Splines and plot_erp

docs/example_data.jl

@@ -6,57 +6,34 @@ using Random
 """
     example_data(String) 
 
-Creates example data. Currently, 7 datasets are available.
-- `TopoPlots.jl` (default) - tidy DataFrame from `TopoPlots.jl` with 2 conditions, 64 channels and 800 ms time range. 
-- `UnfoldLinearModel`
-- `UnfoldLinearModelMultiChannel`
-- `UnfoldLinearModelContinuousTime`
-- `7channels`
-- `UnfoldTimeExpanded`
-- `sort_data` - includes DataFrame EEG recordings `dat` and `evts` with event variables occured during experiment. `evts` could be used for sorting EEG data in ERP image. 
+Creates example data or model. Currently, 3 datasets and 6 models are available.
+
+Datasets:
+- `TopoPlots.jl` (default) - 2 DataFrames from `TopoPlots.jl`:\\
+    - DataFrame with estimate, time, 64 channels, topopositions, sterror and pvalue and 800 ms time range.\\
+    - Posiions for 64 electrodes.
+- `UnfoldLinearModelMultiChannel` - DataFrame with 5 channels, 3 coefnames, sterror, time and estimate.
+- `sort_data` - 2 DataFrames: 
+    - `dat` for EEG recordings  and `evts` with event variables occured during experiment.\\
+    - `evts` could be used for sorting EEG data in ERP image. 
+
+Models:
+- `UnfoldLinearModel` - Model with formula `1 + condition + continuous`.
+- `UnfoldLinearModelContinuousTime` - Model with formula `timeexpand(1 + condition + continuous)` for times [0.0, 0.01 ... 0.5].
+- `UnfoldLinearModelwith1Spline` - Model with formula `1 + condition + spl(continuous, 4)`.
+- `UnfoldLinearModelwith2Splines` - Model with formula ` 1 + condition + spl(continuous, 4) + spl(continuous2, 6)`.
+- `7channels` - Model with formula `timeexpand(1 + condA)` for times [-0.1, -0.09 ... 0.5].
+- `UnfoldTimeExpanded` - Model with formula `timeexpand(1 + condition + continuous)` for times [-0.4, -0.39 ... 0.8].
+
 **Return Value:** `DataFrame`.
 """
 function example_data(example = "TopoPlots.jl")
-
     if example == "UnfoldLinearModel"
-
         # load and generate a simulated Unfold Design
         data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true)
         data = reshape(data, (1, size(data)...))
         f = @formula 0 ~ 1 + condition + continuous
-        # generate ModelStruct
-        se_solver = (x, y) -> Unfold.solver_default(x, y, stderror = true)
-        return fit(
-            UnfoldModel,
-            [Any => (f, range(0, length = size(data, 2), step = 1 / 100))],
-            evts,
-            data;
-            solver = se_solver,
-        )
-    elseif example == "UnfoldLinearModelwith1Spline"
-        # load and generate a simulated Unfold Design
-        data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true)
-        data = reshape(data, (1, size(data)...))
-        evts.continuous2 .=
-            log10.(6 .+ rand(MersenneTwister(1), length(evts.continuous))) .^ 2
-        f = @formula 0 ~ 1 + condition + spl(continuous, 4)
-        # generate ModelStruct
-        se_solver = (x, y) -> Unfold.solver_default(x, y, stderror = true)
-        return fit(
-            UnfoldModel,
-            [Any => (f, range(0, length = size(data, 2), step = 1 / 100))],
-            evts,
-            data;
-            solver = se_solver,
-        )
-    elseif example == "UnfoldLinearModelwith2Splines"
-        # load and generate a simulated Unfold Design
-        data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true)
-        data = reshape(data, (1, size(data)...))
-        evts.continuous2 .=
-            log10.(6 .+ rand(MersenneTwister(1), length(evts.continuous))) .^ 2
-        f = @formula 0 ~ 1 + condition + spl(continuous, 4) + spl(continuous2, 6)
-        # generate ModelStruct
+        # generate ModelStruct 
         se_solver = (x, y) -> Unfold.solver_default(x, y, stderror = true)
         return fit(
             UnfoldModel,
@@ -105,6 +82,38 @@ function example_data(example = "TopoPlots.jl")
         basis = firbasis([0, 0.5], 100)
         # generate ModelStruct
         return fit(UnfoldModel, [Any => (f, basis)], evts, data)
+    elseif example == "UnfoldLinearModelwith1Spline"
+        # load and generate a simulated Unfold Design
+        data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true)
+        data = reshape(data, (1, size(data)...))
+        evts.continuous2 .=
+            log10.(6 .+ rand(MersenneTwister(1), length(evts.continuous))) .^ 2
+        f = @formula 0 ~ 1 + condition + spl(continuous, 4)
+        # generate ModelStruct
+        se_solver = (x, y) -> Unfold.solver_default(x, y, stderror = true)
+        return fit(
+            UnfoldModel,
+            [Any => (f, range(0, length = size(data, 2), step = 1 / 100))],
+            evts,
+            data;
+            solver = se_solver,
+        )
+    elseif example == "UnfoldLinearModelwith2Splines"
+        # load and generate a simulated Unfold Design
+        data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true)
+        data = reshape(data, (1, size(data)...))
+        evts.continuous2 .=
+            log10.(6 .+ rand(MersenneTwister(1), length(evts.continuous))) .^ 2
+        f = @formula 0 ~ 1 + condition + spl(continuous, 4) + spl(continuous2, 6)
+        # generate ModelStruct
+        se_solver = (x, y) -> Unfold.solver_default(x, y, stderror = true)
+        return fit(
+            UnfoldModel,
+            [Any => (f, range(0, length = size(data, 2), step = 1 / 100))],
+            evts,
+            data;
+            solver = se_solver,
+        )
     elseif example == "7channels"
         design =
             SingleSubjectDesign(conditions = Dict(:condA => ["levelA", "levelB"])) |>
@@ -122,7 +131,6 @@ function example_data(example = "TopoPlots.jl")
         f = @formula 0 ~ 1 + condA
         bf_dict = [Any => (f, basisfunction)]
         return fit(UnfoldModel, bf_dict, evnts, df)
-
     elseif example == "UnfoldTimeExpanded"
         df, evts = UnfoldSim.predef_eeg()
         f = @formula 0 ~ 1 + condition + continuous

docs/literate/how_to/mult_vis_in_fig.jl

@@ -89,14 +89,12 @@ plot_erp!(
     res_effects;
     mapping = (; y = :yhat, color = :continuous, group = :continuous => nonnumeric),
     legend = (; nbanks = 2),
-    layout = (; show_legend = true, legend_position = :right),
 )
 
 plot_parallelcoordinates(
     f[3, 2:3],
     uf_5chan;
     mapping = (; color = :coefname),
-    layout = (; legend_position = :right),
 )
 
 plot_erpimage!(f[1, 4:5], times, d_singletrial)

docs/literate/tutorials/erp.jl

@@ -36,6 +36,9 @@ res_effects = effects(Dict(:continuous => -5:0.5:5), m);
 # ## Figure plotting
 plot_erp(results)
 
+# To change legend title use `mapping.color`:
+plot_erp(results, mapping = (; color = :coefname => "Conditions"))
+
 # # Additional features
 
 # ## Effect plot
@@ -53,7 +56,7 @@ plot_erp(results)
 plot_erp(
     res_effects;
     mapping = (; y = :yhat, color = :continuous, group = :continuous),
-    layout = (; show_legend = false),
+    layout = (; use_colorbar = false),
 )
 
 # ## Significance lines

src/docstring_template.jl

@@ -37,8 +37,10 @@ function _docstring(cfg_symb::Symbol)
         :figure => "use `kwargs...` of [`Makie.Figure`](https://docs.makie.org/stable/explanations/figure/)",
         :axis => "use `kwargs...` of  [`Makie.Axis`](https://docs.makie.org/stable/reference/blocks/axis/)",
         :legend => "use `kwargs...` of  [`Makie.Legend`](https://docs.makie.org/stable/reference/blocks/legend/)",
-        :colorbar => "use `kwargs...` of  $cbarstring",
+        :layout => "check this [page](https://unfoldtoolbox.github.io/UnfoldMakie.jl/dev/generated/how_to/hide_deco/)",
+        :mapping => "use any mapping from [`AlgebraOfGraphics`](https://aog.makie.org/stable/layers/mapping/)",
         :visual => "use `kwargs...` of [$(visuallink[cfg_symb])]($(visuallink2[cfg_symb]))",
+        :colorbar => "use `kwargs...` of  $cbarstring",
     )
     for k = 1:length(fn)
         namedtpl = string(Base.getfield(cfg, fn[k]))
@@ -53,7 +55,7 @@ function _docstring(cfg_symb::Symbol)
 
     return """## Shared plot configuration options
         The shared plot options can be used as follows: `type = (; key = value, ...))`.\\
-        For example, `plot_x(...; layout = (; show_legend = true, legend_position = :right))`.\\
+        For example, `plot_x(...; colorbar = (; vertical = true, label = "Test"))`.\\
         Multiple defaults will be cycled until match.
 
         Placing `;` is important!
@@ -63,7 +65,7 @@ function _docstring(cfg_symb::Symbol)
 end
 
 function indiv_docstrings(cfg_symb::Symbol)
-    # plot__splines
+    # plot_splines
     if cfg_symb == :spline_default
         return (;
             ylabel = "Spline value",
@@ -94,5 +96,14 @@ function indiv_docstrings(cfg_symb::Symbol)
         )
     elseif cfg_symb == :sortplot_default
         return (; ylabelvisible = true, yticklabelsvisible = false)
+        # plot_erpgrid
+    elseif cfg_symb == :hlines_grid_default
+        return (; color = :gray, linewidth = 0.5)
+    elseif cfg_symb == :vlines_grid_default
+        return (; color = :gray, linewidth = 0.5, ymin = 0.2, ymax = 0.8)
+    elseif cfg_symb == :lines_grid_default
+        return (; color = :deepskyblue3)
+    elseif cfg_symb == :labels_grid_default
+        return (; color = :gray, fontsize = 12, align = (:left, :top), space = :relative)
     end
 end

src/plot_butterfly.jl

@@ -53,7 +53,7 @@ function plot_butterfly!(
     topomarkersize = 10,
     topopositions_to_color = x -> pos_to_color_RomaO(x),
     topo_axis = (;),
-    mapping = (;), # WTf??
+    mapping = (;),
     kwargs...,
 )
 

src/plot_circular_topoplots.jl

@@ -83,10 +83,9 @@ function plot_circular_topoplots!(
     # setting the colorbar to the bottom right of the box.
     # Relative values got determined by checking what subjectively looks best 
     Colorbar(
-        f[1, 2],
-        colormap = config.colorbar.colormap,
+        f[1, 2];
         colorrange = (min, max),
-        label = config.colorbar.label,
+        config.colorbar...,
         height = @lift Fixed($(pixelarea(ax.scene)).widths[2])
     )
     plot_topo_plots!(
@@ -102,7 +101,6 @@ function plot_circular_topoplots!(
     )
 
     apply_layout_settings!(config; ax = ax)
-
     # set the scene's background color according to config
     #set_theme!(Theme(backgroundcolor = config.axisData.backgroundcolor))
     return f

src/plot_erpgrid.jl

@@ -13,6 +13,22 @@ Plot an ERP image.
     Electrode positions.
 - `ch_names::Vector{String}`\\
     Vector with channel names.
+- `hlines_grid_axis::NamedTuple = (;)`\\
+    Here you can flexibly change configurations of the hline axis.\\
+    To see all options just type `?hlines` in REPL.\\
+    Defaults: $(indiv_docstrings(:hlines_grid_default))
+- `vlines_grid_axis::NamedTuple = (;)`\\
+    Here you can flexibly change configurations of the vline axis.\\
+    To see all options just type `?vlines` in REPL.\\
+    Defaults: $(indiv_docstrings(:vlines_grid_default))
+- `lines_grid_axis::NamedTuple = (;)`\\
+    Here you can flexibly change configurations of the lines axis.\\
+    To see all options just type `?lines` in REPL.\\
+    Defaults: $(indiv_docstrings(:lines_grid_default))
+- `labels_grid_axis::NamedTuple = (;)`\\
+    Here you can flexibly change configurations of the labels axis.\\
+    To see all options just type `?text` in REPL.\\
+    Defaults: $(indiv_docstrings(:labels_grid_default))
 
 ## Keyword arguments (kwargs)
 - `drawlabels::Bool = false`\\
@@ -48,6 +64,10 @@ function plot_erpgrid!(
     ch_names::Vector{String};
     drawlabels = false,
     times = -1:size(data, 2)-2, #arbitrary
+    labels_grid_axis = (;),
+    hlines_grid_axis = (;),
+    vlines_grid_axis = (;),
+    lines_grid_axis = (;),
     kwargs...,
 )
     config = PlotConfig(:erpgrid)
@@ -72,6 +92,8 @@ function plot_erpgrid!(
 
     axlist = []
     rel_zeropoint = argmin(abs.(times)) ./ length(times)
+    labels_grid_axis =
+        update_axis(indiv_docstrings(:labels_grid_default); labels_grid_axis...)
     for (ix, p) in enumerate(eachcol(positions))
         x = p[1]
         y = p[2]
@@ -83,29 +105,25 @@ function plot_erpgrid!(
             valign = y,
         )
         if drawlabels
-            text!(
-                ax,
-                rel_zeropoint + 0.1,
-                1,
-                color = :gray,
-                fontsize = 12,
-                text = ch_names[ix],
-                align = (:left, :top),
-                space = :relative,
-            )
+            text!(ax, rel_zeropoint + 0.1, 1; text = ch_names[ix], labels_grid_axis...)
         end
         # todo: add label if not nothing
 
         push!(axlist, ax)
     end
-    # todo: make optional + be able to specify the linewidth + color
-    hlines!.(axlist, Ref([0.0]), color = :gray, linewidth = 0.5)
-    vlines!.(axlist, Ref([0.0]), color = :gray, linewidth = 0.5)
+    hlines_grid_axis =
+        update_axis(indiv_docstrings(:hlines_grid_default); hlines_grid_axis...)
+    vlines_grid_axis =
+        update_axis(indiv_docstrings(:vlines_grid_default); vlines_grid_axis...)
+    lines_grid_axis = update_axis(indiv_docstrings(:lines_grid_default); lines_grid_axis...)
+
+    hlines!.(axlist, Ref([0.0]); hlines_grid_axis...)
+    vlines!.(axlist, Ref([0.0]); vlines_grid_axis...)
 
     times = isnothing(times) ? (1:size(data, 2)) : times
 
     # todo: add customizable kwargs
-    h = lines!.(axlist, Ref(times), eachrow(data))
+    h = lines!.(axlist, Ref(times), eachrow(data); lines_grid_axis...)
 
     linkaxes!(axlist...)
     hidedecorations!.(axlist)
@@ -119,14 +137,20 @@ function plot_erpgrid!(
     xstart = [Point2f(0), Point2f(0)]
     xdir = [Vec2f(0, 0.1), Vec2f(0.1, 0)]
     arrows!(xstart, xdir, arrowsize = 10)
-    text!(0.02, 0, text = config.axis.xlabel, align = (:left, :top), fontsize = 12)
+    text!(
+        0.02,
+        0,
+        text = config.axis.xlabel,
+        fontsize = config.axis.fontsize,
+        align = (:left, :top),
+    )
     text!(
         -0.008,
         0.01,
         text = config.axis.ylabel,
+        fontsize = config.axis.fontsize,
         align = (:left, :baseline),
         rotation = π / 2,
-        fontsize = 12,
     )
     f
 end

src/plot_splines.jl

@@ -7,8 +7,8 @@ using BSplineKit, Unfold
 Visualization of spline terms in an UnfoldModel. Two subplots are generated for each spline term:\\
 1) the basis function of the spline; 2) the density of the underlying covariate.\\
 
-Multiple spline terms are arranged across columns.
-Dashed lines indicate spline knots. 
+Multiple spline terms are arranged across columns.\\
+Dashed lines indicate spline knots.
 
 ## Arguments:
 

src/plot_topoplot.jl

@@ -50,7 +50,7 @@ function plot_topoplot!(
         @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, show_legend = false))
+        config_kwargs!(config, layout = (; use_colorbar = false))
     else
         config_kwargs!(config, colorbar = (; limits = clims))
     end