"8 plots -2" (#101)

* revised topoplotseries and test all * erp image sorted in test_all * first draft * Update plot_channelimage.jl * first successfull test * upd to main * channelimage in complex plot * strange bug fix * small inconsistency in tests * reverse ERP image trials and sorted ERP image into combined plot * more example_data * del
unfoldtoolbox · Nov 30, 2023 · acff4b9 · acff4b9
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diff --git a/docs/example_data.jl b/docs/example_data.jl
@@ -96,6 +96,14 @@ function example_data(example = "TopoPlots.jl")
         end
         df.time = range(-0.3, 0.5, step = 1 / 500)[Int.(df.time)]
         return df, chanlocs
+    elseif example == "sort_data"
+        dat, evts =
+            UnfoldSim.predef_eeg(; onset = LogNormalOnset(μ = 3.5, σ = 0.4), noiselevel = 5)
+        dat_e, times = Unfold.epoch(dat, evts, [-0.1, 1], 100)
+        evts, dat_e = Unfold.dropMissingEpochs(evts, dat_e)
+        evts.Δlatency = diff(vcat(evts.latency, 0)) *-1
+        dat_e = dat_e[1, :, :]
+        return dat_e, evts, times
     else
         error("unknown example data")
     end

diff --git a/docs/src/how_to/mult_vis_in_fig.md b/docs/src/how_to/mult_vis_in_fig.md
@@ -17,9 +17,8 @@ uf_deconv = example_data("UnfoldLinearModelContinuousTime")
 uf = example_data("UnfoldLinearModel")
 results = coeftable(uf)
 uf_5chan = example_data("UnfoldLinearModelMultiChannel")
-d_singletrial, _ = UnfoldSim.predef_eeg(; return_epoched=true)
-times = -0.099609375:0.001953125:1.0
 data, positions = TopoPlots.example_data()
+dat_e, evts, times = example_data("sort_data")    
 nothing #hide
 ```
 This section discusses how users can incorporate multiple plots into a single figure.
@@ -81,7 +80,7 @@ plot_erp!(f[2, 4:5], res_effects; categorical_color=false, categorical_group=tru
 plot_parallelcoordinates!(f[3, 2:3], uf_5chan, [1, 2, 3, 4, 5]; mapping=(; color=:coefname), 
     layout=(; legend_position=:bottom))
 
-plot_erpimage!(f[1, 4:5], times, d_singletrial)
+plot_erpimage!(f[1, 4:5], times, dat_e; sortvalues=evts.Δlatency)
 plot_circulareegtopoplot!(f[3:4, 4:5], d_topo[in.(d_topo.time, Ref(-0.3:0.1:0.5)), :];
     positions=positions, predictor=:time, predictor_bounds=[-0.3, 0.5])
 

diff --git a/docs/src/tutorials/erpimage.md b/docs/src/tutorials/erpimage.md
@@ -51,7 +51,7 @@ First, generate a data. Second, specify the necessary sorting parameter.
     )
     dat_e, times = Unfold.epoch(dat, evts, [-0.1,1], 100)
     evts, dat_e = Unfold.dropMissingEpochs(evts, dat_e)
-    evts.Δlatency =  diff(vcat(evts.latency, 0))
+    evts.Δlatency =  diff(vcat(evts.latency, 0)) *-1
     dat_e = dat_e[1,:,:]
 
     plot_erpimage(times, dat_e; sortvalues=evts.Δlatency)

diff --git a/src/UnfoldMakie.jl b/src/UnfoldMakie.jl
@@ -43,6 +43,7 @@ include("plot_erpimage.jl")
 include("plot_parallelcoordinates.jl")
 include("plot_circulareegtopoplot.jl")
 include("plot_erpgrid.jl")
+include("plot_channelimage.jl")
 
 include("layout_helper.jl")
 include("eeg_positions.jl")
@@ -71,6 +72,8 @@ export plot_topoplotseries
 export plot_topoplotseries!
 export plot_erpgrid
 export plot_erpgrid!
+export plot_channelimage
+export plot_channelimage!
 
 export to_positions
 export nonnumeric # reexport from AoG

diff --git a/src/docstringtemplate.jl b/src/docstringtemplate.jl
@@ -1,31 +1,32 @@
-function _docstring(cfgsymb::Symbol)
+function _docstring(cfg_symb::Symbol)
     #pad = maximum(length(string(f)) for f in fieldnames(T))
-    cfg = PlotConfig(cfgsymb)
+    cfg = PlotConfig(cfg_symb)
     fn = fieldnames(PlotConfig)
     out = ""
 
     visuallink = Dict(
         :erp =>`Makie.lines`,
         :butterfly =>`Makie.lines`,
         :paracoord =>`Makie.lines`,
+        :erpgrid =>`Makie.lines`,
         :designmat => `Makie.heatmap`,
         :erpimage => `Makie.heatmap`,
         :channelimage => `Makie.heatmap`,
         :circeegtopo => `Topoplot.eeg_topoplot`,
         :topoplot => `Topoplot.eeg_topoplot`,
         :topoplotseries => `Topoplot.eeg_topoplot`
     )
-    cbarstring = (cfgsymb == :erp || cfgsymb == :butterfly) ? "[`AlgebraOfGraphics.colobar!`](@ref)" : "[`Makie.Colorbar`](@ref)"
+    cbarstring = (cfg_symb == :erp || cfg_symb == :butterfly) ? "[`AlgebraOfGraphics.colobar!`](@ref)" : "[`Makie.Colorbar`](@ref)"
     link = Dict(
         :figure => "use `kwargs...` of [`Makie.Figure`](@ref)",
         :axis => "use `kwargs...` of  [`Makie.Axis`](@ref)",
         :legend => "use `kwargs...` of  [`Makie.Legend`](@ref)",
         :colorbar => "use `kwargs...` of  $cbarstring",
-        :visual => "use `kwargs...` of [`$(visuallink[cfgsymb])`](@ref)",
+        :visual => "use `kwargs...` of [`$(visuallink[cfg_symb])`](@ref)",
 
     )
     for k = 1:length(fn)
-        namedtpl = Base.getfield(cfg,fn[k])
+        namedtpl = Base.getfield(cfg, fn[k])
         addlink = ""
         try
             addlink = "- *"*link[fn[k]]*"*"
@@ -36,7 +37,7 @@ function _docstring(cfgsymb::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))`. 
+        `type = (; key=value, ...))` - for example `plot_x(..., layout = (show_legend=true, legend_position=:right))`. 
         Multiple defaults will be cycled until match.
 
         $(out)

diff --git a/src/plot_channelimage.jl b/src/plot_channelimage.jl
@@ -0,0 +1,60 @@
+"""
+    plot_channelimage!(f::Union{GridPosition, GridLayout, Figure}, data::Matrix{<:Real}, position::Vector{Point{2,Float32}}, ch_names::Vector{String}; kwargs...)
+    plot_channelimage(data::Matrix{<:Real}, position::Vector{Point{2,Float32}}, ch_names::Vector{String}; kwargs...)
+        
+Channel image
+
+## Arguments:
+
+- `f::Union{GridPosition, GridLayout, Figure}`: Figure, GridLayout or GridPosition that the plot should be drawn into.
+- `data::DataFrame`: DataFrame with data.
+- `position` (Vector{Point{2,Float32}}): a vector with EEG layout coordinates.
+- `ch_names` (Vector{String}): vector with channel names.
+
+$(_docstring(:channelimage))
+
+## Return Value:
+A figure displaying channel image
+
+"""
+
+plot_channelimage(data::Matrix{<:Real}, position::Vector{Point{2,Float32}}, ch_names::Vector{String}; kwargs...) = 
+    plot_channelimage!(Figure(), data, position, ch_names; kwargs...)
+
+function plot_channelimage!(
+    f::Union{GridPosition,GridLayout,Figure},
+    data::Matrix{<:Real},
+    position::Vector{Point{2,Float32}},
+    ch_names::Vector{String};
+    kwargs...,
+)
+    config = PlotConfig(:channelimage)
+    config_kwargs!(config; kwargs...)
+
+
+    x = [i[1] for i in position]
+    y = [i[2] for i in position]
+
+    x = round.(x; digits = 2)
+    y = Integer.(round.((y .- mean(y)) * 20)) * -1
+    x = Integer.(round.((x .- mean(x)) * 20))
+    d = zip(x, y, ch_names, 1:20)
+    a = sort!(DataFrame(d), [:2, :1], rev = [true, false])
+    b = a[!, :4]
+    c = a[!, :3]
+    c = [string(x) for x in c]
+
+    ix = range(-0.3, 1.2, length = size(data, 2))
+    iy = 1:20
+    iz = mean(data, dims = 3)[b, :, 1]'
+
+    gin = f[1, 1] = GridLayout()
+    ax = Axis(gin[1, 1], xlabel = config.axis.xlabel, ylabel = config.axis.ylabel)
+    hm = Makie.heatmap!(ix, iy, iz, colormap = config.visual.colormap)
+    ax.yticks = iy
+    ax.ytickformat = xc -> c
+    ax.yticklabelsize = config.axis.yticklabelsize
+
+    Makie.Colorbar(gin[1, 2], hm, label = config.colorbar.label, labelrotation = config.colorbar.labelrotation)
+    return f
+end
diff --git a/src/plot_circulareegtopoplot.jl b/src/plot_circulareegtopoplot.jl
@@ -1,6 +1,7 @@
 """
-    plot_circulareegtopoplot(data::DataFrame; kwargs...)
     plot_circulareegtopoplot!(f, data::DataFrame; kwargs...)
+    plot_circulareegtopoplot(data::DataFrame; kwargs...)
+    
 
 Plot a circular EEG topoplot.
 ## Arguments:

diff --git a/src/plot_erpgrid.jl b/src/plot_erpgrid.jl
@@ -12,8 +12,9 @@ Plot an ERP image.
 - `drawlabels` (bool, `false`): draw channels labels over each waveform. 
 - `times`: (Vector, `1:size(data, 2)`): vector of size().
 
+
 ## Return Value:
-The input `f`
+The figure displaying ERP grid
 """
 
 # no figure?

diff --git a/src/plot_erpimage.jl b/src/plot_erpimage.jl
@@ -25,8 +25,7 @@ The input `f`
 """
 
 # no times + no figure?
-plot_erpimage(plot::Matrix{<:Real}; kwargs...) =
-    plot_erpimage!(Figure(), plot; kwargs...)
+plot_erpimage(plot::Matrix{<:Real}; kwargs...) = plot_erpimage!(Figure(), plot; kwargs...)
 
 # no times?
 plot_erpimage!(f::Union{GridPosition,GridLayout,Figure}, plot::Matrix{<:Real}; kwargs...) =

diff --git a/src/plot_topoplot.jl b/src/plot_topoplot.jl
@@ -1,6 +1,6 @@
 """
     plot_topoplot!(f::Union{GridPosition, GridLayout, Figure}, data, ; positions=nothing, labels=nothing,kwargs...)
-    plot_topoplot(data,; positions=nothing, labels=nothing, kwargs...)
+    plot_topoplot(data; positions=nothing, labels=nothing, kwargs...)
 
 Plot a topo plot.
 ## Arguments:

diff --git a/src/plot_topoplotseries.jl b/src/plot_topoplotseries.jl
@@ -1,5 +1,5 @@
 """
-    plot_topoplotseries!(f::Union{GridPosition, GridLayout, Figure}, data::DataFrame, Δbin::Real; kwargs...)
+    plot_topoplotseries(f::Union{GridPosition, GridLayout, Figure}, data::DataFrame, Δbin::Real; kwargs...)
     plot_topoplotseries!(data::DataFrame, Δbin::Real; kwargs...)
         
 Multiple miniature topoplots in regular distances 
@@ -77,7 +77,6 @@ function plot_topoplotseries!(
                 f[1, end+1],
                 colormap = d.colormap,
                 colorrange = d.colorrange,
-                height = config.colorbar.height,
                 flipaxis = config.colorbar.flipaxis,
                 labelrotation  = config.colorbar.labelrotation ,
                 label = config.colorbar.label,
@@ -89,7 +88,6 @@ function plot_topoplotseries!(
                 f[:, :][1, length(axlist)+1],
                 colormap = d.colormap,
                 colorrange = d.colorrange,
-                height = config.colorbar.height,
                 flipaxis = config.colorbar.flipaxis,
                 labelrotation  = config.colorbar.labelrotation ,
                 label = config.colorbar.label,
@@ -98,4 +96,4 @@ function plot_topoplotseries!(
     end
     return f
 
-end
+end
diff --git a/src/plotconfig.jl b/src/plotconfig.jl
@@ -51,28 +51,31 @@ function PlotConfig()# defaults
             tellheight = false,
         ),
     )
-
 end
 
-
 """
 Takes a kwargs named tuple of Key => NamedTuple and merges the fields with the defaults
 """
 function config_kwargs!(cfg::PlotConfig; kwargs...)
-    is_namedtuple = [isa(t,NamedTuple) for t in values(kwargs)]
+    is_namedtuple = [isa(t, NamedTuple) for t in values(kwargs)]
     @debug is_namedtuple
-    @assert(all(is_namedtuple),
-    """ Keyword argument specification (kwargs...) Specified config groups must be NamedTuples', but $(keys(kwargs)[.!is_namedtuple]) was not.
-    Maybe you forgot the semicolon (;) at the beginning of your specification? Compare these strings:
-    
-    plot_example(...; layout = (; use_colorbar=true))
-    
-    plot_example(...; layout = (use_colorbar=true))
-     
-    The first is correct and creates a NamedTuple as required. The second is wrong and its call is ignored.""")
-    list = fieldnames(PlotConfig)#[:layout,:visual,:mapping,:legend,:colorbar,:axis]
+    @assert(
+        all(is_namedtuple),
+        """ Keyword argument specification (kwargs...) Specified config groups must be NamedTuples', but $(keys(kwargs)[.!is_namedtuple]) was not.
+        Maybe you forgot the semicolon (;) at the beginning of your specification? Compare these strings:
+
+        plot_example(...; layout = (; use_colorbar=true))
+
+        plot_example(...; layout = (use_colorbar=true))
+         
+        The first is correct and creates a NamedTuple as required. The second is wrong and its call is ignored."""
+    )
+    list = fieldnames(PlotConfig) #[:layout, :visual, :mapping, :legend, :colorbar, :axis]
     keyList = collect(keys(kwargs))
-    :extra ∈ keyList ? @warn("Extra is deprecated in 0.4 and extra-keyword args have to be used directly as key-word arguments") : ""
+    :extra ∈ keyList ?
+    @warn(
+        "Extra is deprecated in 0.4 and extra-keyword args have to be used directly as key-word arguments"
+    ) : ""
     applyTo = keyList[in.(keyList, Ref(list))]
     for k ∈ applyTo
         setfield!(cfg, k, merge(getfield(cfg, k), kwargs[k]))
@@ -105,13 +108,7 @@ end
 function PlotConfig(T::Val{:topoarray})
     cfg = PlotConfig(:erp)
 
-    config_kwargs!(
-        cfg;
-        layout = (;),
-        colorbar = (;),
-        mapping = (;),
-        axis = (;),
-    )
+    config_kwargs!(cfg; layout = (;), colorbar = (;), mapping = (;), axis = (;))
     return cfg
 end
 
@@ -151,12 +148,7 @@ function PlotConfig(T::Val{:topoplotseries})
     config_kwargs!(
         cfg,
         layout = (use_colorbar = true,),
-        colorbar = (;
-            height = 300, # why even should i made it manually?
-            flipaxis = true, 
-            labelrotation = 4.7, 
-            label = "Voltage [µV]"
-        ), 
+        colorbar = (; flipaxis = true, labelrotation = -π / 2, label = "Voltage [µV]"),
         visual = (;
             label_text = false # true doesnt work again
         ),
@@ -196,12 +188,23 @@ function PlotConfig(T::Val{:erp})
     config_kwargs!(
         cfg;
         mapping = (; color = (:color, :coefname, nothing)),
-        layout = (; show_legend = true,  hidespines = (:r, :t)),
+        layout = (; show_legend = true, hidespines = (:r, :t)),
         legend = (; framevisible = false),
     )
 
     return cfg
 end
+function PlotConfig(T::Val{:channelimage})
+    cfg = PlotConfig()
+    config_kwargs!(
+        cfg;
+        #layout = (; use_colorbar = true),
+        colorbar = (; label = "Voltage [µV]", labelrotation = 4.7),
+        axis = (xlabel = "Time [s]", ylabel = "Channels", yticklabelsize = 14),
+        visual = (; colormap = Reverse("RdBu")), #cork
+    )
+    return cfg
+end
 function PlotConfig(T::Val{:erpimage})
     cfg = PlotConfig()
     config_kwargs!(

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -15,10 +15,14 @@ end
     include("test_butterfly.jl")
 end
 
-@testset "ERP Image" begin
+@testset "ERP image" begin
     include("test_erpimage.jl")
 end
 
+@testset "Channel image" begin
+    include("test_channelimage.jl")
+end
+
 @testset "Topoplot" begin
     include("test_topoplot.jl")
 end

diff --git a/test/test_channelimage.jl b/test/test_channelimage.jl
@@ -0,0 +1,17 @@
+data, pos = TopoPlots.example_data()
+data = data[:, :, 1]
+pos = pos[1:30]
+raw_ch_names = ["FP1", "F3", "F7", "FC3", "C3", "C5", "P3", "P7", "P9", "PO7", 
+"PO3", "O1", "Oz", "Pz", "CPz", "FP2", "Fz", "F4", "F8", "FC4", "FCz", "Cz", 
+"C4", "C6", "P4", "P8", "P10", "PO8", "PO4", "O2"]
+
+@testset "channel image basic" begin
+    plot_channelimage(data, pos, raw_ch_names; )
+
+end
+
+@testset "channel image with Figure" begin
+    f = Figure()
+    plot_channelimage!(f, data, pos, raw_ch_names; )
+
+end