Merge branch 'main' into joss_paper

CITATION.cff

@@ -23,4 +23,4 @@ identifiers:
     value: 10.5281/zenodo.14192333
 repository-code: 'https://github.com/unfoldtoolbox/UnfoldMakie.jl'
 version: 0.5.10
-date-released: '2023-10-24'
+date-released: '2023-10-24'

README.md

@@ -8,7 +8,7 @@
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://unfoldtoolbox.github.io/UnfoldMakie.jl/dev)
 [![Build Status](https://github.com/unfoldtoolbox/UnfoldMakie.jl/workflows/CI/badge.svg)](https://github.com/unfoldtoolbox/UnfoldMakie.jl/actions)
 [![Coverage](https://codecov.io/gh/behinger/UnfoldMakie.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/behinger/UnfoldMakie.jl)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10235220.svg)](https://doi.org/10.5281/zenodo.10235220)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14192333.svg)](https://doi.org/10.5281/zenodo.14192333)
 
 
 

docs/make.jl

@@ -34,8 +34,8 @@ makedocs(;
         assets = String[],
     ),
     pages = [
-        "UnfoldMakie Documentation" => "index.md",
         "Intro" => [
+            "UnfoldMakie Highlights" => "index.md",
             "Installation" => "generated/intro/installation.md",
             "Plot types" => "generated/intro/plot_types.md",
             "Code principles" => "generated/intro/code_principles.md",

docs/src/index.md

@@ -1,22 +1,26 @@
-# UnfoldMakie Documentation
+# Highlights of UnfoldMakie.jl
 
 ```@raw html
 <img src="assets/complex_plot.png" width="300" align="right"/>
 ```
 
-This is the documentation of the UnfoldMakie.jl package for the Julia programming language. 
-
-## Highlights of UnfoldMakie.jl
-
-- **11 plot functions for displaying ERPs.**
-Each plot emphasizes certain dimensions while collapsing others.
-- **Fast plotting**
-Plot one figure with 20 topoplots in 1 second? No problemo!
-- **Highly adaptable.**
-The package is primarily based on [Unfold.jl](https://github.com/unfoldtoolbox/unfold.jl/) and [Makie.jl](https://makie.juliaplots.org/stable/).
-- **Many usage examples**
-You can find many user-friendly examples of how to use and adapt the plots in this documentation.
-- **Scientific colormaps by default**
-According to our study [(Mikheev, 2024)](https://apertureneuro.org/article/116386-the-art-of-brainwaves-a-survey-on-event-related-potential-visualization-practices), 40% of EEG researchers do not know about the issue of scientific color maps. As default color maps we use `Reverse(:RdBu)` (based on [colorbrewer](https://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3)) and `Roma` (based on [Scientific Colormaps](https://www.fabiocrameri.ch/colourmaps/) by Fabio Crameri).
-- **Interactivity** 
-Several plots make use of `Observables.jl` which allows fast updating of the underlying data. Several plots already have predefined interactive features, e.g. you can click on labels to enable / disable them. See `plot_topoplotseries` and `plot_erpimage` for examples.
+`UnfoldMakie.jl` excels in various fields:
+
+- **Focused.** `UnfoldMakie.jl` focuses exclusively on visualizing (r)ERPs, unlike other toolboxes such as `EEGLAB`, `FieldTrip`, `Brainstorm`, or `MNE`. This makes it easier to understand, use, and maintain the package in the future.
+
+- **Customizable.** The majority of EEG researchers perceive the flexibility of coding as the most important feature of the EEG toolbox. Consequently, users `UnfoldMakie.jl` have great flexibility in customizing most aspects of the plots, such as colors, line styles, and axis decorations. 
+
+- **Combining plots.** The layout system for subplots in `Makie.jl` makes it easy to combine and align various plot types.
+- **Flexible mapping.** With `AlgebraOfGraphics.jl`, it is easy to map conditions, groups, channels, or other features, to a large variety of aesthetics like linestyle, color, marker and others. It works similar to the popular R package `ggplot2`.
+
+- **Flexible data input.** All functions support basic `Arrays` and tidy `DataFrames`.
+
+- **Fast.** Julia and `Makie.jl` allows fast plotting of figures with very complex layout. As an example, it is able to plot one figure with 50 topoplots in 1.9 seconds (1.6 sec with DelaunayMesh interpolation), which is ~20 times faster, compared to `EEGLAB`. Although, the Python-based `MNE` is faster by one second. For more details check [this page](https://unfoldtoolbox.github.io/UnfoldMakie.jl/dev/generated/intro/speed/)
+
+- **Faster updating.** `Makie.jl` is incredibly fast at updating figures, which is beneficial for developing interactive tools and creating animations. `UnfoldMakie.jl` can create and save a topoplot gif file with 50 frames in 1.7 times less time than `MNE` (Table 2).
+
+- **Interactive.** Several plots in our package have interactive features. They are supported by `Observables.jl`, which allows for fast data exchange and quick plot updating.
+
+- **Scientific color maps.** According to our previous study [(Mikheev, 2024)](https://apertureneuro.org/article/116386-the-art-of-brainwaves-a-survey-on-event-related-potential-visualization-practices), 40% of EEG researchers are not aware of the issue of perceptually non-uniform color maps. `UnfoldMakie.jl` uses scientific color maps throughout.
+
+- **Documented.** There is extensive documentation with many usage examples and docstrings.

joss_paper/paper.md

@@ -116,4 +116,3 @@ Only the main dependencies are listed here. The dependencies of the dependencies
 
 # References
 
-

joss_paper/paper_UM.bib

@@ -289,5 +289,5 @@ @software{Schepers_UnfoldSim_jl
   title = {{UnfoldSim.jl}},
   year={2024},
   doi={10.5281/zenodo.13933412},
-  url = {https://github.com/unfoldtoolbox/UnfoldSim.jl}
-}
+  url = {https://github.com/unfoldtoolbox/UnfoldSim.jl
+  }