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ERP Plot

ERP plot is plot type for visualisation of Event-related potentials. It can fully represent time and experimental condition dimensions using lines.

Setup

Package loading

using Unfold
using UnfoldMakie
using DataFrames
using CairoMakie
using DataFramesMeta
using UnfoldSim
using UnfoldMakie
include("../../../example_data.jl")
Main.example_data

Data generation

Let's generate some data. We'll fit a model with a 2 level categorical predictor and a continuous predictor with interaction.

data, evts = UnfoldSim.predef_eeg(; noiselevel = 12, return_epoched = true)
data = reshape(data, (1, size(data)...))
f = @formula 0 ~ 1 + condition + continuous
se_solver = (x, y) -> Unfold.solver_default(x, y, stderror = true);

m = fit(
    UnfoldModel,
    Dict(Any => (f, range(0, step = 1 / 100, length = size(data, 2)))),
    evts,
    data,
    solver = se_solver,
)
results = coeftable(m)
res_effects = effects(Dict(:continuous => -5:0.5:5), m);
┌ Warning: using `Dict(:A=>(@formula,times/basisfunction))` is deprecated, please use `[:A=>(@formula,times/basisfunction)]` from now on
└ @ Unfold ~/.julia/packages/Unfold/qjDWM/src/fit.jl:53

Figure plotting

plot_erp(results)
Example block output

Additional features

Effect plot

Effect plot shows how ERP voltage is affected by variation of some variable (here: :contionous).

  • categorical_color::Bool = true

    Treat :color as continuous or categorical variable in case of numeric :color column.

  • categorical_group::Bool = true

    Treat :group as categorical variable by default in case of numeric :group column.

plot_erp(
    res_effects;
    mapping = (; y = :yhat, color = :continuous, group = :continuous),
    legend = (; nbanks = 2),
    layout = (; show_legend = true, legend_position = :right),
    categorical_color = false, # perceives color (here: continuous) as contionus
    categorical_group = true, # separates lines, if `false` all lines will be connected
)
Example block output

P-value lines

  • pvalue (Array, []): show a pvalue (see below).

Here we manually specify p-value lines. If array is not empty, plot shows colored lines under the plot representing the p-values. Below is an example in which p-values are given:

m = example_data("UnfoldLinearModel")
results = coeftable(m)
pvals = DataFrame(
    from = [0.1, 0.3],
    to = [0.5, 0.7],
    coefname = ["(Intercept)", "condition: face"], # if coefname not specified, line should be black
)
plot_erp(results; :pvalue => pvals)
Example block output

Error ribbons

  • stderror (bool, false): add an error ribbon, with lower and upper limits based on the :stderror column.

Display a colored band on the graph to indicate lower and higher estimates based on the standard error. For the generalizability of your results, it is always better to include error bands.

f = Figure()
results.coefname =
    replace(results.coefname, "condition: face" => "face", "(Intercept)" => "car")
results = filter(row -> row.coefname != "continuous", results)
plot_erp!(
    f[1, 1],
    results;
    axis = (title = "Bad example", titlegap = 12),
    :stderror => false,
    mapping = (; color = :coefname => "Conditions"),
)

plot_erp!(
    f[2, 1],
    results;
    axis = (title = "Good example", titlegap = 12),
    :stderror => true,
    mapping = (; color = :coefname => "Conditions"),
)

ax = Axis(f[2, 1], width = Relative(1), height = Relative(1))
xlims!(ax, [-0.04, 1])
ylims!(ax, [-0.04, 1])
hidespines!(ax)
hidedecorations!(ax)
text!(0.98, 0.2, text = "* Confidence\nintervals", align = (:right, :top))
f
Example block output

There are two ways to implement it. First is using :stderror = true' after;`.

results.se_low = results.estimate .- 0.5
results.se_high = results.estimate .+ 0.15
plot_erp(select(results, Not(:stderror)); stderror = true)
Example block output

Second way is to specify manually lower and higher borders of the error bands.

Note

:stderror has precedence over :se_low/:se_high.

Faceting

Creation of column facets for each channel.

m7 = example_data("7channels")
results7 = coeftable(m7)
plot_erp(results7, mapping = (; col = :channel, group = :channel))
Example block output

Configurations of ERP plot

UnfoldMakie.plot_erp — Function
plot_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 to draw the plot.
  • data::Union{DataFrame, Vector{Float32}}
    Data for the Line plot visualization.
  • kwargs...
    Additional styling behavior.
    Often used as: plot_erp(df; mapping = (; color = :coefname, col = :conditionA)).

Keyword argumets (kwargs)

  • categorical_color::Bool = true
    Treat :color as continuous or categorical variable in case of numeric :color column.
  • categorical_group::Bool = true
    Treat :group as categorical variable by default in case of numeric :group column.
  • stderror::Bool = false
    Add an error ribbon, with lower and upper limits based on the :stderror column.
  • pvalue::DataFrame = nothing
    Show a p-values as a horizontal bars.
    Example: DataFrame(from = [0.1, 0.3], to=[0.5, 0.7], coefname=["(Intercept)", "condition:face"]).
    If coefname is not specified, the significance lines will be black.

Internal use only:

  • butterfly::Bool = true
    A butterfly plot instead of an ERP plot. See plot_butterfly

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.

Placing ; is important!

figure = NamedTuple() - use kwargs... of Makie.Figure

axis = (xlabel = "Time [s]", ylabel = "Voltage [µV]", yticklabelsize = 14) - use kwargs... of Makie.Axis

layout = (show_legend = true, legend_position = :right, xlabelFromMapping = :x, ylabelFromMapping = :y, use_colorbar = false, hidespines = (:r, :t), hidedecorations = Dict{Symbol, Bool}(:grid => 1, :label => 0, :ticks => 0, :ticklabels => 0))

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: Figure displaying the ERP plot.

source

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