix the visualization issues:
-
-
-![Fixed PCP](../images/fixed_PCP.png)
+By setting these manually through trial and error we can fix the visualization issues

docs/src/how_to/hide_deco.md

@@ -24,13 +24,16 @@ For more information on the input of these functions refer to the [Makie dokumen
 
 Since some plots hide features by default, the hiding can be reverted by setting the variables to `nothing`
 
-```
-plot_xxx(...;layout=(;
+```@example main
+using TopoPlots
+using UnfoldMakie
+using CairoMakie
+
+data, positions = TopoPlots.example_data()
+plot_topoplot(data[:,340,1]; 
+    positions = positions, 
+    layout=(;
     hidespines = nothing,
     hidedecorations = nothing
-)
+    ),)
 ```
-
-
-![Topoplot with all axis spines and decorations enabled](../images/spine_topo.png)
-

docs/src/how_to/show_oob_labels.md

@@ -9,7 +9,6 @@ We start with the "label-limited" time-expanded designmatrix from the [correspon
 plot_designmatrix(designmatrix!(ufCont,evts), cDesign; xTicks=10, sortData=false)
 ```
 
-#![Label Limited Timeexpanded Designmatrix](../images/designmatrix_te_12_labels.png)
 
 While the plot automatically sets its height according to the labels, the labels are cut off on the left side.
 
@@ -27,5 +26,3 @@ plot_design(f[1,2:6], designmatrix!(ufCont, evts), cDesign; setExtraValues=(xTic
 
 f
 ```
-
-#![Label Limited Timeexpanded Designmatrix](../images/label_fix.png)

docs/src/tutorials/butterfly.md

@@ -39,8 +39,6 @@ plot_butterfly(df; positions=pos)
 
 Since butterfly plots use a `DataFrame` as input, the library needs to know the names of the columns used for plotting. You can set these mapping values by calling `plot_butterfly(...; mapping=(; :x=:time,))`, that is, by specifying a `NamedTuple` (note the `;` right after the opening parentheses).
 
-For more information on mapping values, see the [Mapping Data](@ref config_mapping) section of the documentation.
-
 While there are several default values that will be checked in that order if they exist in the `DataFrame`, a custom name may need to be chosen:
 
 

docs/src/tutorials/parallelcoordinates.md

@@ -35,8 +35,6 @@ plot_parallelcoordinates(results_plot, [5,3,2]; # this selects channel 5,3 & 2
 
 Since PCPs use a `DataFrame` as an input, the library needs to know the names of the columns used for plotting.
 
-For more informations about mapping values, look into the [Mapping Data](@ref config_mapping) section of the documentation.
-
 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:
 
 ### y

docs/src/tutorials/topoplot.md

@@ -43,9 +43,7 @@ To get the positions from the labels we use a [database](https://raw.githubuserc
 
 ## Column Mappings for Topo Plots
 
-When using topo plots with a `DataFrame` as an input, the library needs to know the names of the columns used for plotting.
-
-For more informations about mapping values look into the [Mapping Data](@ref config_mapping) section of the documentation.
+When using topo plots with a `DataFrame` as an input, the library needs to know the names of the columns used for plotting. This is specified using the `mapping=(;)` kwargs.
 
 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: