Erpgrid (#92)

* Update plot_erp.jl

* new tests, combined plot in docs

* del

* additional docs problems

* little detail

* dead links

* docstring warnings

* cross-refs again

* test

* pp_plot fixed

* docs errors should be resolved

* Update hide_deco.md

* colorbar docs

* liting

* add Voltage label

* linting + name consistency

* formatter

* no extra for circular

* no extra toposeries

* test for design matrix and no extra

* test

* no extra for erp

* del extra in erpimage and parplot

* g

* citability

* failed, but I will save it

* fixed

* fixed colorbar in toposeries

* small test

* review of current test

* del chanNum argument

---------

Co-authored-by: behinger (s-ccs 001) <[email protected]>

Project.toml

@@ -44,7 +44,7 @@ GeometryBasics = "0.4"
 GridLayoutBase = "0.9"
 ImageFiltering = "0.7"
 LinearAlgebra = "1"
-Makie = "0.17,0.18,0.19"
+Makie = "0.17, 0.18, 0.19"
 PyMNE = "0.2"
 SparseArrays = "1"
 StaticArrays = "1"

docs/run_liveserver.jl

@@ -1,3 +1,3 @@
 using LiveServer
-servedocs(skip_dir=joinpath("src","generated"),literate_dir=joinpath("literate"),foldername=".")
+servedocs(skip_dir=joinpath("src","generated"),literate_dir=joinpath("literate"),literate=joinpath("literate"),foldername=".")
 

src/UnfoldMakie.jl

@@ -42,6 +42,7 @@ include("plot_topoplot.jl")
 include("plot_erpimage.jl")
 include("plot_parallelcoordinates.jl")
 include("plot_circulareegtopoplot.jl")
+include("plot_erpgrid.jl")
 
 include("layout_helper.jl")
 include("eeg_positions.jl")
@@ -68,6 +69,8 @@ export plot_circulareegtopoplot!
 
 export plot_topoplotseries
 export plot_topoplotseries!
+export plot_erpgrid
+export plot_erpgrid!
 
 export to_positions
 export nonnumeric # reexport from AoG

src/eeg_series.jl

@@ -130,9 +130,10 @@ function eeg_topoplot_series!(
     select_col = isnothing(col) ? 1 : unique(data_mean[:, col])
     select_row = isnothing(row) ? 1 : unique(data_mean[:, row])
 
+    axlist = []
     for r = 1:length(select_row)
         for c = 1:length(select_col)
-            ax = Axis(fig[r, c]; axisOptions...)
+            ax = Axis(fig[:, :][r, c]; axisOptions...)
             # select one topoplot
             sel = 1 .== ones(size(data_mean, 1)) # select all
             if !isnothing(col)
@@ -159,14 +160,15 @@ function eeg_topoplot_series!(
             end
             if c == 1 && length(select_row) > 1 && row_labels
                 #@show df_single
-                ax.ylabel = string(df_single.row[1])
+                ax.ylabel = string(df_single[1, row])
                 ax.ylabelvisible = true
             end
+            push!(axlist, ax)
         end
     end
     colgap!(fig.layout, 0)
 
-    return fig
+    return fig, axlist
 end
 
 """

src/plot_erp.jl

@@ -149,10 +149,6 @@ function plot_erp!(
         mapp = mapp * mapping(; config.mapping.group)
     end
 
-
-
-
-
     # remove x / y
     mappingOthers = deleteKeys(config.mapping, [:x, :y])
 
@@ -169,7 +165,7 @@ function plot_erp!(
 
     # add the pvalues
     if !isempty(pvalue)
-        basic = basic + addPvalues(plotData, pvalue,config)
+        basic = basic + addPvalues(plotData, pvalue, config)
     end
 
     plotEquation = basic * mapp
@@ -268,7 +264,7 @@ function topoplotLegend(axis, topomarkersize, topoPositionToColorFunction, allPo
     return topoplot
 end
 
-function addPvalues(plotData, pvalue,config)
+function addPvalues(plotData, pvalue, config)
     p = deepcopy(pvalue)
 
     # for now, add them to the fixed effect

src/plot_erpgrid.jl

@@ -0,0 +1,87 @@
+"""
+    function plot_erpgrid!(f::Union{GridPosition, Figure}, data::Matrix{<:Real}, pos::Vector{Point{2,Float}}; kwargs...)
+    function plot_erpgrid(data::Matrix{<:Real}, pos::Vector{Point{2,Float}}; kwargs...)
+
+Plot an ERP image.
+## Arguments:
+- `f::Union{GridPosition, Figure}`: Figure or GridPosition that the plot should be drawn into;
+- `plotData::Matrix{<:Real}`: Data for the plot visualization;
+- `pos::Vector{Point{2,Float}}`: electrode positions.
+        
+## Keyword Arguments
+- `drawLabels` (bool, `false`) - Draw channels labels over each waveform. 
+- `times`: (Vector, `1:size(plotData, 2)`) - Vector of size()
+
+## Return Value:
+The input `f`
+"""
+
+# no figure?
+plot_erpgrid(plotData::Matrix{<:Real}, pos; kwargs...) =
+    plot_erpgrid!(Figure(), plotData, pos; kwargs...)
+
+function plot_erpgrid!(
+    f::Union{GridPosition,Figure},
+    plotData::Matrix{<:Real},
+    pos;
+    drawLabels = false,
+    times = -1:size(plotData, 2)-2, #arbitrary strat just for fun
+    kwargs...,
+)
+    chanNum = size(plotData, 1)
+    println(size(plotData, 1), " ", size(plotData, 2))
+    plotData = plotData[1:chanNum, :]
+    pos = hcat([[p[1], p[2]] for p in pos]...)
+
+    pos = pos[:, 1:chanNum]
+    minmaxrange = (maximum(pos, dims = 2) - minimum(pos, dims = 2))
+    pos = (pos .- mean(pos, dims = 2)) ./ minmaxrange .+ 0.5
+
+    axlist = []
+    #ax = Axis(f[1, 1],backgroundcolor=:green)#
+
+    rel_zeropoint = argmin(abs.(times)) ./ length(times)
+
+    for (ix, p) in enumerate(eachcol(pos))
+        x = p[1] #- 0.1
+        y = p[2] #- 0.1
+        # todo: 0.1 should go into plot config
+        ax = Axis(
+            f[1, 1],
+            width = Relative(0.2),
+            height = Relative(0.2),
+            halign = x,
+            valign = y,
+        )# title = raw_ch_names[1:30])
+        if drawLabels
+            text!(
+                ax,
+                rel_zeropoint + 0.1,
+                1,
+                color = :gray,
+                fontsize = 12,
+                text = string.(ix),
+                align = (:left, :top),
+                space = :relative,
+            )
+        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)
+
+    times = isnothing(times) ? (1:size(plotData, 2)) : times
+
+    # todo: add customizable kwargs
+    h = lines!.(axlist, Ref(times), eachrow(plotData))
+
+    linkaxes!(axlist...)
+    hidedecorations!.(axlist)
+    hidespines!.(axlist)
+
+    f
+
+end

src/plot_erpimage.jl

@@ -35,15 +35,8 @@ plot_erpimage!(f::Union{GridPosition,Figure}, plotData::Matrix{<:Real}; kwargs..
 
 
 # no figure?
-plot_erpimage(times::AbstractVector, plotData::Matrix{<:Real}; kwargs...) = plot_erpimage!(
-    Figure(),
-    times,
-    plotData;
-    sortix = nothing,
-    meanPlot = false,
-    erpBlur = 10,
-    kwargs...,
-)
+plot_erpimage(times::AbstractVector, plotData::Matrix{<:Real}; kwargs...) =
+    plot_erpimage!(Figure(), times, plotData; kwargs...)
 
 function plot_erpimage!(
     f::Union{GridPosition,Figure},

src/plot_topoplotseries.jl

@@ -2,9 +2,10 @@
     plot_topoplotseries!(f::Union{GridPosition, Figure}, plotData::DataFrame,Δbin::Real;kwargs...)
     plot_topoplotseries!(plotData::DataFrame, Δbin::Real;kwargs...)
         
+Multiple miniature topoplots in regular distances 
 
-Plot a Topoplot Series.
 ## Arguments:
+
 - `f::Union{GridPosition, Figure}`: Figure or GridPosition that the plot should be drawn into
 - `plotData::DataFrame`: DataFrame with data, needs a `time` column
 - `Δbin::Real`: A number for how large one bin should be. Δbin is in units of the `plotData.time` column
@@ -23,7 +24,6 @@ The input `f`
 plot_topoplotseries(plotData::DataFrame, Δbin::Real; kwargs...) =
     plot_topoplotseries!(Figure(), plotData, Δbin; kwargs...)
 
-
 function plot_topoplotseries!(
     f::Union{GridPosition,Figure},
     plotData::DataFrame,
@@ -36,6 +36,7 @@ function plot_topoplotseries!(
     rasterize_heatmaps = true,
     kwargs...,
 )
+
     config = PlotConfig(:topoplotseries)
     config_kwargs!(config; kwargs...)
 
@@ -51,7 +52,7 @@ function plot_topoplotseries!(
     end
 
 
-    ftopo = eeg_topoplot_series!(
+    ftopo, axlist = eeg_topoplot_series!(
         f,
         plotData,
         Δbin;
@@ -68,13 +69,8 @@ function plot_topoplotseries!(
     )
 
     if config.layout.useColorbar
-        #println(fieldnames(typeof(ftopo.layout.content[5].content.content[2].content)))
-        #@show "colorbar"
         if typeof(ftopo) == Figure
-
             d = ftopo.content[1].scene.plots[1]
-            #println(d.colorrange)
-            #println(d.colormap)
             Colorbar(
                 f[1, end+1],
                 colormap = d.colormap,
@@ -83,20 +79,17 @@ function plot_topoplotseries!(
                 flipaxis = false,
                 label = "Voltage [µV]",
             )
-        else # temporal
-            if length(ftopo.layout.content) > 2
-                d = ftopo.layout.content[5].content.content[2].content.scene.plots[1].attributes
-            else
-                d = ftopo.layout.content[2].content.content[1].content.scene.plots[1].plots[1].attributes
-            end
+        else
+            # println(fieldnames(typeof((axlist[1]))))
+            d = axlist[1].scene.plots[1].attributes
             Colorbar(
-                f[1, ftopo.layout.size[2]+1],
+                f[:, :][1, length(axlist)+1],
                 colormap = d.colormap,
                 colorrange = d.colorrange,
                 height = 100,
                 flipaxis = false,
                 label = "Voltage [µV]",
-            ) # why end is not working????
+            )
         end
     end
     return f

test/runtests.jl

@@ -1,4 +1,4 @@
-
+using UnfoldMakie
 include("setup.jl")
 #include("../src/UnfoldMakie.jl")
 

test/setup.jl

@@ -1,4 +1,3 @@
-using UnfoldMakie
 using UnfoldSim
 using Test
 using CairoMakie

test/test_butterfly.jl

@@ -1,19 +1,21 @@
 
+@testset "basic" begin
+    include("../docs/example_data.jl")
+    data, pos = example_data("TopoPlots.jl")
+    plot_butterfly(data; positions = pos)
+end
+
 @testset "markersize change" begin
     include("../docs/example_data.jl")
     data, pos = example_data("TopoPlots.jl")
     plot_butterfly(
         data;
         positions = pos,
-        markersize = 10,
+        topomarkersize = 10,
         topoheigth = 0.4,
         topowidth = 0.4,
     )
 end
 
 
-@testset "markersize change" begin
-    include("../docs/example_data.jl")
-    data, pos = example_data("TopoPlots.jl")
-    plot_butterfly(data; positions = pos)
-end
+

test/test_erp.jl

@@ -1,4 +1,4 @@
-@testset "testing standart" begin
+@testset "basic with results" begin
     data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true)
     data = reshape(data, (1, size(data)...))
     f = @formula 0 ~ 1 + condition + continuous
@@ -19,7 +19,7 @@
 end
 
 
-@testset "testing standart with more arguments" begin
+@testset "basic with res_effects" begin
     data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true)
     data = reshape(data, (1, size(data)...))
     f = @formula 0 ~ 1 + condition + continuous

test/test_erpgrid.jl

@@ -0,0 +1,17 @@
+data, pos = TopoPlots.example_data()
+data = data[:, :, 1]
+
+#times = -0.099609375:0.001953125:1.0
+
+@testset "basic erpgrid: one plot is out of the border" begin
+    plot_erpgrid(data[1:3, 1:20], pos)
+end
+
+@testset "basic erpgrid" begin
+    plot_erpgrid(data[1:6, 1:20], pos)
+end
+
+@testset "erpgrid with GridPosition" begin
+    f = Figure()
+    plot_erpgrid!(f[1, 1], data, pos)
+end

test/test_erpimage.jl

@@ -1,21 +1,20 @@
 #include("setup.jl")
-@testset "testing no bottom erp plot" begin
+@testset "basic" begin
     data, evts = UnfoldSim.predef_eeg(; noiselevel = 10, return_epoched = true)
     plot_erpimage(data;)
 end
 
-@testset "testing with bottom erp plot" begin
+@testset "with mean erp plot" begin
     data, evts = UnfoldSim.predef_eeg(; noiselevel = 10, return_epoched = true)
     plot_erpimage(data; meanPlot = true)
 end
 
-@testset "testing no bottom erp plot in extra mode" begin
+@testset "changing erpBlur to zero" begin
     data, evts = UnfoldSim.predef_eeg(; noiselevel = 10, return_epoched = true)
-    plot_erpimage(data; meanPlot = true)
+    plot_erpimage(data; meanPlot = true, erpBlur = 0)
 end
 
-
-@testset "testing no bottom erp plot in extra mode" begin
+@testset "GridPosition" begin
     f = Figure()
     data, evts = UnfoldSim.predef_eeg(; noiselevel = 10, return_epoched = true)
     plot_erpimage!(f[1, 1], data; meanPlot = true)

test/test_pp.jl

@@ -1,7 +1,18 @@
 
-@testset "markersize change" begin
+@testset "Figure, 3 channels, 1 condition" begin
     include("../docs/example_data.jl")
     results_plot, positions = example_data();
-    plot_parallelcoordinates(results_plot, [5,3,2]; # this selects channel 5,3 & 2 
+    plot_parallelcoordinates(results_plot, [5, 3, 2]; # this selects channel 5,3 & 2 
         mapping = (color = :coefname, y = :estimate))
 end
+
+
+@testset "GridPosition" begin
+    uf_5chan = example_data("UnfoldLinearModelMultiChannel")
+    d_singletrial, _ = UnfoldSim.predef_eeg(; return_epoched=true)
+
+    f = Figure()
+    plot_parallelcoordinates!(f[1, 1], uf_5chan, [1, 2, 3, 4, 5]; 
+        mapping=(; color=:coefname), layout=(; legendPosition=:bottom))
+    f
+end