Merge pull request #292 from unfoldtoolbox/uncertain

Horizontal colorbars and other topoplot issues
- `Cite this repository` is updated for a JOOS paper
- issue #288 fixed
- adding horizontal colorbars
- using `LinRange` for ticks in ERPimage
- #251 fixed

CITATION.cff

@@ -1,24 +1,31 @@
-# This CITATION.cff file was generated with cffinit.
-# Visit https://bit.ly/cffinit to generate yours today!
-
-cff-version: 1.2.1
-title: 'UnfoldMakie.jl: EEG/ERP visualization package'
-message: 'If you use this page, please cite it as below.'
-type: software
-journal: 'Journal of Open Source Software'
-volume : 10
-number: 105
-pages: 7560
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
 authors:
 - given-names: Vladimir
   family-names: Mikheev
   orcid: 'https://orcid.org/0000-0002-4738-6655'
 - given-names: Benedikt
   family-names: Ehinger
   orcid: 'https://orcid.org/0000-0002-6276-3332'
-identifiers:
-  - type: doi
-    value: https://doi.org/10.21105/joss.07560
-repository-code: 'https://github.com/unfoldtoolbox/UnfoldMakie.jl'
+title: 'UnfoldMakie.jl: EEG/ERP visualization package'
 version: 0.5.10
+doi: 10.21105/joss.07560
 date-released: '2025-01-10'
+url: 'https://github.com/unfoldtoolbox/UnfoldMakie.jl'
+preferred-citation:
+  type: article
+  authors:
+  - given-names: Vladimir
+    family-names: Mikheev
+    orcid: 'https://orcid.org/0000-0002-4738-6655'
+  - given-names: Benedikt
+    family-names: Ehinger
+    orcid: 'https://orcid.org/0000-0002-6276-3332'
+  doi: 10.21105/joss.07560
+  journal: 'Journal of Open Source Software'
+  month: 1
+  title: 'UnfoldMakie.jl: EEG/ERP visualization package'
+  volume : 10
+  number: 105
+  pages: 7560
+  year: 2025

docs/literate/intro/speed.jl

@@ -106,6 +106,7 @@ end
 # ![](topoplot_animation_UM.gif)
 
 # MNE with .gif
+# Note that due to some bugs in (probably) `CondaPkg` topoplot is blac and white. 
 @benchmark begin
     fig, anim = simulated_epochs.animate_topomap(
         times = Py(timestamps),

docs/literate/tutorials/topoplot.jl

@@ -106,6 +106,16 @@ end
 # # Highlighting channels
 plot_topoplot(dat[:, 50, 1]; positions, high_chan = [1, 2])
 
+
+# # Horizontal colorbars
+# Just switch `colorbar.vertical` to `false`
+plot_topoplot(
+    dat[:, 50, 1];
+    positions,
+    axis = (; xlabel = "50 ms"),
+    colorbar = (; vertical = false, width = 180, label = "Voltage estimate"),
+)
+
 # # Configurations of Topoplot
 
 # ```@docs

src/eeg_series.jl

@@ -31,7 +31,7 @@ The function takes the `combinefun = mean` over the `:time` column of `data`.
 - `topo_attributes::NamedTuple = (;)`\\
     Here you can flexibly change configurations of the topoplot interoplation.\\
     To see all options just type `?Topoplot.topoplot` in REPL.\\
-    Defaults: $(supportive_defaults(:topo_default_attributes)).
+    Defaults: $(replace(string(supportive_defaults(:topo_default_attributes; docstring = true)), "_" => "\\_")).
 - `positions::Vector{Point{2, Float32}}`\\
     Channel positions. The list of x and y positions for all unique electrodes. 
 

src/plot_erpimage.jl

@@ -12,7 +12,7 @@ Plot an ERP image.
     `Figure`, `GridLayout`, or `GridPosition` to draw the plot.
 - `data::Union{DataFrame, Vector{Float32}}`\\
     Data for the plot visualization.
-        
+         
 ## Keyword arguments (kwargs) 
 - `erpblur::Number = 10`\\
     Number indicating how much blur is applied to the image. \\
@@ -93,13 +93,8 @@ function plot_erpimage!(
     !isnothing(to_value(sortindex)) ? @assert(to_value(sortindex) isa Vector{Int}) : ""
     ax = Axis(ga[1:4, 1:4]; config.axis...)
 
-    ax.yticks = [
-        1,
-        size(to_value(data), 2) ÷ 4,
-        size(to_value(data), 2) ÷ 2,
-        size(to_value(data), 2) - (size(to_value(data), 2) ÷ 4),
-        size(to_value(data), 2),
-    ]
+    ax.yticks = LinRange(1, size(to_value(data), 2), 5)
+
     ax.yticklabelsvisible = true
     sortindex = sortindex_management(sortindex, sortvalues, data)
     filtered_data = @lift(
@@ -138,10 +133,14 @@ function ei_meanplot(ax, data, config, f, ga, times, meanplot_axis)
 
     trace = @lift(mean($data, dims = 2)[:, 1])
     meanplot_axis = update_axis(supportive_defaults(:meanplot_default); meanplot_axis...)
+    xticks = @lift(round.(LinRange(minimum($times), maximum($times), 5), digits = 2))
+    yticks = @lift(round.(LinRange(minimum($trace), maximum($trace), 5), digits = 1))
 
     axbottom = Axis(
         ga[5, 1:4];
         ylabel = config.colorbar.label === nothing ? "" : config.colorbar.label,
+        xticks = xticks,
+        yticks = yticks,
         limits = @lift((
             minimum($times),
             maximum($times),
@@ -172,10 +171,9 @@ function ei_sortvalue(sortvalues, f, ax, hm, config, sortval_xlabel, sortplot_ax
         axleft = Axis(
             gb[1:4, 1:5];
             xlabel = sortval_xlabel,
-            xticks = @lift([
-                round(minimum($sortvalues), digits = 2),
-                round(maximum($sortvalues), digits = 2),
-            ]),
+            xticks = @lift(
+                round.(LinRange(minimum($sortvalues), maximum($sortvalues), 2), digits = 2)
+            ),
             limits = @lift((
                 minimum($sortvalues) - (maximum($sortvalues) / 100 * 3),
                 maximum($sortvalues) + (maximum($sortvalues) / 100 * 3),

src/plot_topoplot.jl

@@ -22,7 +22,7 @@ Plot a topoplot.
 - `topo_attributes::NamedTuple = (;)`\\
     Here you can flexibly change configurations of the topoplot interoplation.\\
     To see all options just type `?Topoplot.topoplot` in REPL.\\
-    Defaults: $(supportive_defaults(:topo_default_attributes))
+    Defaults: $(replace(string(supportive_defaults(:topo_default_attributes; docstring = true)), "_" => "\\_"))
 $(_docstring(:topoplot))
 
 **Return Value:** `Figure` displaying the Topoplot.
@@ -56,7 +56,7 @@ function plot_topoplot!(
     config = PlotConfig(:topoplot)
     config_kwargs!(config; kwargs...) # potentially should be combined
 
-    outer_axis = Axis(f[1, 1]; config.axis...)
+    outer_axis = Axis(f[1:4, 1:2]; config.axis...)
     hidespines!(outer_axis)
     hidedecorations!(outer_axis, label = false)
 
@@ -72,7 +72,8 @@ function plot_topoplot!(
     topo_attributes =
         update_axis(supportive_defaults(:topo_default_attributes); topo_attributes...)
     topo_axis = update_axis(supportive_defaults(:topo_default_single); topo_axis...)
-    inner_axis = Axis(f[1, 1]; topo_axis...)
+    inner_axis = Axis(f[1:4, 1:2]; topo_axis...)
+
     if isa(high_chan, Int) || isa(high_chan, Vector{Int64})
         x = zeros(length(positions))
         isa(high_chan, Int) ? x[high_chan] = 1 : x[high_chan] .= 1
@@ -100,18 +101,27 @@ function plot_topoplot!(
         )
     end
 
-
-    if config.layout.use_colorbar == true
-        Colorbar(f[:, 2]; colormap = config.visual.colormap, config.colorbar...)
-    end
     clims = @lift (min($data...), max($data...))
     if clims[][1] ≈ clims[][2]
         @warn """The min and max of the value represented by the color are the same, it seems that the data values are identical. 
 We disable the color bar in this figure.
 Note: The identical min and max may cause an interpolation error when plotting the topoplot."""
         config_kwargs!(config, layout = (; use_colorbar = false))
     else
-        config_kwargs!(config, colorbar = (; limits = clims))
+        ticks = LinRange(clims[][1], clims[][2], 5)
+        rounded_ticks = round.(ticks, digits = 2)  # Round to 2 decimal places
+        config_kwargs!(
+            config,
+            colorbar = (; ticks = (ticks, string.(rounded_ticks)), limits = clims),
+        )
+    end
+    if config.layout.use_colorbar == true
+        if config.colorbar.vertical == true
+            Colorbar(f[1:4, 2]; colormap = config.visual.colormap, config.colorbar...)
+        else
+            config_kwargs!(config, colorbar = (; labelrotation = 2π, flipaxis = false))
+            Colorbar(f[5, 1:2]; colormap = config.visual.colormap, config.colorbar...)
+        end
     end
     apply_layout_settings!(config; fig = f)
     return f

src/plot_topoplotseries.jl

@@ -47,7 +47,7 @@ Multiple miniature topoplots in regular distances.
 - `topo_attributes::NamedTuple = (;)`\\
     Here you can flexibly change configurations of the topoplot interoplation.\\
     To see all options just type `?Topoplot.topoplot` in REPL.\\
-    Defaults: $(supportive_defaults(:topo_default_attributes))
+    Defaults: $(replace(string(supportive_defaults(:topo_default_attributes; docstring = true)), "_" => "\\_"))
 
 $(_docstring(:topoplotseries))
 

src/supportive_defaults.jl

@@ -8,7 +8,7 @@ Such supporting axes allow users to flexibly see defaults in docstrings and mani
 For developers: to make them updateable in the function, use `update_axis`.
 **Return value:** `NamedTuple`.
 """
-function supportive_defaults(cfg_symb::Symbol)
+function supportive_defaults(cfg_symb::Symbol; docstring = false)
     # plot_splines
     if cfg_symb == :spline_default
         return (;
@@ -62,10 +62,14 @@ function supportive_defaults(cfg_symb::Symbol)
             height = Relative(1),
             halign = 0.05,
             valign = 0.95,
-            aspect = 1,
+            aspect = DataAspect(),
         )
     elseif cfg_symb == :topo_default_attributes
-        return (; interp_resolution = (128, 128), interpolation = CloughTocher())
+        if docstring == false
+            return (; interp_resolution = (128, 128), interpolation = CloughTocher())
+        else
+            return string("interp_resolution = (128, 128), interpolation = CloughTocher()")
+        end
         # plot_topoplotseries
     elseif cfg_symb == :topo_default_series
         return (;

test/test_topoplot.jl

@@ -104,3 +104,34 @@ end
     dat_obs[] = dat[:, 30, 1]
     plot_topoplot(dat_obs; positions = positions)
 end
+
+
+@testset "topoplot: horizontal colorbar" begin
+    plot_topoplot(
+        dat[:, 50, 1];
+        positions,
+        colorbar = (; vertical = false, width = 180, label = "Voltage estimate"),
+        axis = (; xlabel = "50 ms"),
+    )
+end
+
+@testset "topoplot: std errors" begin
+    f = Figure()
+    plot_topoplot!(
+        f[:, 1],
+        dat[:, 50, 1];
+        positions,
+        colorbar = (; vertical = false, width = 180, label = "Voltage estimate"),
+        axis = (; xlabel = "50 ms"),
+    )
+    plot_topoplot!(
+        f[:, 2],
+        dat[:, 50, 2];
+        positions,
+        colorbar = (; vertical = false, width = 180, label = "Voltage uncertainty"),
+        axis = (; xlabel = "50 ms"),
+        visual = (; colormap = :viridis),
+    )
+    colgap!(f.layout, 0)
+    f
+end