UnfoldMakie.cart3d_to_spherical — Methodconvert x/y/z electrode montage positions to spherical coordinate representation. output is a matrixUnfoldMakie.config_kwargs! — MethodTakes a kwargs named tuple of Key => NamedTuple and merges the fields with the defaults
UnfoldMakie.df_timebin — Methodfunction dftimebin(df, Δbin; coly=:erp, fun=mean, grouping=[]) Split or combine dataframe according to equally spaced time bins
dfAbstractTable with columns:timeandcol_y(default:erp), and all columns ingrouping;Δbinbin size in:timeunits;col_ydefault :erp, the column to combine over (withfun);funfunction to combine, default ismean;grouping(vector of symbols/strings) default empty vector, columns to group the data by before aggregating. Values ofnothingare ignored.
UnfoldMakie.eeg_matrix_to_dataframe — MethodHelper function converting a matrix (channel x times) to a tidy dataframe with columns :estimate, :time and :label
UnfoldMakie.eeg_topoplot_series! — Methodeegtopoplotseries!(fig, data::DataFrame, Δbin; kwargs..) In place plotting of topoplot series see eegtopoplotseries(data, Δbin) for help
UnfoldMakie.eeg_topoplot_series — Methodfunction eegtopoplotseries(data::DataFrame, Δbin; y=:estimate, label=:label, col=:time, row=nothing, figure = NamedTuple(), combinefun=mean, rowlabels = false, collabels = false, topoplot_attributes... )
Plot a series of topoplots. The function automatically takes the combinefun=mean over the :time column of data in Δbin steps.
- The data frame
dataneeds the columns:timeandy(=:erp), andlabel(=:label). Ifdatais a matrix, it is automatically cast to a dataframe, time bins are in samples, labels arestring.(1:size(data,1)). - Δbin in
:timeunits, specifying the time steps. All other keyword arguments are passed to the EEG_TopoPlot recipe. In most cases, the user should specify the electrode positions withpositions=pos. - The
colandrowarguments specify the field to be divided into columns and rows. The default iscol=:timeto split by the time field androw=nothing. Useful
to split by a condition, e.g. ...(..., col=:time, row=:condition) would result in multiple (as many as different values in df.condition) rows of topoplot series.
- The
figureoption allows you to include information for plotting the figure. Alternatively, you can pass a fig objecteeg_topoplot_series!(fig, data::DataFrame, Δbin; kwargs..). row_labelsandcol_labelsindicate whether there should be labels in the plots in the first column to indicate the row value and in the last row to indicate the time (typically timerange).
Examples
Desc
julia > df = DataFrame(:erp => repeat(1:63, 100), :time => repeat(1:20, 5 * 63), :label => repeat(1:63, 100)) # fake data
+API · UnfoldMakie.jl UnfoldMakie.cart3d_to_spherical — Methodconvert x/y/z electrode montage positions to spherical coordinate representation. output is a matrix
sourceUnfoldMakie.config_kwargs! — MethodTakes a kwargs named tuple of Key => NamedTuple and merges the fields with the defaults
sourceUnfoldMakie.df_timebin — Methodfunction dftimebin(df, Δbin; coly=:erp, fun=mean, grouping=[]) Split or combine dataframe according to equally spaced time bins
df AbstractTable with columns :time and col_y (default :erp), and all columns in grouping;Δbin bin size in :time units;col_y default :erp, the column to combine over (with fun);fun function to combine, default is mean;grouping (vector of symbols/strings) default empty vector, columns to group the data by before aggregating. Values of nothing are ignored.
sourceUnfoldMakie.eeg_matrix_to_dataframe — MethodHelper function converting a matrix (channel x times) to a tidy dataframe with columns :estimate, :time and :label
sourceUnfoldMakie.eeg_topoplot_series! — Methodeegtopoplotseries!(fig, data::DataFrame, Δbin; kwargs..) In place plotting of topoplot series see eegtopoplotseries(data, Δbin) for help
sourceUnfoldMakie.eeg_topoplot_series — Methodfunction eegtopoplotseries(data::DataFrame, Δbin; y=:estimate, label=:label, col=:time, row=nothing, figure = NamedTuple(), combinefun=mean, rowlabels = false, collabels = false, topoplot_attributes... )
Plot a series of topoplots. The function automatically takes the combinefun=mean over the :time column of data in Δbin steps.
- The data frame
data needs the columns :time and y(=:erp), and label(=:label). If data is a matrix, it is automatically cast to a dataframe, time bins are in samples, labels are string.(1:size(data,1)). - Δbin in
:time units, specifying the time steps. All other keyword arguments are passed to the EEG_TopoPlot recipe. In most cases, the user should specify the electrode positions with positions=pos. - The
col and row arguments specify the field to be divided into columns and rows. The default is col=:time to split by the time field and row=nothing. Useful
to split by a condition, e.g. ...(..., col=:time, row=:condition) would result in multiple (as many as different values in df.condition) rows of topoplot series.
- The
figure option allows you to include information for plotting the figure. Alternatively, you can pass a fig object eeg_topoplot_series!(fig, data::DataFrame, Δbin; kwargs..). row_labels and col_labels indicate whether there should be labels in the plots in the first column to indicate the row value and in the last row to indicate the time (typically timerange).
Examples
Desc
julia > df = DataFrame(:erp => repeat(1:63, 100), :time => repeat(1:20, 5 * 63), :label => repeat(1:63, 100)) # fake data
julia > pos = [(1:63) ./ 63 .* (sin.(range(-2 * pi, 2 * pi, 63))) (1:63) ./ 63 .* cos.(range(-2 * pi, 2 * pi, 63))] .* 0.5 .+ 0.5 # fake electrode positions
julia > pos = [Point2.(pos[k, 1], pos[k, 2]) for k in 1:size(pos, 1)]
-julia > eeg_topoplot_series(df, 5; positions=pos)
sourceUnfoldMakie.plot_butterfly — MethodPlot a butterfly plot
kwargs (...; ...):
butterfly (bool, true): create a butterfly plot.topolegend (bool, true): show an inlay topoplot with corresponding electrodes.topomarkersize (Real, 10): change the size of the markers, topoplot-inlay electrodes.topowidth (Real, 0.25): change the size of the inlay topoplot width.topoheigth (Real, 0.25): change the size of the inlay topoplot height.topopositions_to_color (function, ´x -> posToColorRomaO(x)´).
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = NamedTuple() - use kwargs... of Makie.Axis
layout = (showlegend = false, legendposition = :right, xlabelFromMapping = :x, ylabelFromMapping = :y, use_colorbar = false, hidespines = (:r, :t))
mapping = (x = (:time,), y = (:estimate, :yhat, :y), color = (:channel, :channels, :trial, :trials), positions = (:pos, :positions, :position, :topo_positions, :x, nothing), labels = (:labels, :label, :topoLabels, :sensor, nothing))
visual = (colormap = :roma,) - use kwargs... of $Makie.lines$
legend = (orientation = :vertical, tellwidth = true, tellheight = false, framevisible = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of AlgebraOfGraphics.colobar!
see also plot_erp
sourceUnfoldMakie.plot_circulareegtopoplot — Methodplot_circulareegtopoplot(data::DataFrame; kwargs...)
-plot_circulareegtopoplot!(f, data::DataFrame; kwargs...)
Plot a circular EEG topoplot.
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure, GridLayout or GridPosition that the plot should be drawn into
data::DataFrame: DataFrame with keys for data (looks for :y, :yhat, :estimate), and :position (looks for :pos, :position, :positions),
predictor (optional; default: predictor): the circular predictor value, defines position of topoplot, is mapped around predictor_bounds
predictor_bounds (default: [0,360]): the bounds of the predictor. This is relevant for the axis labels.
positions (default: nothing): positions for the plot_topoplot
center_label (default: ""): the text in the center of the cricle
labels (default: nothing): labels for the plot_topoplot
kwargs...: additional styling behavior, see below.
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = (aspect = Makie.DataAspect(), label = "") - use kwargs... of Makie.Axis
layout = (showlegend = false, legendposition = :right, xlabelFromMapping = nothing, ylabelFromMapping = nothing, use_colorbar = true, hidespines = (), hidedecorations = ())
mapping = (x = (nothing,), y = (:estimate, :yhat, :y), positions = (:pos, :positions, :position, nothing), labels = (:labels, :label, :sensor, nothing))
visual = (colormap = Makie.Reverse{Symbol}(:RdBu), contours = (color = :white, linewidth = 2), labelscatter = true, labeltext = true, boundinggeometry = GeometryBasics.Circle) - *use kwargs... of [``Topoplot.eegtopoplot``](@ref)*
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false, label = "Voltage [µV]", colormap = Makie.Reverse{Symbol}(:RdBu)) - use kwargs... of Makie.Colorbar
Return Value:
A figure containing the circular topoplot at given layout position
sourceUnfoldMakie.plot_designmatrix — Methodplot_designmatrix!(f::Union{GridPosition, GridLayout, Figure}, data::Unfold.DesignMatrix; kwargs...)
-plot_designmatrix(data::Unfold.DesignMatrix; kwargs...)
Plot a designmatrix.
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure or GridPosition (e.g. f[2, 3]) in which the plot will be placed into. A new axis is created.data::Unfold.DesignMatrix: data for the plot visualization.
kwargs
standardize_data (bool,true): indicates whether the data is standardized by pointwise division of the data with its sampled standard deviation.sort_data (bool, true): indicates whether the data is sorted; using sortslices() of Base Julia. xticks (nothing): returns the number of labels on the x-axis. Behavior is set in the configuration:xticks = 0: no labels are placed.xticks = 1: first possible label is placed.xticks = 2: first and last possible labels are placed.- 2 <
xticks < number of labels: equally distribute the labels. xticks ≥ number of labels: all labels are placed.
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = (xticklabelrotation = 0.39269908169872414,) - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = nothing, ylabelFromMapping = nothing, use_colorbar = true)
mapping = (x = (:time,), y = (:estimate, :yhat, :y))
visual = (colormap = :roma,) - use kwargs... of $Makie.heatmap$
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of Makie.Colorbar
Return Value:
A figure displaying the designmatrix.
sourceUnfoldMakie.plot_erp — Methodplot_erp!(f::Union{GridPosition, GridLayout, Figure}, plot_data::DataFrame; kwargs...)
-plot_erp(plot_data::DataFrame; kwargs...)
Plot an ERP plot.
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure, GridLayout or GridPosition that the plot should be drawn into.plot_data::DataFrame: Data for the line plot visualization.kwargs...: Additional styling behavior. Often used: plot_erp(df; mapping=(; color=:coefname, col=:conditionA)).
kwargs (...; ...):
categorical_color (bool, true): in case of numeric :color column, treat :color as continuous or categorical variable.categorical_group (bool, true): in case of numeric :group column, treat :group as categorical variable by default.topolegend (bool, false): add an inlay topoplot with corresponding electrodes.stderror (bool, false): add an error ribbon, with lower and upper limits based on the :stderror column.pvalue (Array, []): show a pvalue.- example:
DataFrame(from=[0.1, 0.3], to=[0.5, 0.7], coefname=["(Intercept)", "condition:face"]) - if coefname is not specified, the lines will be black
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = NamedTuple() - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = :x, ylabelFromMapping = :y, use_colorbar = false, hidespines = (:r, :t))
mapping = (x = (:time,), y = (:estimate, :yhat, :y), color = (:color, :coefname, nothing))
visual = (colormap = :roma,) - use kwargs... of $Makie.lines$
legend = (orientation = :vertical, tellwidth = true, tellheight = false, framevisible = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of AlgebraOfGraphics.colobar!
Return Value:
- f - Figure() or the inputed
f
sourceUnfoldMakie.plot_new — Methodplot_new() -> String
-
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = NamedTuple() - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = :x, ylabelFromMapping = :y, use_colorbar = false, hidespines = (:r, :t))
mapping = (x = (:time,), y = (:estimate, :yhat, :y), color = (:color, :coefname, nothing))
visual = (colormap = :roma,) - use kwargs... of $Makie.lines$
legend = (orientation = :vertical, tellwidth = true, tellheight = false, framevisible = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of AlgebraOfGraphics.colobar!
sourceUnfoldMakie.plot_parallelcoordinates — Methodplot_parallelcoordinates!(f::Union{GridPosition, GridLayout, Figure},
- data::DataFrame, config::PlotConfig; channels::Vector{Int64})
Plot a PCP (parallel coordinates plot).
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure or GridPosition that the plot should be drawn into.data::DataFrame: data for the plot visualization.config::PlotConfig: instance of PlotConfig being applied to the visualization.channels::Vector{Int64}: vector with all the channels representing an axis used in the PCP in given order.
PCP has problems with size changes of the view window. By adapting the padding, aspect ratio and tick label size in px for a new use case, the PCP can even be added into a complex figures.
pc_aspect_ratio (default: 0.55) -pc_right_padding (default: 15) -pc_left_padding (default: 25) -pc_top_padding (default: 26) -pc_bottom_padding (default: 16) -pc_tick_label_size (default: 14) -
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = NamedTuple() - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = :channel, ylabelFromMapping = :y, use_colorbar = false, hidespines = (), hidedecorations = (label = false,))
mapping = (x = (:time,), y = (:estimate, :yhat, :y), channel = :channel, category = :category, time = :time)
visual = (colormap = :roma,) - use kwargs... of $Makie.lines$
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of Makie.Colorbar
Return Value:
The input f
sourceUnfoldMakie.plot_topoplot — Methodplot_topoplot!(f::Union{GridPosition, GridLayout, Figure}, data, ; positions=nothing, labels=nothing,kwargs...)
-plot_topoplot(data,; positions=nothing, labels=nothing, kwargs...)
Plot a topo plot.
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure or GridPosition (e.g. f[2, 3]) that the plot should be drawn into. New axis is created.data::Union{DataFrame, Vector{Float32}}: data for the plot visualization.positions::Vector{Point{2, Float32}}=nothing: positions used if data is not a DataFrame. If this is the case and positions=nothing then positions are generated from labels.labels::Vector{String} = nothing: labels used if data is not a DataFrame.
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = (aspect = Makie.DataAspect(),) - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = nothing, ylabelFromMapping = nothing, use_colorbar = true, hidespines = (), hidedecorations = ())
mapping = (x = (nothing,), y = (:estimate, :yhat, :y), positions = (:pos, :positions, :position, nothing), labels = (:labels, :label, :sensor, nothing))
visual = (colormap = Makie.Reverse{Symbol}(:RdBu), contours = (color = :white, linewidth = 2), labelscatter = true, labeltext = true, boundinggeometry = GeometryBasics.Circle) - *use kwargs... of [``Topoplot.eegtopoplot``](@ref)*
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of Makie.Colorbar
Return Value:
A figure displaying the topo plot.
sourceUnfoldMakie.plot_topoplotseries — Methodplot_topoplotseries!(f::Union{GridPosition, GridLayout, Figure}, data::DataFrame, Δbin::Real; kwargs...)
-plot_topoplotseries!(data::DataFrame, Δbin::Real; kwargs...)
Multiple miniature topoplots in regular distances
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure or GridPosition that the plot should be drawn into.data::DataFrame: DataFrame with data, needs a time column.Δbin::Real: A number for how large one time bin should be. Δbin is in units of the data.time column.combinefun (default: mean) - can be used to specify how the samples within Δbin are combined.rasterize_heatmaps (default: true) - enforce rasterization of the plot heatmap when saving in svg format. This has the benefit that all lines/points are vectors, except the interpolated heatmap. This is typically what you want, otherwise you get ~500x500 vectors per topoplot, which makes everything super slow.col_labels, row_labels - shows column and row labels. - labels (default:
nothing) - . - positions (default:
nothing) - .
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = (aspect = Makie.DataAspect(),) - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = nothing, ylabelFromMapping = nothing, use_colorbar = true, hidespines = (), hidedecorations = ())
mapping = (x = (nothing,), y = (:estimate, :yhat, :y), positions = (:pos, :positions, :position, nothing), labels = (:labels, :label, :sensor, nothing), col = (:time,), row = (nothing,))
visual = (colormap = Makie.Reverse{Symbol}(:RdBu), contours = (color = :white, linewidth = 2), labelscatter = true, labeltext = false, boundinggeometry = GeometryBasics.Circle) - *use kwargs... of [``Topoplot.eegtopoplot``](@ref)*
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false, height = 300, flipaxis = true, labelrotation = 4.7, label = "Voltage [µV]") - use kwargs... of Makie.Colorbar
Return Value:
The input f
sourceUnfoldMakie.rel_to_abs_bbox — Methodreltoabs_bbox(org,rel)
Takes a rectangle org and applies the relative transformation tuple rel Returns a Makie.BBox
sourceUnfoldMakie.to_positions — Methodtopositions(x,y,z;sphere=[0,0,0.]) topositions(pos::AbstractMatrix;sphere=[0,0,0.]) Projects 3D electrode positions to a 2D layout.
The matrix case, assumes size(pos) = (3,nChannels) Re-implementation of the MNE algorithm.
Tipp: You can directly get positions from an MNE object after loading PyMNE and thus activating the UnfoldMakie PyMNE extension
sourceUnfoldMakie.valType_to_symbol — MethodVal{:bu}() to => :bu
sourceInternally, we use a PlotConfig struct to keep track of common plot options, in order to have a similar API to all functions
UnfoldMakie.PlotConfig — TypePlotConfig(<plotname>)
-holds various different fields, that can modify various different plotting aspects.
sourceSettings
This document was generated with Documenter.jl version 1.1.2 on Monday 20 November 2023. Using Julia version 1.9.4.
UnfoldMakie.plot_butterfly — MethodPlot a butterfly plot
kwargs (...; ...):
butterfly(bool,true): create a butterfly plot.topolegend(bool,true): show an inlay topoplot with corresponding electrodes.topomarkersize(Real,10): change the size of the markers, topoplot-inlay electrodes.topowidth(Real,0.25): change the size of the inlay topoplot width.topoheigth(Real,0.25): change the size of the inlay topoplot height.topopositions_to_color(function, ´x -> posToColorRomaO(x)´).
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = NamedTuple() - use kwargs... of Makie.Axis
layout = (showlegend = false, legendposition = :right, xlabelFromMapping = :x, ylabelFromMapping = :y, use_colorbar = false, hidespines = (:r, :t))
mapping = (x = (:time,), y = (:estimate, :yhat, :y), color = (:channel, :channels, :trial, :trials), positions = (:pos, :positions, :position, :topo_positions, :x, nothing), labels = (:labels, :label, :topoLabels, :sensor, nothing))
visual = (colormap = :roma,) - use kwargs... of $Makie.lines$
legend = (orientation = :vertical, tellwidth = true, tellheight = false, framevisible = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of AlgebraOfGraphics.colobar!
see also plot_erp
UnfoldMakie.plot_circulareegtopoplot — Methodplot_circulareegtopoplot(data::DataFrame; kwargs...)
+plot_circulareegtopoplot!(f, data::DataFrame; kwargs...)Plot a circular EEG topoplot.
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure, GridLayout or GridPosition that the plot should be drawn intodata::DataFrame: DataFrame with keys for data (looks for:y, :yhat, :estimate), and :position (looks for:pos, :position, :positions),predictor(optional; default: predictor): the circular predictor value, defines position of topoplot, is mapped aroundpredictor_boundspredictor_bounds(default:[0,360]): the bounds of the predictor. This is relevant for the axis labels.positions(default: nothing): positions for theplot_topoplotcenter_label(default: ""): the text in the center of the criclelabels(default: nothing): labels for theplot_topoplotkwargs...: additional styling behavior, see below.
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = (aspect = Makie.DataAspect(), label = "") - use kwargs... of Makie.Axis
layout = (showlegend = false, legendposition = :right, xlabelFromMapping = nothing, ylabelFromMapping = nothing, use_colorbar = true, hidespines = (), hidedecorations = ())
mapping = (x = (nothing,), y = (:estimate, :yhat, :y), positions = (:pos, :positions, :position, nothing), labels = (:labels, :label, :sensor, nothing))
visual = (colormap = Makie.Reverse{Symbol}(:RdBu), contours = (color = :white, linewidth = 2), labelscatter = true, labeltext = true, boundinggeometry = GeometryBasics.Circle) - *use kwargs... of [``Topoplot.eegtopoplot``](@ref)*
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false, label = "Voltage [µV]", colormap = Makie.Reverse{Symbol}(:RdBu)) - use kwargs... of Makie.Colorbar
Return Value:
A figure containing the circular topoplot at given layout position
UnfoldMakie.plot_designmatrix — Methodplot_designmatrix!(f::Union{GridPosition, GridLayout, Figure}, data::Unfold.DesignMatrix; kwargs...)
+plot_designmatrix(data::Unfold.DesignMatrix; kwargs...)Plot a designmatrix.
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure or GridPosition (e.g. f[2, 3]) in which the plot will be placed into. A new axis is created.data::Unfold.DesignMatrix: data for the plot visualization.
kwargs
standardize_data(bool,true): indicates whether the data is standardized by pointwise division of the data with its sampled standard deviation.sort_data(bool,true): indicates whether the data is sorted; using sortslices() of Base Julia.xticks(nothing): returns the number of labels on the x-axis. Behavior is set in the configuration:xticks= 0: no labels are placed.xticks= 1: first possible label is placed.xticks= 2: first and last possible labels are placed.- 2 <
xticks<number of labels: equally distribute the labels. xticks≥number of labels: all labels are placed.
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = (xticklabelrotation = 0.39269908169872414,) - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = nothing, ylabelFromMapping = nothing, use_colorbar = true)
mapping = (x = (:time,), y = (:estimate, :yhat, :y))
visual = (colormap = :roma,) - use kwargs... of $Makie.heatmap$
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of Makie.Colorbar
Return Value:
A figure displaying the designmatrix.
UnfoldMakie.plot_erp — Methodplot_erp!(f::Union{GridPosition, GridLayout, Figure}, plot_data::DataFrame; kwargs...)
+plot_erp(plot_data::DataFrame; kwargs...)Plot an ERP plot.
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure, GridLayout or GridPosition that the plot should be drawn into.plot_data::DataFrame: Data for the line plot visualization.kwargs...: Additional styling behavior. Often used:plot_erp(df; mapping=(; color=:coefname, col=:conditionA)).
kwargs (...; ...):
categorical_color(bool,true): in case of numeric:colorcolumn, treat:coloras continuous or categorical variable.categorical_group(bool,true): in case of numeric:groupcolumn, treat:groupas categorical variable by default.topolegend(bool,false): add an inlay topoplot with corresponding electrodes.stderror(bool,false): add an error ribbon, with lower and upper limits based on the:stderrorcolumn.pvalue(Array,[]): show a pvalue.- example:
DataFrame(from=[0.1, 0.3], to=[0.5, 0.7], coefname=["(Intercept)", "condition:face"])- if coefname is not specified, the lines will be black
- example:
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = NamedTuple() - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = :x, ylabelFromMapping = :y, use_colorbar = false, hidespines = (:r, :t))
mapping = (x = (:time,), y = (:estimate, :yhat, :y), color = (:color, :coefname, nothing))
visual = (colormap = :roma,) - use kwargs... of $Makie.lines$
legend = (orientation = :vertical, tellwidth = true, tellheight = false, framevisible = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of AlgebraOfGraphics.colobar!
Return Value:
- f - Figure() or the inputed
f
UnfoldMakie.plot_new — Methodplot_new() -> String
+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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = NamedTuple() - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = :x, ylabelFromMapping = :y, use_colorbar = false, hidespines = (:r, :t))
mapping = (x = (:time,), y = (:estimate, :yhat, :y), color = (:color, :coefname, nothing))
visual = (colormap = :roma,) - use kwargs... of $Makie.lines$
legend = (orientation = :vertical, tellwidth = true, tellheight = false, framevisible = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of AlgebraOfGraphics.colobar!
UnfoldMakie.plot_parallelcoordinates — Methodplot_parallelcoordinates!(f::Union{GridPosition, GridLayout, Figure},
+ data::DataFrame, config::PlotConfig; channels::Vector{Int64})Plot a PCP (parallel coordinates plot).
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure or GridPosition that the plot should be drawn into.data::DataFrame: data for the plot visualization.config::PlotConfig: instance of PlotConfig being applied to the visualization.channels::Vector{Int64}: vector with all the channels representing an axis used in the PCP in given order.
PCP has problems with size changes of the view window. By adapting the padding, aspect ratio and tick label size in px for a new use case, the PCP can even be added into a complex figures.
pc_aspect_ratio(default:0.55) -pc_right_padding(default:15) -pc_left_padding(default:25) -pc_top_padding(default:26) -pc_bottom_padding(default:16) -pc_tick_label_size(default:14) -
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = NamedTuple() - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = :channel, ylabelFromMapping = :y, use_colorbar = false, hidespines = (), hidedecorations = (label = false,))
mapping = (x = (:time,), y = (:estimate, :yhat, :y), channel = :channel, category = :category, time = :time)
visual = (colormap = :roma,) - use kwargs... of $Makie.lines$
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of Makie.Colorbar
Return Value:
The input f
UnfoldMakie.plot_topoplot — Methodplot_topoplot!(f::Union{GridPosition, GridLayout, Figure}, data, ; positions=nothing, labels=nothing,kwargs...)
+plot_topoplot(data,; positions=nothing, labels=nothing, kwargs...)Plot a topo plot.
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure or GridPosition (e.g. f[2, 3]) that the plot should be drawn into. New axis is created.data::Union{DataFrame, Vector{Float32}}: data for the plot visualization.positions::Vector{Point{2, Float32}}=nothing: positions used ifdatais not a DataFrame. If this is the case andpositions=nothingthen positions are generated fromlabels.labels::Vector{String} = nothing: labels used ifdatais not a DataFrame.
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = (aspect = Makie.DataAspect(),) - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = nothing, ylabelFromMapping = nothing, use_colorbar = true, hidespines = (), hidedecorations = ())
mapping = (x = (nothing,), y = (:estimate, :yhat, :y), positions = (:pos, :positions, :position, nothing), labels = (:labels, :label, :sensor, nothing))
visual = (colormap = Makie.Reverse{Symbol}(:RdBu), contours = (color = :white, linewidth = 2), labelscatter = true, labeltext = true, boundinggeometry = GeometryBasics.Circle) - *use kwargs... of [``Topoplot.eegtopoplot``](@ref)*
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false) - use kwargs... of Makie.Colorbar
Return Value:
A figure displaying the topo plot.
UnfoldMakie.plot_topoplotseries — Methodplot_topoplotseries!(f::Union{GridPosition, GridLayout, Figure}, data::DataFrame, Δbin::Real; kwargs...)
+plot_topoplotseries!(data::DataFrame, Δbin::Real; kwargs...)Multiple miniature topoplots in regular distances
Arguments:
f::Union{GridPosition, GridLayout, Figure}: Figure or GridPosition that the plot should be drawn into.data::DataFrame: DataFrame with data, needs atimecolumn.Δbin::Real: A number for how large one time bin should be. Δbin is in units of thedata.timecolumn.combinefun(default:mean) - can be used to specify how the samples withinΔbinare combined.rasterize_heatmaps(default:true) - enforce rasterization of the plot heatmap when saving in svg format. This has the benefit that all lines/points are vectors, except the interpolated heatmap. This is typically what you want, otherwise you get ~500x500 vectors per topoplot, which makes everything super slow.col_labels,row_labels- shows column and row labels.- labels (default:
nothing) - . - positions (default:
nothing) - .
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)). Multiple defaults will be cycled until match.
figure = NamedTuple() - use kwargs... of Makie.Figure
axis = (aspect = Makie.DataAspect(),) - use kwargs... of Makie.Axis
layout = (showlegend = true, legendposition = :right, xlabelFromMapping = nothing, ylabelFromMapping = nothing, use_colorbar = true, hidespines = (), hidedecorations = ())
mapping = (x = (nothing,), y = (:estimate, :yhat, :y), positions = (:pos, :positions, :position, nothing), labels = (:labels, :label, :sensor, nothing), col = (:time,), row = (nothing,))
visual = (colormap = Makie.Reverse{Symbol}(:RdBu), contours = (color = :white, linewidth = 2), labelscatter = true, labeltext = false, boundinggeometry = GeometryBasics.Circle) - *use kwargs... of [``Topoplot.eegtopoplot``](@ref)*
legend = (orientation = :vertical, tellwidth = true, tellheight = false) - use kwargs... of Makie.Legend
colorbar = (vertical = true, tellwidth = true, tellheight = false, height = 300, flipaxis = true, labelrotation = 4.7, label = "Voltage [µV]") - use kwargs... of Makie.Colorbar
Return Value:
The input f
UnfoldMakie.rel_to_abs_bbox — Methodreltoabs_bbox(org,rel)
Takes a rectangle org and applies the relative transformation tuple rel Returns a Makie.BBox
UnfoldMakie.to_positions — Methodtopositions(x,y,z;sphere=[0,0,0.]) topositions(pos::AbstractMatrix;sphere=[0,0,0.]) Projects 3D electrode positions to a 2D layout.
The matrix case, assumes size(pos) = (3,nChannels) Re-implementation of the MNE algorithm.
Tipp: You can directly get positions from an MNE object after loading PyMNE and thus activating the UnfoldMakie PyMNE extension
UnfoldMakie.valType_to_symbol — MethodVal{:bu}() to => :bu
Internally, we use a PlotConfig struct to keep track of common plot options, in order to have a similar API to all functions
UnfoldMakie.PlotConfig — TypePlotConfig(<plotname>)
+holds various different fields, that can modify various different plotting aspects.