diff --git a/.github/workflows/video-dry.yml b/.github/workflows/video-dry.yml index 43ae802d384213..1926078310d336 100644 --- a/.github/workflows/video-dry.yml +++ b/.github/workflows/video-dry.yml @@ -67,4 +67,4 @@ jobs: echo "Software Versions" $FFMPEG_PATH/ffmpeg -version - $(npm bin)/editly --version + ./node_modules/.bin/editly --version diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 6e64e8aa30b6e8..49f8251c6a70a5 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -393,6 +393,10 @@ cutsort: name: Frederick Tan joined: 2023-06 +cxli233: + name: Chenxin Li + joined: 2023-11 + d-salgado: name: David Salgado joined: 2022-10 diff --git a/Makefile b/Makefile index 102d7e493608e9..7c256a576aee72 100644 --- a/Makefile +++ b/Makefile @@ -217,17 +217,17 @@ _site/%/tutorial.pdf: _site/%/tutorial.html _site/%/slides.pdf: _site/%/slides.html $(ACTIVATE_ENV) && \ - $(shell npm bin)/http-server _site -p 9876 & \ + ./node_modules/.bin/http-server _site -p 9876 & \ docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@ _site/%/slides_ES.pdf: _site/%/slides_ES.html $(ACTIVATE_ENV) && \ - $(shell npm bin)/http-server _site -p 9876 & \ + ./node_modules/.bin/http-server _site -p 9876 & \ docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@ _site/%/slides_CAT_ES.pdf: _site/%/slides_CAT_ES.html $(ACTIVATE_ENV) && \ - $(shell npm bin)/http-server _site -p 9876 & \ + ./node_modules/.bin/http-server _site -p 9876 & \ docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@ video: ## Build all videos diff --git a/_layouts/base_slides.html b/_layouts/base_slides.html index d873855862496e..5774ef69311558 100644 --- a/_layouts/base_slides.html +++ b/_layouts/base_slides.html @@ -104,7 +104,7 @@
{% icon last_modification %} {{locale['last-modification'] | default: "Updated"}}: {{ page.last_modified_at | date: "%b %-d, %Y"}}   - {% icon purl %}PURL: gxy.io/GTN:{{ page.short_id }} + {% if page.short_id %}{% icon purl %}PURL: gxy.io/GTN:{{ page.short_id }}{% endif %}
@@ -177,8 +177,8 @@ {% endif %} - -{{ locale['license-tutorial'] | default: "This material is licensed under the Creative Commons Attribution 4.0 International License" }}. +{{ locale['license-framework'] | default: "Tutorial Content is licensed under" }} {% if page.license%} {{ page.license }}.{% else %}Creative Commons Attribution 4.0 International License.{% endif %}
+{% if page.copyright %}{{ page.copyright }}{% endif %} {% if page.layout == "base_slides" %} .footnote[Found a typo? Something is wrong in this tutorial?
Edit it on [GitHub]({{ site.github_repository }}/tree/main{{ page.url }})] diff --git a/_layouts/base_slides_ai4life.html b/_layouts/base_slides_ai4life.html index 103550615ca66d..8d0498f85a8e89 100644 --- a/_layouts/base_slides_ai4life.html +++ b/_layouts/base_slides_ai4life.html @@ -171,8 +171,8 @@ {% endif %} - -{{ locale['license-tutorial'] | default: "This material is licensed under the Creative Commons Attribution 4.0 International License" }}. +{{ locale['license-framework'] | default: "Tutorial Content is licensed under" }} {% if page.license %} {{ page.license }}. +{% else %}Creative Commons Attribution 4.0 International License.{% endif %} {% if page.layout == "base_slides" %} .footnote[Found a typo? Something is wrong in this tutorial?
Edit it on [GitHub]({{ site.github_repository }}/tree/main{{ page.url }})] diff --git a/_layouts/slides-plain.html b/_layouts/slides-plain.html index 51d2ce291791fd..872d3df326f751 100644 --- a/_layouts/slides-plain.html +++ b/_layouts/slides-plain.html @@ -78,7 +78,12 @@

Thank you!

{% endif %} {% endif %} -This material is licensed under the Creative Commons Attribution 4.0 International License. +{{ locale['license-framework'] | default: "Tutorial Content is licensed under" }} +{% if page.license %} + {{ page.license }}. +{% else %} + Creative Commons Attribution 4.0 International License. +{% endif %} {% if page.cited %} diff --git a/_layouts/tutorial_hands_on.html b/_layouts/tutorial_hands_on.html index 290c8062da5b7d..bdc727bac98937 100644 --- a/_layouts/tutorial_hands_on.html +++ b/_layouts/tutorial_hands_on.html @@ -154,11 +154,13 @@

Under Development!

{% if page.copyright %} {{ page.copyright }}. {% endif %} + {{ locale['license-framework'] | default: "Tutorial Content is licensed under" }} {% if page.license %} - Tutorial Content is licensed under {{ page.license }}. + {{ page.license }}. {% else %} - {{ locale['license-framework'] | default: "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License" }}. - {% endif %} The GTN Framework is licensed under MIT + Creative Commons Attribution 4.0 International License. + {% endif %} + The GTN Framework is licensed under MIT {% if page.short_id %}
{% icon purl %} PURL: https://gxy.io/GTN:{{ page.short_id }}
diff --git a/_plugins/gtn/contributors.rb b/_plugins/gtn/contributors.rb index 922489fdb2f8d1..5c5403397a5875 100644 --- a/_plugins/gtn/contributors.rb +++ b/_plugins/gtn/contributors.rb @@ -61,7 +61,7 @@ def self.get_non_authors(material) # from disk ourselves. def self._load_file(site, category) if site.nil? - Jekyll.logger.warning "[GTN/Contributor] Loading #{category} from disk, this access could be improved" + Jekyll.logger.warn "[GTN/Contributor] Loading #{category} from disk, this access could be improved" File.open("_data/#{category}.yml", 'r') { |f| YAML.safe_load(f) } else site.data[category] @@ -84,10 +84,10 @@ def self.fetch(site, c) elsif _load_file(site, 'funders').key?(c) return ['funder', site.data['funders'][c]] else - Jekyll.logger.error "Contributor #{c} not found" + Jekyll.logger.warn "Contributor #{c} not found" end - [nil, nil] + ['contributor', { 'name' => c }] end ## diff --git a/bin/ari-make.sh b/bin/ari-make.sh index c09752a8442ed0..4cb3cf14e79631 100755 --- a/bin/ari-make.sh +++ b/bin/ari-make.sh @@ -15,7 +15,7 @@ else changed_slides="$(echo "$videos" | xargs ./bin/filter-resource-metadata video)" fi -$(npm bin)/http-server -p 9876 _site & +./node_modules/.bin/http-server -p 9876 _site & for slides in $changed_slides; do echo "====== $slides ======" diff --git a/bin/ari.sh b/bin/ari.sh index 043e8fe0d5ff78..78645666ca9ed4 100755 --- a/bin/ari.sh +++ b/bin/ari.sh @@ -82,9 +82,9 @@ ruby bin/ari-prep-script.rb "${build_dir}" "${engine}" echo " Extracting slides" convert "${slides}" -resize 1920x1080 "${build_dir}/slides.%03d.png" -echo " Building Video | $(npm bin)/editly --json ${build_dir}/editly.json5" +echo " Building Video | ./node_modules/.bin/editly --json ${build_dir}/editly.json5" $FFMPEG_PATH/ffmpeg -version -$(npm bin)/editly --json "${build_dir}/editly.json5" +./node_modules/.bin/editly --json "${build_dir}/editly.json5" # Mux it together echo " Muxing" diff --git a/bin/schema-slides.yaml b/bin/schema-slides.yaml index cc1e276da31404..1e7ac71196c1e1 100644 --- a/bin/schema-slides.yaml +++ b/bin/schema-slides.yaml @@ -372,6 +372,16 @@ mapping: type: str description: | URL of the external resource + copyright: + type: str + description: | + A copyright attribution string, as required by some licenses. + examples: + - © Copyright 2021-2023 University of Technology Sydney, The University of Manchester UK and RO-Crate contributors + license: + type: str + description: | + An [SPDX](https://spdx.org/) identifier for the alternative license that is used for that particular material. This is **only** relevant for materials which have been imported from an external source and were originally licensed under another license. For new materials we strongly encourage contributors to not use this key as materials are CC-BY, by default. draft: type: bool description: | diff --git a/metadata/lang/es.yml b/metadata/lang/es.yml index 3003eb4182b96f..2574cf6c32587c 100644 --- a/metadata/lang/es.yml +++ b/metadata/lang/es.yml @@ -49,7 +49,7 @@ recommended-followup: "Continúa tu aprendizaje completando uno de nuestros entr license: "Licencia" # "License" -license-tutorial: "El contenido de este tutorial tiene la licencia Creative Commons Attribution 4.0 International License." # "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License." +license-tutorial: "El contenido de este tutorial tiene la licencia" # "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License." license-framework: "GTN Framework tiene licencia del MIT" # "The GTN Framework is licensed under MIT" diff --git a/metadata/lang/fr.yml b/metadata/lang/fr.yml index f9d76348b3c4b3..6fbf6dfce7fe42 100644 --- a/metadata/lang/fr.yml +++ b/metadata/lang/fr.yml @@ -49,7 +49,7 @@ recommended-followup: "Poursuivez votre apprentissage en suivant l'une de nos fo license: "Licence" # "License" -license-tutorial: "Le contenu de ce didacticiel est sous licence Creative Commons Attribution 4.0 International License." # "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License." +license-tutorial: "Le contenu de ce didacticiel est sous licence" # "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License." license-framework: "Le Framework GTN est sous licence MIT" # "The GTN Framework is licensed under MIT diff --git a/topics/visualisation/metadata.yaml b/topics/visualisation/metadata.yaml index 640e8a389f9b8b..95a09cafff158e 100644 --- a/topics/visualisation/metadata.yaml +++ b/topics/visualisation/metadata.yaml @@ -5,10 +5,6 @@ title: "Visualisation" summary: "Training material for data visualisation in Galaxy" edam_ontology: ["topic_0337"] -requirements: - - type: "internal" - topic_name: introduction - editorial_board: - shiltemann - hexylena diff --git a/topics/visualisation/tutorials/bad-graphs/images/Abstract_R_2022_11_24.png b/topics/visualisation/tutorials/bad-graphs/images/Abstract_R_2022_11_24.png new file mode 100644 index 00000000000000..aa699daad9d39f Binary files /dev/null and b/topics/visualisation/tutorials/bad-graphs/images/Abstract_R_2022_11_24.png differ diff --git a/topics/visualisation/tutorials/bad-graphs/images/Abstract_R_2022_11_24.svg b/topics/visualisation/tutorials/bad-graphs/images/Abstract_R_2022_11_24.svg new file mode 100644 index 00000000000000..65b4601bf16b58 --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/images/Abstract_R_2022_11_24.svg @@ -0,0 +1,1202 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/topics/visualisation/tutorials/bad-graphs/images/AvoidBarPlotMeadow.png b/topics/visualisation/tutorials/bad-graphs/images/AvoidBarPlotMeadow.png new file mode 100644 index 00000000000000..c715b1de5cc497 Binary files /dev/null and b/topics/visualisation/tutorials/bad-graphs/images/AvoidBarPlotMeadow.png differ diff --git a/topics/visualisation/tutorials/bad-graphs/images/AvoidBarPlotMeadow.svg b/topics/visualisation/tutorials/bad-graphs/images/AvoidBarPlotMeadow.svg new file mode 100644 index 00000000000000..10c06a58716591 --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/images/AvoidBarPlotMeadow.svg @@ -0,0 +1,874 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +a +a +a +ab +ab +ab +ab +ab +ab +ab +abc +abc +abc +abc +abcd +abcd +bcde +cdef +defg +efgh +fgh +gh +gh +h +i +i +i + + + +0 +50 +100 +150 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Alias.T1.cut stem +Bright.T1.cut stem +Rococo.T1.cut stem +Alias.T5.cut stem +Bright.T5.cut stem +Rococo.T5.cut stem +Alias.T10.cut stem +Bright.T10.cut stem +Rococo.T10.cut stem +Alias.T1.inverted stem +Bright.T1.inverted stem +Rococo.T1.inverted stem +Alias.T5.inverted stem +Bright.T5.inverted stem +Rococo.T5.inverted stem +Alias.T10.inverted stem +Bright.T10.inverted stem +Rococo.T10.inverted stem +Alias.T1.split stem +Bright.T1.split stem +Rococo.T1.split stem +Alias.T5.split stem +Bright.T5.split stem +Rococo.T5.split stem +Alias.T10.split stem +Bright.T10.split stem +Rococo.T10.split stem +Mean +Classic bar plot meadow +y ~ Variety:Treatment:Explant +This is horrendous. +What am I looking at? + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +a +a +a + + + + + + + + + + + + + + + + + + + + + + + + + +a +ab +b + + + + + + + + + + + + + + + + + + + + + + + + + +a +a +ab + + + + + + + + + + + + + + + + + + + + + + + + + +a +a +a + + + + + + + + + + + + + + + + + + + + + + + + + +a +a +a + + + + + + + + + + + + + + + + + + + + + + + + + +a +a +b + + + + + + + + + + + + + + + + + + + + + + + + + +b +bc +c + + + + + + + + + + + + + + + + + + + + + + + + + +c +c +c + + + + + + + + + + + + + + + + + + + + + + + + + +c +c +c + + + + + + + + + + + + + + + + +Bright + + + + + + + + + +cut stem + + + + + + + + + + + + + + + + + + +Bright + + + + + + + + + +inverted stem + + + + + + + + + + + + + + + + + + +Bright + + + + + + + + + +split stem + + + + + + + + + + + + + + + + + + +Alias + + + + + + + + + +cut stem + + + + + + + + + + + + + + + + + + +Alias + + + + + + + + + +inverted stem + + + + + + + + + + + + + + + + + + +Alias + + + + + + + + + +split stem + + + + + + + + +T1 +T5 +T10 + + + + +T1 +T5 +T10 + + + + +T1 +T5 +T10 + + + + +T1 +T5 +T10 + + + + +T1 +T5 +T10 + + + + +T1 +T5 +T10 + + + + + + + + + + + + + + +Rococo + + + + + + + + + +cut stem + + + + + + + + + + + + + + + + + + +Rococo + + + + + + + + + +inverted stem + + + + + + + + + + + + + + + + + + +Rococo + + + + + + + + + +split stem + + + + + + + + +T1 +T5 +T10 + + + + +T1 +T5 +T10 + + + + +T1 +T5 +T10 + +0 +50 +100 +150 +200 + + + + + + +0 +50 +100 +150 +200 + + + + + + +0 +50 +100 +150 +200 + + + + + +Response +Better designed for multifactorial experiments +y ~ Treatment:Explant | Variety +That's better. +Reader's attention is more focused. + + diff --git a/topics/visualisation/tutorials/bad-graphs/images/Beware_of_small_n_box_violin_plot.png b/topics/visualisation/tutorials/bad-graphs/images/Beware_of_small_n_box_violin_plot.png new file mode 100644 index 00000000000000..7409e3a5fa611a Binary files /dev/null and b/topics/visualisation/tutorials/bad-graphs/images/Beware_of_small_n_box_violin_plot.png differ diff --git a/topics/visualisation/tutorials/bad-graphs/images/Beware_of_small_n_box_violin_plot.svg b/topics/visualisation/tutorials/bad-graphs/images/Beware_of_small_n_box_violin_plot.svg new file mode 100644 index 00000000000000..8bb7d1fb22138f --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/images/Beware_of_small_n_box_violin_plot.svg @@ -0,0 +1,188 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-1 +0 +1 +2 +3 + + + + + + + + + +group1 +group2 +group3 +Group +Response +Points are median. +The distributions are different! +I wonder what's going on. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-1 +0 +1 +2 +3 + + + + + + + + + +group1 +group2 +group3 +Group +Response +Boxes span IQR. +The quartiles are different! +I wonder what's going on. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-1 +0 +1 +2 +3 + + + + + + + + + +group1 +group2 +group3 +Group +Response +n = 5 +Never mind... +Too little data to say anything. + + diff --git a/topics/visualisation/tutorials/bad-graphs/images/Broken_axis.png b/topics/visualisation/tutorials/bad-graphs/images/Broken_axis.png new file mode 100644 index 00000000000000..3d7a8c01aeabbf Binary files /dev/null and b/topics/visualisation/tutorials/bad-graphs/images/Broken_axis.png differ diff --git a/topics/visualisation/tutorials/bad-graphs/images/Broken_axis.svg b/topics/visualisation/tutorials/bad-graphs/images/Broken_axis.svg new file mode 100644 index 00000000000000..056018d699cf8a --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/images/Broken_axis.svg @@ -0,0 +1,234 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +10 +20 +30 +450 +500 + + + +400 +450 +500 +550 + + + + + + + + + + + + + + + + + + + + + + + + + + + +10 +20 +30 +450 +500 + + + +0 +10 +20 +30 +40 +50 + + + + + + + + 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b/topics/visualisation/tutorials/bad-graphs/images/dont_bar_plot.png differ diff --git a/topics/visualisation/tutorials/bad-graphs/images/dont_bar_plot.svg b/topics/visualisation/tutorials/bad-graphs/images/dont_bar_plot.svg new file mode 100644 index 00000000000000..8cdcc478ff292a --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/images/dont_bar_plot.svg @@ -0,0 +1,369 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.0 +0.3 +0.6 +0.9 + + + + + + + +group1 +group2 +Group +Response +group1: mean = 0.93; sd = 1 +group2: mean = 0.98; sd = 0.93 +They are the same! +P = 0.76 (t test) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-2 +0 +2 +4 +6 + + + + + + + + +group1 +group2 +Group +Response +group1: median = 0.95; IQR = 1.5 +group2: median = 0.62; IQR = 1 +Hmmmmm... +P = 0.78 (Wilcoxon rank sum test) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +-2 +0 +2 +4 +6 + + + + + + + + +group1 +group2 +Group +Response +group1: median = 0.95; IQR = 1.5 +group2: median = 0.62; IQR = 1 +OH!!! +P = 0.037 (Kolmogorov–Smirnov test) + + diff --git a/topics/visualisation/tutorials/bad-graphs/images/dont_concentric_donuts.png b/topics/visualisation/tutorials/bad-graphs/images/dont_concentric_donuts.png new file mode 100644 index 00000000000000..d91689ae929ce1 Binary files /dev/null and b/topics/visualisation/tutorials/bad-graphs/images/dont_concentric_donuts.png differ diff --git a/topics/visualisation/tutorials/bad-graphs/images/dont_concentric_donuts.svg b/topics/visualisation/tutorials/bad-graphs/images/dont_concentric_donuts.svg new file mode 100644 index 00000000000000..0fc3256db2bc26 --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/images/dont_concentric_donuts.svg @@ -0,0 +1,157 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Group1 +Group2 +Group3 +25 +50 +75 +0/100 + + + + +Type I +Type II +Arc lenghts are misleading +Outer rings = much longer arcs + + + + + + + + + + + + + + + + + + + + + + + + +Group1 +Group2 +Group3 +25 +50 +75 +0/100 + + + + +Type I +Type II +Ring order matters +Shorter arcs can have larger values + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +25 +50 +75 +100 + + + + + + + + + +1 +2 +3 +Group +% + + + +Type I +Type II +Just unwrap the donuts! +Simple but better + + diff --git a/topics/visualisation/tutorials/bad-graphs/images/dont_pie_chart.png b/topics/visualisation/tutorials/bad-graphs/images/dont_pie_chart.png new file mode 100644 index 00000000000000..ef49ccd6d04b73 Binary files /dev/null and b/topics/visualisation/tutorials/bad-graphs/images/dont_pie_chart.png differ diff --git a/topics/visualisation/tutorials/bad-graphs/images/dont_pie_chart.svg b/topics/visualisation/tutorials/bad-graphs/images/dont_pie_chart.svg new file mode 100644 index 00000000000000..1b0f9805a7fe53 --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/images/dont_pie_chart.svg @@ -0,0 +1,170 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Group 1 + + +Pie charts: +Arc lengths & area +represent data + + + + + + + + + + + +Group 2 + + +Hard to compare groups. +Arc length redundant with area. + + + + + + + + + + + + + + + + + + + + +Group 1 + + +Donut charts: +Arc lengths +represent data + + + + + + + + + + + +Group 2 + + +Still hard to compare +groups. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +25 +50 +75 +100 + + + + + + + + +1 +2 +Groups +Percentage + + + + + +Type I +Type II +Type III +Type IV +Stacked Bars: +Just unwrap +the polar coordinate! +Easier to compare groups. +Data represented by bar heights. + + diff --git a/topics/visualisation/tutorials/bad-graphs/slides.bib b/topics/visualisation/tutorials/bad-graphs/slides.bib new file mode 100644 index 00000000000000..30ef0f41b8d689 --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/slides.bib @@ -0,0 +1,36 @@ +@article{Weissgerber_2015, + title = {Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm}, + author = {Weissgerber, Tracey L. and Milic, Natasa M. and Winham, Stacey J. and Garovic, Vesna D.}, + year = 2015, + month = apr, + journal = {PLOS Biology}, + publisher = {Public Library of Science (PLoS)}, + volume = 13, + number = 4, + pages = {e1002128}, + doi = {10.1371/journal.pbio.1002128}, + issn = {1545-7885}, + url = {http://dx.doi.org/10.1371/journal.pbio.1002128}, +} +@article{Matand_2020, + title = {High frequency in vitro regeneration of adventitious shoots in daylilies (Hemerocallis sp) stem tissue using thidiazuron}, + author = {Matand, Kanyand and Shoemake, Meordrick and Li, Chenxin}, + year = 2020, + month = jan, + journal = {BMC Plant Biology}, + publisher = {Springer Science and Business Media LLC}, + volume = 20, + number = 1, + doi = {10.1186/s12870-020-2243-7}, + issn = {1471-2229}, + url = {http://dx.doi.org/10.1186/s12870-020-2243-7}, +} +@article{Li_2022, + title = {Single-cell multi-omics enabled discovery of alkaloid biosynthetic pathway genes in the medical plant Catharanthus roseus}, + author = {Li, Chenxin and Wood, Joshua C. and Vu, Anh Hai and Hamilton, John P. and Rodriguez Lopez, Carlos Eduardo and Payne, Richard M. E. and Serna Guerrero, Delia Ayled and Yamamoto, Kotaro and Vaillancourt, Brieanne and Caputi, Lorenzo and O’Connor, Sarah E. and Buell, C. Robin}, + year = 2022, + month = jul, + publisher = {Cold Spring Harbor Laboratory}, + doi = {10.1101/2022.07.04.498697}, + url = {http://dx.doi.org/10.1101/2022.07.04.498697}, +} diff --git a/topics/visualisation/tutorials/bad-graphs/slides.html b/topics/visualisation/tutorials/bad-graphs/slides.html new file mode 100644 index 00000000000000..1351b1599f43b4 --- /dev/null +++ b/topics/visualisation/tutorials/bad-graphs/slides.html @@ -0,0 +1,287 @@ +--- +layout: tutorial_slides +logo: "GTN" + +license: MIT +copyright: © Copyright 2022 C. Li +title: Friends Don't Let Friends Make Bad Graphs +contributions: + authorship: + - cxli233 + editing: + - hexylena +video: true +--- + +# Friends Don't Let Friends Make Bad Graphs + +This is an *opinionated* essay about good and bad practices in data visualization. + +This material is MIT licensed and adapted from [cxli233/FriendsDontLetFriends](https://github.com/cxli233/FriendsDontLetFriends). + +R Code for generating the graphs is available in that repository. + +??? + +- This is an opinionated essay about good and bad practices in data visualization. +- This material is MIT licensed and adapted from cxli233's work +- Please see the linked repository for the source for each of these graphs as well as more links and details. + +--- + +## 1. Friends Don't Let Friends Make Bar Plots for Means Separation + + +![No Bar Plots for Means Separation](images/dont_bar_plot.png) + +.footnote[inspired by many tweets the author saw on limitations of the bar graph. See e.g. {% cite Weissgerber_2015 %}] + +??? + +- This has to be the first one. +- Means separation plots are some of the most common in scientific publications. +- We have two or more groups, which contains multiple observations; they may have different means, variances, and distributions. +- The task of the visualization is to show the means and the spread (dispersion) of the data. +- In this example, two groups have similar means and standard deviations, but quite different distributions. +- Are they really "the same"? +- Just don't use bar plot for means separation, or at least check a couple things before settling down on a bar plot. +- It's worth mentioning that I was inspired by many researchers who have tweeted on the limitation of bar graphs. + +--- + +## 2. Friends Don't Let Friends Make Violin Plots for Small Sample Sizes + +![Beware of Violin Plots for Small Sample Sizes](images/Beware_of_small_n_box_violin_plot.png) + +??? + +- This is quite common in the literature as well, but unfortunately, violin plots (or any sort of smoothed distribution curves) make no sense for small n. +- Distributions and quartiles can vary widely with small n, even if the underlying observations are similar. +- Distribution and quartiles are only meaningful with large n. +- I did an experiment before, where I sampled the same normal distribution several times and computed the quartiles for each sample. +- The quartiles only stablize when n gets larger than 50. + +--- + +## 3. Friends Don't Let Friends Use Bidirectional Color Scales for Unidirectional Data + +![Are You Using the Right Color Scale for Your Data?](images/ColorScales.png) + +??? + +- Excuse my language, but this is a truly data visualization sin, and again quite common. +- I can understand why this error is common, because it appears that many of us have not spent a lot of thoughts on this issue. +- Color scales are pretty, but we have to be extra careful. +- When color scales (or color gradients) are used to represent numerical data, the darkest and lightest colors should have special meanings. +- You can decide what those special meanings are: e.g., max, min, mean, zero. But they should represent something meaningful. +- A data visualization sin for heat maps/color gradients is when the lightest or darkers colors are some arbitrary numbers. +- This is as bad as the longest bar in a bar chart not being the largest value. Can you imagine that? + +--- + +## 4. Friends Don't Let Friends Make Bar Plot Meadow + +![Horrendous Giant Bar Plot vs. Better Designed Plot](images/AvoidBarPlotMeadow.png) + +.footnote[Data from {% cite Matand_2020 %}] + +??? + +- We talked about no bar charts for mean separation, but this is a different issue. +- It has to do with presenting results of a multi-factorial experiment. +- Bar plot meadows are very common in scientific publications and unfortunately also ineffective in communicating the results. +- Bar plot meadows are common because multi-factorial experiments are common. +- However, a bar plot meadow is poorly designed for its purpose. +- To communicate results of a multi-factorial experiment, it requires thoughtful designs regarding grouping/faceting by factors of interest. +- In this example, I focus on comparing the effect of `Treatment` & `Explant` on `Response` at the level of each `Variety`. +- However, if the focus is the effect of `Treatment` & `Variety` on `Response` at the level of each `Exaplant`, then it will require a different layout. + +--- + +## 5. Friends Don't Let Friends Make Heatmap without (Considering) Reordering Rows & Columns + +![A Heatmap before and after reordering rows and columns](images/Reorder_rows_and_columns_for_heatmap.png) + +.footnote[Data from {% cite Li_2022 %}] + +??? + +- Heatmaps are very common in scientific publications, and very very common in omics papers. +- However, for heatmaps to be effective, we have to consider the ordering of rows and columns. +- In this example, I have cells as columns and features as rows. Grids are showing z scores. +- It is impossible to get anything useful out of the heatmap without reordering rows and columns. +- We can reorder rows and columns using clustering, but that is not the only way. +- Of course, if the rows and columns are mapping to physical entities (rows and columns of a 96-well plate), then you can't reorder them. +- But it is a very good idea to at least consider reordering rows and columns. + +--- + +### Bonus: heatmaps can be very pretty + + +![aRt with Heatmap](images/Abstract_R_2022_11_24.png) + +.footnote[ + [R Code](https://github.com/cxli233/FriendsDontLetFriends/blob/main/Scripts/Abstract_aRt.R), + [Tutorial on reordering](https://github.com/cxli233/FriendsDontLetFriends/blob/main/Heatmap_tutorial.md) +] + +??? + +- Heatmaps can be very pretty...if you are good are reordering rows/columns and choosing color gradients. +- Here is an example "abstract aRt" generated from simulated data. + + +## 6. Friends Don't Let Friends Make Heatmap without Checking Outliers + + +![Did you check outliers](images/Check_outliers_for_heatmap.png) + +??? + +- Outliers in heatmap can really change how we perceive and interpret the visualization. +- This generalizes to all sort of visualizations that use colors to represent numeric data. +- Let me show you an example: +- In this example, I have 2 observations. For each observations, I measured 20 features. +- Without checking for outliers, it may appear that the 2 observations are overall similar, except at 2 features. +- However, after maxing out the color scale around 95th percentile of the data, it reveals that the two observations are distinct across all features. + +--- + +## 7. Friends Don't Let Friends Forget to Check Data Range at Each Factor Level + + +![Did you check data range at each factor level](images/Check_range_at_factor_level.png) + +??? + +- This is a common issue that many of us have encountered. +- In a multifactor experiment, sometimes the range of the response variable changes widely between different factor levels. +- This hypothetical experiment measured 3 compounds across 2 groups (control vs. treatment). +- Without checking data range for each compound, you will likely have missed that the treatment had a strong effect on compound 1. +- This is because the concentration of compound 1 has a much narrower range than the other compounds in this experiment. + +--- + +## 8. Friends Don't Let Friends Make Network Graphs without Trying Different Layouts + + +![Try different network layouts](images/TryDifferentLayouts.png) + +.footnote[Data from {% cite Li_2022 %}] + +??? + +- Network graphs are common in scientific publications. They are super useful in presenting relationship data. +- However, the apparence (not the topology) of the network can make a huge difference in determing if a network graph is effective. +- Layouts can drastically change the appearance of networks, making them easier or harder to interpret. +- Here are 3 network graphs from the same data. They look very different from each other. + +--- + +## 9. Friends Don't Let Friends Confuse Position-based Visualizations with Length-based Visualizations + +![Position vs. length based visualizations](images/Position_and_length_based_visualizations.png) + +??? + +- This is always the elephant in the room and the essence of many misleading visualizations. +- In this example, I measured a response variable across 3 time points. +- Two of the following graphs are fine, but one of them is a data visualization crime. Can you see why? +- In dot and line plots, values are represented by positions along the x and y axis. +- The same idea applies to other position based visualizations, such as box plots. +- In bar plots, values are represented by the distance from the x axis, and thus the length of the bar. +- The 3rd graph is not 0-based, which makes the bar length at time point 2 about 3x longer than that at time point 1. +- In fact, the true difference in means is closer to 1.6x. +- I hope you can see how confusing length and position based visualizations can lead to misleading graphs. + +--- + +### Watch out for bar plots with broken axis + +![Broken axis](images/Broken_axis.png) + +.footnote[[Example R Code](https://github.com/cxli233/FriendsDontLetFriends/blob/main/Scripts/Broken_axis.R)] + +??? + +- Broken axis may be useful for depicting data across a wide range of numeric values. +- (Alternatively, log scaled axis can be used instead.) +- Broken axis are fine for position based graphics, because the data are represented by positions along the axis. +- However, we must be very careful with bar plots that have broken axis. Here is an example. +- In this example, two graphs (left vs. right) are showing the same data. +- However, by changing where the axis is broken, one can make certain bars looks longer or shorter. +- In this example, the length of bar "d" can look really different. +- The illusion of bar "d" being very short on the right graph boils down to bar plot being a length based graphics, not a position based graphics. + +--- + +## 10. Friends Don't Let Friends Make Pie Chart + +![Don't make pie charts](images/dont_pie_chart.png) + +??? + +- Pie chart is a common type of visualization for fractional data, where fractions add up to 100%. +- This is achieved by dividing a circle into sectors, and the sectors add up to a full circle. +- Pie charts have been criticized, because human are much worse in reading angles and area than reading lengths. +- In this example, we have two groups, each contains 4 sub-categories. +- In classic pie charts, the angles (and thus arc lengths & sector area) represent the data. +- The problem is that it is very difficult to compare between groups. +- We can visually simplify the pie chart into donut charts, where the data are now represented by arc lengths. +- However, if we want to use lengths to represent the data, why don't we just unwrap the donut and make stacked bars? +- In stacked bar graphs, bars are shown side-by-side and thus easier to compare across groups. +- Fun fact: the scripts underlying stacked bars are much simpler than those underlying the pie charts and donut charts. +- If you want to produce sub-optimal graph types with ggplot, you actually have to work extra hard. + +--- + +## 11. Friends Don't Let Friends Make Concentric Donuts + +![Don't make concentric donuts](images/dont_concentric_donuts.png) + +??? + +- In this example, we have 3 groups, each of which contains two sub-categories (Type I or Type II). +- In concentric donuts, you might be tempted to say the data are represented by the arc lengths, which is in fact inaccurate. +- The arc lengths on the outer rings are much longer than those in the inner rings. +- Group 2 and Group 3 have the same exact values, but the arc lengths of Group 3 are much longer. +- In fact the data are represented by the arc angles, which we are bad at reading. +- Since outer rings are longer, the ordering of the groups (which group goes to which ring) has a big impact on the impression of the plot. +- It can lead to the apparent paradox where larger values have shorter arcs. +- The better (and simpler!) alternative is just unwrap the donuts and make a good old stacked bar plot. +- BTW, this is also my main issue with circos plots and other circular plot layouts. + +--- + +## 12. Friends Don't Let Friends Use Red/Green and Rainbow color scales + +![are you making a "safe" heatmap?](images/Color_blind_grey_scale_safe_heatmap.png) + +??? + +- Deuteranomaly is the most common type of red/green colorblindness, occurring in 1/16 male and 1/256 female. +- Any color scales that use shades of red and shades of green in the same time would be a problem for a person with red/green colorblindness (third column of the figure). +- In addition, red/green and rainbow do not preserve information well at all when printed on black/white (grey scale, second column in figure). +- Many scientific software still use red/green or rainbow as the default color scales, which drives me crazy. +- More "modern" color scales, such as viridis are both colorblind-friendly and grey scale-safe (third row of figure). +- And they look nice too. + +--- + +## 13. Friends Don't Let Friends Forget to Reorder Stacked Bar Plot + +![Reorder your stacked bars](images/Reorder_stacked_bars.png) + +.footnote[[Tutorial on optimising](https://github.com/cxli233/FriendsDontLetFriends/blob/main/Scripts/stacked_bars_optimization.Rmd).] + +??? + +- Stacked bar plots are useful for visualizing proportion data. +- Stacked bar plots are commonly used to visualize community structure or population structure or admixture analysis. +- This kind of visualization boils down to a collection of samples, where each sample contains multiple classes of members. +- However, when we have many samples and many classes, stacked bar plots need to be optimized to be effective. +- And by "optimize" I mean the grouping and ordering of samples. +- Here we have an example data with 100 samples and 8 classes of member. +- Due to the number of samples and classes, it is very hard to discern anything from this graph without optimizing the order of bars. What the heck am I looking at? +- After reordering the bars, wow, that really made a difference, don't you think?