Clay documentation

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About

Clay is a minimalistic Clojure tool for data visualization and literate programming, compatible with the Kindly convention. It allows to conduct visual data explorations and create documents (HTML pages like this one, books, blog posts, reports, slideshows) from source code and comments.

Source: (GitHub repo)

Artifact: (Clojars coordinates)

Status: The project has moved into Beta stage (March 2024).

Clay is developed by Timothy Pratley & Daniel Slutsky in parallel and in coordination with Claykind, a tool with similar goals which is build in a more thoughtful process, aiming at a more modular structure.

Goals

  • Easily explore & share data visualizations and notebooks for others to easily pick & use.
  • Encourage writing Kindly-compatible notes for future compatiblity with other tools.
  • Flow with the REPL: encourage user interactions that flow naturally with the typical use of Clojure in editors and REPLs.

Getting started

Add Clay to your project dependencies: (Clojars coordinates)

(If you like to use aliases, you may add under it to the extra dependencies under an alias. See, for example, the deps.edn file of Noj. If you do not know what this means, just add it under the main :deps section of your deps.edn file.)

To render a given Clojure namespace, say "notebooks/index.clj", you may run the following in the REPL:

(require '[scicloj.clay.v2.api :as clay])
(clay/make! {:source-path "notebooks/index.clj"})

This will render an HTML page and serve it in Clay’s browser view. Note that Clay does not need to be mentioned in the namespace we wish to render.

See the API and Configuration subsections for more options and variations.

See the Setup section and recent Videos for details about integrating Clay with your editor so you do not need to call make! yourself.

Projects using Clay

Videos

Dec. 17th 2023 Cursive integration, API, configuration - blogging demo
Dec. 17th 2023 CIDER integration - image processing demo
Dec. 16th 2023 Calva integration - datavis demo
Dec. 12th 2023 Demo & Clay overview - London Clojurians - see Tim's part
Dec. 1st 2023 Kindly & Clay overview - visual-tools group - see Daniel's & Tim's parts
June 10th 2023 An early overview - babashka-conf

Setup

See the example project for a concrete example.

To enjoy Clay’s dynamic interaction, you also need to inform it about code evaluations. This requires some setup at the your editor.

To use Quarto-related actions, it is necessary to have the Quarto CLI installed in your system.

See the suggested setup for popular editors below. If your favourite editor is not supported yet, let us talk and make it work.

VSCode Calva

If you now run a REPL with Clay version in your classpath, then Calva will have the relevant custom REPL commands, as defined here.

name function
Clay make Namespace as HTML will genenrate an HTML rendering of the current namespace.
Clay make Namespace as Quarto, then HTML will generate a Quarto .qmd rendering of the current namespace, then render it as HTML through Quarto.
Clay make Namespace as Quarto, then reveal.js will generate a Quarto .qmd rendering of the current namespace, then render it as a reveal.js slideshow through Quarto.
Clay make current form as HTML will generate an HTML rendering of the current form, in the context of the current namespace.

Emacs CIDER

See the clay.el package for the relevant interactive functions.

IntelliJ Cursive

Under preferences, search for “REPL Commands” (or use the menu IntelliJ -> Preferences -> Languages and Frameworks -> Clojure -> REPL Commands)

Add a global command, and edit it with these settings:

Name: Send form to Clay
Execution: Command

(do (require '[scicloj.clay.v2.api :as clay])
    (clay/make! {:single-form '~form-before-caret
                 :source-path ["~file-path"]}))

You might also like to create a command to compile the namespace:

(do (require '[scicloj.clay.v2.api :as clay])
    (clay/make! {:source-path ["~file-path"]}))

Or a top-level-form (replace form-before-caret with top-level-form).

You can then add keybindings under Preferences -> Keymap for the new commands.

For more information about commands, see the Cursive documentation on REPL commands and substitutions.

Example notebook namespace

This notebook is created by a Clojure namespace. Here is the namespace definition and a few examples of what such a namespace may contain.

(ns index
  (:require [scicloj.kindly.v4.kind :as kind]
            [scicloj.kindly.v4.api :as kindly]
            [tablecloth.api :as tc]
            [scicloj.metamorph.ml :as ml]
            [scicloj.metamorph.ml.toydata :as toydata]
            [scicloj.noj.v1.stats :as noj.stats]
            [scicloj.noj.v1.vis.hanami :as hanami]
            [aerial.hanami.templates :as ht]
            [scicloj.clay.v2.quarto.themes :as quarto.themes]
            [scicloj.clay.v2.quarto.highlight-styles :as quarto.highlight-styles]
            [clojure.math :as math]))

A Hiccup spec:

(kind/hiccup
 [:div {:style {:background "#efe9e6"
                :border-style :solid}}
  [:ul
   [:li "one"]
   [:li "two"]
   [:li "three"]]])
  • one
  • two
  • three

A dataset using Tablecloth:

(-> {:x (range 5)
     :y (repeatedly 5 rand)}
    tc/dataset
    (tc/set-dataset-name "my dataset"))

my dataset [5 2]:

:x :y
0 0.58619955
1 0.20611535
2 0.31655674
3 0.98632060
4 0.76140255

A plot using Hanami and Noj:

(-> (toydata/iris-ds)
    (hanami/plot ht/rule-chart
                 {:X "sepal_width"
                  :X2 "sepal_length"
                  :Y "petal_width"
                  :Y2 "petal_length"
                  :COLOR "species"
                  :SIZE 3
                  :OPACITY 0.2}))

API

(require '[scicloj.clay.v2.api :as clay])

The entry point of the Clay API is the scicloj.clay.v2.api/make! function. Here are some usage examples.

Evaluate and render the namespace in "notebooks/index.clj" as HTML and show it at the browser:

(comment
  (clay/make! {:format [:html]
               :source-path "notebooks/index.clj"}))

Do the same as above (since :format [:html] is the default):

(comment
  (clay/make! {:source-path "notebooks/index.clj"}))

Evaluate and render the namespace in "notebooks/index.clj" as HTML and do not show it at the browser:

(comment
  (clay/make! {:source-path "notebooks/index.clj"
               :show false}))

Evaluate and render the namespaces in "notebooks/slides.clj" "notebooks/index.clj" as HTML and do not show it at the browser:

(comment
  (clay/make! {:source-path ["notebooks/slides.clj"
                             "notebooks/index.clj"]
               :show false}))

Evaluate and render a single form in the context of the namespace in "notebooks/index.clj" as HTML and show it at the browser:

(comment
  (clay/make! {:source-path "notebooks/index.clj"
               :single-form '(kind/cytoscape
                              cytoscape-example
                              {:element/style {:width "300px"
                                               :height "300px"}})}))

Evaluate and render a single form in the context of the current namespace (*ns*) as HTML and show it at the browser:

(comment
  (clay/make! {:single-form '(kind/cytoscape
                              cytoscape-example
                              {:element/style {:width "300px"
                                               :height "300px"}})}))

Render a single value as HTML and show it at the browser:

(comment
  (clay/make! {:single-value (kind/cytoscape
                              cytoscape-example
                              {:element/style {:width "300px"
                                               :height "300px"}})}))

Evaluate and render the namespace in "notebooks/index.clj" as a Quarto qmd file then, using Quarto, render that file as HTML and show it at the browser:

(comment
  (clay/make! {:format [:quarto :html]
               :source-path "notebooks/index.clj"}))

Evaluate and render the namespace in "notebooks/index.clj" as a Quarto qmd file and show it at the browser:

(comment
  (clay/make! {:format [:quarto :html]
               :source-path "notebooks/index.clj"
               :run-quarto false}))

Evaluate and render the namespace in "notebooks/slides.clj" as a Quarto qmd file (using its namespace-specific config from the ns metadata) then, using Quarto, render that file as HTML and show it at the browser:

(comment
  (clay/make! {:format [:quarto :html]
               :source-path "notebooks/slides.clj"}))

Evaluate and render the namespace in "notebooks/slides.clj" as a Quarto qmd file (using its namespace-specific config from the ns metadata) then, using Quarto, render that file as a reveal.js slideshow and show it at the browser:

(comment
  (clay/make! {:format [:quarto :revealjs]
               :source-path "notebooks/slides.clj"}))

Evaluate and render the namespace in "notebooks/index.clj" as a Quarto qmd file with a custom Quarto config then, using Quarto, render that file as HTML and show it at the browser:

(comment
  (clay/make! {:format [:quarto :html]
               :source-path "notebooks/index.clj"
               :quarto {:highlight-style :nord
                        :format {:html {:theme :journal}}}}))

Evaluate and render the namespace in "notebooks/index.clj" as a Quarto qmd file with a custom Quarto config where the higlight style is fetched from the scicloj.clay.v2.quarto.highlight-styles namespace, and the theme is fetched from the scicloj.clay.v2.quarto.themes namespace, then, using Quarto, render that file as HTML and show it at the browser:

(comment
  (require '[scicloj.clay.v2.quarto.highlight-styles :as quarto.highlight-styles]
           '[scicloj.clay.v2.quarto.themes :as quarto.themes])
  (clay/make! {:format [:quarto :html]
               :source-path "notebooks/index.clj"
               :quarto {:highlight-style quarto.highlight-styles/nord
                        :format {:html {:theme quarto.themes/journal}}}}))

Evaluate and render the namespace in "index.clj" under the "notebooks" directory as HTML and show it at the browser:

(comment
  (clay/make! {:base-source-path "notebooks/"
               :source-path "index.clj"}))

Create a Quarto book with a default generated index page:

(comment
  (clay/make! {:format [:quarto :html]
               :base-source-path "notebooks"
               :source-path ["chapter.clj"
                             "another_chapter.md"
                             "a_chapter_with_R_code.Rmd"
                             "test.ipynb"]
               :base-target-path "book"
               :book {:title "Book Example"}
               ;; Empty the target directory first:
               :clean-up-target-dir true}))

Create a Quarto book with a specified index page:

(comment
  (clay/make! {:format [:quarto :html]
               :base-source-path "notebooks"
               :source-path ["index.clj"
                             "chapter.clj"
                             "another_chapter.md"]
               :base-target-path "book"
               :book {:title "Book Example"}
               ;; Empty the target directory first:
               :clean-up-target-dir true}))

Reopen the Clay view in the browser (in case you closed the browser tab previously opened):

(comment
  (clay/browse!))

Configuration

Calls to the make! function are affected by various parameters which collected as one nested map. This map is the result of deep-merging four sources:

  • the default configuration: clay-default.edn under Clay’s resources

  • the user configuration: clay.edn at the top

  • the namespace configuration: the :clay member of the namespace metadata

  • the call configuration: the argument to make!

Here are some of the parameters worth knowing about:

(to be documented soon)

Kinds

The way things should be visualized is determined by the advice of Kindly.

In this namespace we demonstrate Kindly’s default advice. User-defined Kindly advices should work as well.

Kindly advises tools (like Clay) about the kind of way a given context should be displayed, by assigning to it a so-called kind.

Please refer to the Kindly documentation for details about specifying and using kinds.

Examples

Plain values

By default, when there is no kind information provided by Kindly, values are simply pretty-printed.

(+ 4 5)
9
(str "abcd" "efgh")
"abcdefgh"

Hidden

Values of :kind/hidden are not shown.

(kind/hidden 9)

Hiccup

Hiccup, a popular Clojure way to represent HTML, can be specified by kind:

(kind/hiccup
 [:ul
  [:li [:p "hi"]]
  [:li [:big [:big [:p {:style ; https://www.htmlcsscolor.com/hex/7F5F3F
                        {:color "#7F5F3F"}}
                    "hello"]]]]])
  • hi

  • hello

As we can see, this kind is displayed by converting Hiccup to HTML.

Reagent

(kind/reagent
 ['(fn [numbers]
     [:p {:style {:background "#d4ebe9"}}
      (pr-str (map inc numbers))])
  (vec (range 40))])

From the reagent tutorial:

(kind/reagent
 ['(fn []
     (let [*click-count (reagent.core/atom 0)]
       (fn []
         [:div
          "The atom " [:code "*click-count"] " has value: "
          @*click-count ". "
          [:input {:type "button" :value "Click me!"
                   :on-click #(swap! *click-count inc)}]])))])

HTML

Raw html can be represented as a kind too:

(kind/html "<div style='height:40px; width:40px; background:purple'></div> ")
(kind/html
 "
<svg height=100 width=100>
<circle cx=50 cy=50 r=40 stroke='purple' stroke-width=3 fill='floralwhite' />
</svg> ")

Markdown

Markdown text (a vector of strings) can be handled using a kind too.

(kind/md
 "This is [markdown](https://www.markdownguide.org/).")

This is markdown.

(kind/md
 ["
* This is [markdown](https://www.markdownguide.org/).
  * *Isn't it??*"
  "
* Here is **some more** markdown."])
  • This is markdown.
    • Isn’t it??
  • Here is some more markdown.

When rendering through Quarto, LaTeX formulae are supported as well.

(kind/md
 "Let $x=9$. Then $$x+11=20$$")

Let \(x=9\). Then \[x+11=20\]

One current known issue is that LaTeX would not render correctly when nesting kind/md inside other kinds.

Images

Java BufferedImage objects are displayed as images.

(import javax.imageio.ImageIO
        java.net.URL)
java.net.URL
(defonce clay-image
  (->  "https://upload.wikimedia.org/wikipedia/commons/2/2c/Clay-ss-2005.jpg"
       (URL.)
       (ImageIO/read)))
clay-image

Plain data structures

Plain data structures (lists and sequnces, vectors, sets, maps) are pretty printed if there isn’t any value inside which needs to be displayed in special kind of way.

(def people-as-maps
  (->> (range 29)
       (mapv (fn [i]
               {:preferred-language (["clojure" "clojurescript" "babashka"]
                                     (rand-int 3))
                :age (rand-int 100)}))))
(def people-as-vectors
  (->> people-as-maps
       (mapv (juxt :preferred-language :age))))
(take 5 people-as-maps)
({:preferred-language "clojure", :age 68}
 {:preferred-language "clojurescript", :age 39}
 {:preferred-language "clojurescript", :age 58}
 {:preferred-language "clojure", :age 62}
 {:preferred-language "babashka", :age 62})
(take 5 people-as-vectors)
(["clojure" 68]
 ["clojurescript" 39]
 ["clojurescript" 58]
 ["clojure" 62]
 ["babashka" 62])
(->> people-as-vectors
     (take 5)
     set)
#{["clojure" 62]
  ["clojurescript" 39]
  ["clojurescript" 58]
  ["babashka" 62]
  ["clojure" 68]}

When something inside needs to be displayed in a special kind of way, the data structures are printed in a way that makes that clear.

(def nested-structure-1
  {:vector-of-numbers [2 9 -1]
   :vector-of-different-things ["hi"
                                (kind/hiccup
                                 [:big [:big "hello"]])]
   :map-of-different-things {:markdown (kind/md ["*hi*, **hi**"])
                             :number 9999}
   :hiccup (kind/hiccup
            [:big [:big "bye"]])
   :dataset (tc/dataset {:x (range 3)
                         :y [:A :B :C]})})
nested-structure-1

{

:vector-of-numbers [2 9 -1]
:vector-of-different-things

[

"hi"
hello

]

:map-of-different-things

{

:markdown

hi, hi

:number 9999

}

:hiccup
bye
:dataset

_unnamed [3 2]:

:x :y
0 :A
1 :B
2 :C

}

Pretty printing

The :kind/pprint kind makes sure to simply pretty-print values:

(kind/pprint nested-structure-1)
{:vector-of-numbers [2 9 -1],
 :vector-of-different-things ["hi" [:big [:big "hello"]]],
 :map-of-different-things {:markdown ["*hi*, **hi**"], :number 9999},
 :hiccup [:big [:big "bye"]],
 :dataset _unnamed [3 2]:

| :x | :y |
|---:|----|
|  0 | :A |
|  1 | :B |
|  2 | :C |
}

Datasets

tech.ml.dataset datasets currently use the default printing of the library,

Let us create such a dataset using Tablecloth.

(require '[tablecloth.api :as tc])
(-> {:x (range 6)
     :y [:A :B :C :A :B :C]}
    tc/dataset)

_unnamed [6 2]:

:x :y
0 :A
1 :B
2 :C
3 :A
4 :B
5 :C
(-> {:x [1 [2 3] 4]
     :y [:A :B :C]}
    tc/dataset)

_unnamed [3 2]:

:x :y
1 :A
[2 3] :B
4 :C
(-> [{:x 1 :y 2 :z 3}
     {:y 4 :z 5}]
    tc/dataset)

_unnamed [2 3]:

:x :y :z
1 2 3
4 5
(-> people-as-maps
    tc/dataset)

_unnamed [29 2]:

:preferred-language :age
clojure 68
clojurescript 39
clojurescript 58
clojure 62
babashka 62
clojurescript 33
clojure 67
babashka 80
clojurescript 21
clojure 99
clojure 88
babashka 38
clojure 51
babashka 22
babashka 28
clojurescript 37
clojure 82
babashka 79
babashka 81
babashka 31
clojurescript 53

Tables

The :kind/table kind can be handy for an interactive table view. :kind/table understands many structures which can be rendered as a table.

A map containing either :row-vectors (sequence of sequences) or row-maps (sequence of maps) keys with optional :column-names.

(kind/table
 {:column-names [:preferred-language :age]
  :row-vectors people-as-vectors})
preferred-language age
clojure 68
clojurescript 39
clojurescript 58
clojure 62
babashka 62
clojurescript 33
clojure 67
babashka 80
clojurescript 21
clojure 99
clojure 79
clojure 25
babashka 68
clojure 29
babashka 54
babashka 73
babashka 53
clojure 41
clojure 88
babashka 38
clojure 51
babashka 22
babashka 28
clojurescript 37
clojure 82
babashka 79
babashka 81
babashka 31
clojurescript 53

Lack of column names produces table without a header.

(kind/table
 {:row-vectors (take 5 people-as-vectors)})
clojure 68
clojurescript 39
clojurescript 58
clojure 62
babashka 62

Column names are inferred from a sequence of maps

(kind/table
 {:row-maps (take 5 people-as-maps)})
preferred-language age
clojure 68
clojurescript 39
clojurescript 58
clojure 62
babashka 62

We can limit displayed columns for sequence of maps case.

(kind/table
 {:column-names [:preferred-language]
  :row-maps (take 5 people-as-maps)})
preferred-language
clojure
clojurescript
clojurescript
clojure
babashka

Sequence of sequences and sequence of maps also work

(kind/table (take 5 people-as-vectors))
clojure 68
clojurescript 39
clojurescript 58
clojure 62
babashka 62
(kind/table (take 5 people-as-maps))
preferred-language age
clojure 68
clojurescript 39
clojurescript 58
clojure 62
babashka 62

Additionally map of sequences is supported (unless it contains :row-vectors or :row-maps key, see such case above).

(kind/table {:x (range 6)
             :y [:A :B :C :A :B :C]})
x y
0 A
1 B
2 C
3 A
4 B
5 C

A dataset can be also treated as a table input.

(def people-as-dataset
  (tc/dataset people-as-maps))
(-> people-as-dataset
    kind/table)
preferred-language age
clojure 68
clojurescript 39
clojurescript 58
clojure 62
babashka 62
clojurescript 33
clojure 67
babashka 80
clojurescript 21
clojure 99
clojure 79
clojure 25
babashka 68
clojure 29
babashka 54
babashka 73
babashka 53
clojure 41
clojure 88
babashka 38
clojure 51
babashka 22
babashka 28
clojurescript 37
clojure 82
babashka 79
babashka 81
babashka 31
clojurescript 53

Additional options may hint at way the table should be rendered.

(-> people-as-dataset
    (kind/table {:element/max-height "300px"}))
preferred-language age
clojure 68
clojurescript 39
clojurescript 58
clojure 62
babashka 62
clojurescript 33
clojure 67
babashka 80
clojurescript 21
clojure 99
clojure 79
clojure 25
babashka 68
clojure 29
babashka 54
babashka 73
babashka 53
clojure 41
clojure 88
babashka 38
clojure 51
babashka 22
babashka 28
clojurescript 37
clojure 82
babashka 79
babashka 81
babashka 31
clojurescript 53

It is possible to use datatables to reneder kind/table, and in this case the user may specify datatables options (see the full list).

(-> people-as-maps
    tc/dataset
    (kind/table {:use-datatables true}))
preferred-languageage
clojure68
clojurescript39
clojurescript58
clojure62
babashka62
clojurescript33
clojure67
babashka80
clojurescript21
clojure99
clojure79
clojure25
babashka68
clojure29
babashka54
babashka73
babashka53
clojure41
clojure88
babashka38
clojure51
babashka22
babashka28
clojurescript37
clojure82
babashka79
babashka81
babashka31
clojurescript53
(-> people-as-dataset
    (kind/table {:use-datatables true
                 :datatables {:scrollY 300}}))
preferred-languageage
clojure68
clojurescript39
clojurescript58
clojure62
babashka62
clojurescript33
clojure67
babashka80
clojurescript21
clojure99
clojure79
clojure25
babashka68
clojure29
babashka54
babashka73
babashka53
clojure41
clojure88
babashka38
clojure51
babashka22
babashka28
clojurescript37
clojure82
babashka79
babashka81
babashka31
clojurescript53

ML models

(-> (toydata/iris-ds)
    (noj.stats/linear-regression-model :sepal_length
                                       [:sepal_width
                                        :petal_width
                                        :petal_length])
    ml/thaw-model)
Linear Model:

Residuals:
       Min          1Q      Median          3Q         Max
   -0.8282     -0.2202      0.0191      0.1992      0.8457

Coefficients:
                  Estimate Std. Error    t value   Pr(>|t|)
Intercept           1.8560     0.2508     7.4010     0.0000 ***
sepal_width         0.6508     0.0666     9.7654     0.0000 ***
petal_width        -0.5565     0.1275    -4.3629     0.0000 ***
petal_length        0.7091     0.0567    12.5025     0.0000 ***
---------------------------------------------------------------------
Significance codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.3145 on 146 degrees of freedom
Multiple R-squared: 0.8586,    Adjusted R-squared: 0.8557
F-statistic: 295.5391 on 4 and 146 DF,  p-value: 8.588e-62

Vega and Vega-Lite

(defn vega-lite-point-plot [data]
  (-> {:data {:values data},
       :mark "point"
       :encoding
       {:size {:field "w" :type "quantitative"}
        :x {:field "x", :type "quantitative"},
        :y {:field "y", :type "quantitative"},
        :fill {:field "z", :type "nominal"}}}
      kind/vega-lite))
(defn random-data [n]
  (->> (repeatedly n #(- (rand) 0.5))
       (reductions +)
       (map-indexed (fn [x y]
                      {:w (rand-int 9)
                       :z (rand-int 9)
                       :x x
                       :y y}))))
(defn random-vega-lite-plot [n]
  (-> n
      random-data
      vega-lite-point-plot))
(random-vega-lite-plot 9)

When the vega/vega-lite data is given in CSV format, Clay will serve it in a separate CSV file alongside the generated HTML.

(-> {:data {:values "x,y
1,1
2,4
3,9
-1,1
-2,4
-3,9"
            :format {:type :csv}},
     :mark "point"
     :encoding
     {:x {:field "x", :type "quantitative"}
      :y {:field "y", :type "quantitative"}}}
    kind/vega-lite)

Cytoscape

See the Cytoscape docs.

(def cytoscape-example
  {:elements {:nodes [{:data {:id "a" :parent "b"} :position {:x 215 :y 85}}
                      {:data {:id "b"}}
                      {:data {:id "c" :parent "b"} :position {:x 300 :y 85}}
                      {:data {:id "d"} :position {:x 215 :y 175}}
                      {:data {:id "e"}}
                      {:data {:id "f" :parent "e"} :position {:x 300 :y 175}}]
              :edges [{:data {:id "ad" :source "a" :target "d"}}
                      {:data {:id "eb" :source "e" :target "b"}}]}
   :style [{:selector "node"
            :css {:content "data(id)"
                  :text-valign "center"
                  :text-halign "center"}}
           {:selector "parent"
            :css {:text-valign "top"
                  :text-halign "center"}}
           {:selector "edge"
            :css {:curve-style "bezier"
                  :target-arrow-shape "triangle"}}]
   :layout {:name "preset"
            :padding 5}})
(kind/cytoscape
 cytoscape-example)
(-> cytoscape-example
    (kind/cytoscape {:element/style
                     {:width "100px"
                      :height "100px"}}))

ECharts

This example is taken from Apache ECharts’ Getting Started.

(def echarts-example
  {:title {:text "Echarts Example"}
   :tooltip {}
   :legend {:data ["sales"]}
   :xAxis {:data ["Shirts", "Cardigans", "Chiffons",
                  "Pants", "Heels", "Socks"]}
   :yAxis {}
   :series [{:name "sales"
             :type "bar"
             :data [5 20 36
                    10 10 20]}]})
(kind/echarts
 echarts-example)
(-> echarts-example
    (kind/echarts {:element/style
                   {:width "500px"
                    :height "200px"}}))

Plotly

See the plotly.js docs.

(def plotly-example
  {:data [{:x [0 1 3 2]
           :y [0 6 4 5]
           :z [0 8 9 7]
           :type :scatter3d
           :mode :lines+markers
           :opacity 0.5
           :line {:width 5}
           :marker {:size 4
                    :colorscale :Viridis}}]
   :layout {:title "Plotly example"}})
(kind/plotly
 plotly-example)
(-> plotly-example
    (kind/plotly {:element/style
                  {:width "300px"
                   :height "300px"}}))

Highcharts

(kind/highcharts
 {:title {:text "Line chart"}
  :subtitle {:text "By Job Category"}
  :yAxis {:title {:text "Number of Employees"}}
  :series [{:name "Installation & Developers"
            :data [43934, 48656, 65165, 81827, 112143, 142383,
                   171533, 165174, 155157, 161454, 154610]}

           {:name "Manufacturing",
            :data [24916, 37941, 29742, 29851, 32490, 30282,
                   38121, 36885, 33726, 34243, 31050]}

           {:name "Sales & Distribution",
            :data [11744, 30000, 16005, 19771, 20185, 24377,
                   32147, 30912, 29243, 29213, 25663]}

           {:name "Operations & Maintenance",
            :data [nil, nil, nil, nil, nil, nil, nil,
                   nil, 11164, 11218, 10077]}

           {:name "Other",
            :data [21908, 5548, 8105, 11248, 8989, 11816, 18274,
                   17300, 13053, 11906, 10073]}]

  :xAxis {:accessibility {:rangeDescription "Range: 2010 to 2020"}}

  :legend {:layout "vertical",
           :align "right",
           :verticalAlign "middle"}

  :plotOptions {:series {:label {:connectorAllowed false},
                         :pointStart 2010}}

  :responsive {:rules [{:condition {:maxWidth 500},
                        :chartOptions {:legend {:layout "horizontal",
                                                :align "center",
                                                :verticalAlign "bottom"}}}]}})

Observable

Observable visualizations are supported when rendering through Quarto.

The following is adapted from the Penguins example in Quarto’s documentation.

Note that you can save your Clojure data as a csv file and refer to it from within your Observable code. See Referring to files for more information. In this case, we are using the local file, "notebooks/datasets/palmer-penguins.csv", which is transparently copied by Clay alongside the target HTML.

(kind/observable
 "
//| panel: input
viewof bill_length_min = Inputs.range(
                                      [32, 50],
                                      {value: 35, step: 1, label: 'Bill length (min):'}
                                      )
viewof islands = Inputs.checkbox(
                                 ['Torgersen', 'Biscoe', 'Dream'],
                                 { value: ['Torgersen', 'Biscoe'],
                                  label: 'Islands:'
                                  }
                                 )

Plot.rectY(filtered,
            Plot.binX(
                      {y: 'count'},
                      {x: 'body_mass_g', fill: 'species', thresholds: 20}
                      ))
 .plot({
        facet: {
                data: filtered,
                x: 'sex',
                y: 'species',
                marginRight: 80
                },
        marks: [
                Plot.frame(),
                ]
        }
       )
Inputs.table(filtered)
penguins = FileAttachment('notebooks/datasets/palmer-penguins.csv').csv({ typed: true })
filtered = penguins.filter(function(penguin) {
                                           return bill_length_min < penguin.bill_length_mm &&
                                           islands.includes(penguin.island);
                                           })
")

More examples from Quarto’s Observable documentation:

(kind/observable
 "athletes = FileAttachment('notebooks/datasets/athletes.csv').csv({typed: true})")
(kind/observable
 "athletes")
(kind/observable
 "Inputs.table(athletes)")
(kind/observable
 "
Plot.plot({
  grid: true,
  facet: {
    data: athletes,
    y: 'sex'
  },
  marks: [
    Plot.rectY(
      athletes,
      Plot.binX({y: 'count'}, {x: 'weight', fill: 'sex'})
    ),
    Plot.ruleY([0])
  ]
})
")
(kind/observable
 "population = FileAttachment('notebooks/datasets/population.json').json()")
(kind/observable
 "population")
(kind/observable
 " import { chart } with { population as data } from '@d3/zoomable-sunburst'
 chart")

Leaflet

This example was adapted from the Leaflet website. Note we are defining a tile layer using leaflet-providers.

(kind/reagent
 ['(fn []
     [:div {:style {:height "200px"}
            :ref (fn [el]
                   (let [m (-> js/L
                               (.map el)
                               (.setView (clj->js [51.505 -0.09])
                                         13))]
                     (-> js/L
                         .-tileLayer
                         (.provider "OpenStreetMap.Mapnik")
                         (.addTo m))
                     (-> js/L
                         (.marker (clj->js [51.5 -0.09]))
                         (.addTo m)
                         (.bindPopup "A pretty CSS popup.<br> Easily customizable.")
                         (.openPopup))))}])]
 ;; Note we need to mention the dependency:
 {:html/deps [:leaflet]})

D3

The following example is adapted from hiccup-d3. The code is a bit different, e.g. (.scaleOrdinal js/d3 (.-schemeCategory10 js/d3)) instead of (d3/scaleOrdinal d3/schemeCategory10). We still need to figure out how to make hiccup-d3’s examples work as they are.

(let [letter-frequencies [{:letter "A", :frequency 0.08167}
                          {:letter "B", :frequency 0.01492}
                          {:letter "C", :frequency 0.02782}
                          {:letter "D", :frequency 0.04253}
                          {:letter "E", :frequency 0.12702}
                          {:letter "F", :frequency 0.02288}
                          {:letter "G", :frequency 0.02015}
                          {:letter "H", :frequency 0.06094}
                          {:letter "I", :frequency 0.06966}
                          {:letter "J", :frequency 0.00153}
                          {:letter "K", :frequency 0.00772}
                          {:letter "L", :frequency 0.04025}
                          {:letter "M", :frequency 0.02406}
                          {:letter "N", :frequency 0.06749}
                          {:letter "O", :frequency 0.07507}
                          {:letter "P", :frequency 0.01929}
                          {:letter "Q", :frequency 0.00095}
                          {:letter "R", :frequency 0.05987}
                          {:letter "S", :frequency 0.06327}
                          {:letter "T", :frequency 0.09056}
                          {:letter "U", :frequency 0.02758}
                          {:letter "V", :frequency 0.00978}
                          {:letter "W", :frequency 0.0236}
                          {:letter "X", :frequency 0.0015}
                          {:letter "Y", :frequency 0.01974}
                          {:letter "Z", :frequency 0.00074}]]
  (kind/reagent
   ['(fn [data]
       (let [size 400
             x (-> js/d3
                   .scaleLinear
                   (.range (into-array [0 size]))
                   (.domain (into-array [0 (apply max (map :frequency data))])))
             y (-> js/d3
                   .scaleBand
                   (.domain (into-array (map :letter data)))
                   (.range (into-array [0 size])))
             color (.scaleOrdinal js/d3 (.-schemeCategory10 js/d3))]
         [:svg
          {:viewBox (str "0 0 " size " " size)}
          (map
           (fn
             [{:keys [letter frequency]}]
             [:g
              {:key letter, :transform (str "translate(" 0 "," (y letter) ")")}
              [:rect
               {:x (x 0),
                :height (.bandwidth y),
                :fill (color letter),
                :width (x frequency)}]])
           data)]))
    letter-frequencies]
   {:html/deps [:d3]}))

ggplotly

(WIP)

Clay supports rendering plots through the JS client side of ggplotly - an R package offering a Plotly fronted for ggplot2’s grammar of graphics implementation. This package is part of the htmlwidgets ecosystem, and we represent that in the kind’s name.

The following is a work-in-progress attempt to generate JSON specs of the kind consumed by ggplotly’s client side.

The following spec function was generaged by mimicking R’s ggplotly(ggplot(mtcars, aes(wt, mpg)) + geom_point()). Therefore, some parts are hard-coded and require generalization. Other parts are missing (e.g., specifying colours).

(defn ->ggplotly-spec [{:keys [layers labels]}]
  (kind/htmlwidgets-ggplotly
   (let [;; assuming a single layer for now:
         {:keys [data xmin xmax ymin ymax]} (first layers)
         ;; an auxiliary function to compute tick values:
         ->tickvals (fn [l r]
                      (let [jump (-> (- r l)
                                     (/ 6)
                                     math/floor
                                     int
                                     (max 1))]
                        (-> l
                            math/ceil
                            (range r jump))))]
     {:x
      {:config
       {:doubleClick "reset",
        :modeBarButtonsToAdd ["hoverclosest" "hovercompare"],
        :showSendToCloud false},
       :layout
       {:plot_bgcolor "rgba(235,235,235,1)",
        :paper_bgcolor "rgba(255,255,255,1)",
        :legend
        {:bgcolor "rgba(255,255,255,1)",
         :bordercolor "transparent",
         :borderwidth 1.88976377952756,
         :font {:color "rgba(0,0,0,1)", :family "", :size 11.689497716895}},
        :xaxis (let [tickvals (->tickvals xmin xmax)
                     ticktext (mapv str tickvals)
                     range-len (- xmax xmin)
                     range-expansion (* 0.1 range-len)
                     expanded-range [(- xmin range-expansion)
                                     (+ xmax range-expansion)]]
                 {:linewidth 0,
                  :nticks nil,
                  :linecolor nil,
                  :ticklen 3.65296803652968,
                  :tickcolor "rgba(51,51,51,1)",
                  :tickmode "array",
                  :gridcolor "rgba(255,255,255,1)",
                  :automargin true,
                  :type "linear",
                  :tickvals tickvals
                  :zeroline false,
                  :title
                  {:text (:x labels),
                   :font {:color "rgba(0,0,0,1)", :family "", :size 14.6118721461187}},
                  :tickfont {:color "rgba(77,77,77,1)", :family "", :size 11.689497716895},
                  :autorange false,
                  :showticklabels true,
                  :showline false,
                  :showgrid true,
                  :ticktext ticktext
                  :ticks "outside",
                  :gridwidth 0.66417600664176,
                  :anchor "y",
                  :domain [0 1],
                  :hoverformat ".2f",
                  :tickangle 0,
                  :tickwidth 0.66417600664176,
                  :categoryarray ticktext,
                  :categoryorder "array",
                  :range expanded-range},)
        :font {:color "rgba(0,0,0,1)", :family "", :size 14.6118721461187},
        :showlegend false,
        :barmode "relative",
        :yaxis (let [tickvals (->tickvals ymin ymax)
                     ticktext (mapv str tickvals)
                     range-len (- ymax ymin)
                     range-expansion (* 0.1 range-len)
                     expanded-range [(- ymin range-expansion)
                                     (+ ymax range-expansion)]]
                 {:linewidth 0,
                  :nticks nil,
                  :linecolor nil,
                  :ticklen 3.65296803652968,
                  :tickcolor "rgba(51,51,51,1)",
                  :tickmode "array",
                  :gridcolor "rgba(255,255,255,1)",
                  :automargin true,
                  :type "linear",
                  :tickvals tickvals,
                  :zeroline false,
                  :title
                  {:text (:y labels),
                   :font {:color "rgba(0,0,0,1)", :family "", :size 14.6118721461187}},
                  :tickfont {:color "rgba(77,77,77,1)", :family "", :size 11.689497716895},
                  :autorange false,
                  :showticklabels true,
                  :showline false,
                  :showgrid true,
                  :ticktext ticktext,
                  :ticks "outside",
                  :gridwidth 0.66417600664176,
                  :anchor "x",
                  :domain [0 1],
                  :hoverformat ".2f",
                  :tickangle 0,
                  :tickwidth 0.66417600664176,
                  :categoryarray ticktext,
                  :categoryorder "array",
                  :range expanded-range},)
        :hovermode "closest",
        :margin
        {:t 25.7412480974125,
         :r 7.30593607305936,
         :b 39.6955859969559,
         :l 37.2602739726027},
        :shapes
        [{:yref "paper",
          :fillcolor nil,
          :xref "paper",
          :y1 1,
          :type "rect",
          :line {:color nil, :width 0, :linetype []},
          :y0 0,
          :x1 1,
          :x0 0}]},
       :highlight
       {:on "plotly_click",
        :persistent false,
        :dynamic false,
        :selectize false,
        :opacityDim 0.2,
        :selected {:opacity 1},
        :debounce 0},
       :base_url "https://plot.ly",
       :cur_data "1f2fea5b54d146",
       :source "A",
       :shinyEvents
       ["plotly_hover"
        "plotly_click"
        "plotly_selected"
        "plotly_relayout"
        "plotly_brushed"
        "plotly_brushing"
        "plotly_clickannotation"
        "plotly_doubleclick"
        "plotly_deselect"
        "plotly_afterplot"
        "plotly_sunburstclick"],
       :attrs {:1f2fea5b54d146 {:x {}, :y {}, :type "scatter"}},
       :data
       [{:y (:y data)
         :hoveron "points",
         :frame nil,
         :hoverinfo "text",
         :marker
         {:autocolorscale false,
          :color "rgba(0,0,0,1)",
          :opacity 1,
          :size 5.66929133858268,
          :symbol "circle",
          :line {:width 1.88976377952756, :color "rgba(0,0,0,1)"}},
         :mode "markers"
         :type "scatter",
         :xaxis "x",
         :showlegend false,
         :yaxis "y",
         :x (:x data)
         :text (-> data
                   (tc/select-columns [:x :y])
                   (tc/rows :as-maps)
                   (->> (mapv pr-str)))}]},
      :evals [],
      :jsHooks []})))
(require '[tech.v3.datatype.functional :as fun])

A random walk example:

(let [n 100
      xs (range n)
      ys (reductions + (repeatedly n #(- (rand) 0.5)))
      xmin (fun/reduce-min xs)
      xmax (fun/reduce-max xs)
      ymin (fun/reduce-min ys)
      ymax (fun/reduce-max ys)
      data (tc/dataset {:x xs
                        :y ys})]
  (->ggplotly-spec
   {:layers [{:data data
              :xmin xmin :xmax xmax
              :ymin ymin :ymax ymax}]
    :labels {:x "wt"
             :y "mpg"}}))

3DMol.js

Embedding a 3Dmol Viewer (original example):

(kind/reagent
 ['(fn [{:keys [data-pdb]}]
     [:div {:style {:height "400px"
                    :width "400px"
                    :position :relative}
            :class "viewer_3Dmoljs"
            :data-pdb data-pdb
            :data-backgroundcolor "0xffffff"
            :data-style "stick"
            :data-ui true}])
  {:data-pdb "2POR"}]
 ;; Note we need to mention the dependency:
 {:html/deps [:three-d-mol]})

Using 3Dmol within your code (inspired by these examples):

(defonce pdb-2POR
(slurp "https://files.rcsb.org/download/2POR.pdb"))
(kind/reagent
['(fn [{:keys [pdb-data]}]
    [:div
     {:style {:width "100%"
              :height "500px"
              :position "relative"}
      :ref (fn [el]
             (let [config (clj->js
                           {:backgroundColor "0xffffff"})
                   viewer (.createViewer js/$3Dmol el)]
               (.setViewStyle viewer (clj->js
                                      {:style "outline"}))
               (.addModelsAsFrames viewer pdb-data "pdb")
               (.addSphere viewer (clj->js
                                   {:center {:x 0
                                             :y 0
                                             :z 0}
                                    :radius 5
                                    :color "green"
                                    :alpha 0.2}))
               (.zoomTo viewer)
               (.render viewer)
               (.zoom viewer 0.8 2000)))}])
 {:pdb-data pdb-2POR}]
;; Note we need to mention the dependency:
{:html/deps [:three-d-mol]})

Video

(kind/video {:youtube-id "DAQnvAgBma8"})
(kind/video {:youtube-id "DAQnvAgBma8"
             :allowfullscreen false})
(kind/video {:youtube-id "DAQnvAgBma8"
             :iframe-width 480
             :iframe-height 270})
(kind/video {:youtube-id "DAQnvAgBma8"
             :embed-options {:mute 1
                             :controls 0}})

See, e.g., HTML Youtube Videos on w3schools.

Embedded Portal

We may embed Portal’s data-navigating viewers using kind/portal.

(kind/portal {:x (range 3)})

Note that kind/portal applies the kind-portal adapter to nested kinds.

(kind/portal
[(kind/hiccup [:img {:height 50 :width 50
                     :src "https://clojure.org/images/clojure-logo-120b.png"}])
 (kind/hiccup [:img {:height 50 :width 50
                     :src "https://raw.githubusercontent.com/djblue/portal/fbc54632adc06c6e94a3d059c858419f0063d1cf/resources/splash.svg"}])])
(kind/portal
[(kind/hiccup [:big [:big "a plot"]])
 (random-vega-lite-plot 9)])

Nesting kinds in Hiccup

Kinds are treated recursively inside Hiccup:

(kind/hiccup
 [:div {:style {:background "#f5f3ff"
                :border "solid"}}

  [:hr]
  [:pre [:code "kind/md"]]
  (kind/md "*some text* **some more text**")

  [:hr]
  [:pre [:code "kind/code"]]
  (kind/code "{:x (1 2 [3 4])}")

  [:hr]
  [:pre [:code "kind/dataset"]]
  (tc/dataset {:x (range 33)
               :y (map inc (range 33))})

  [:hr]
  [:pre [:code "kind/table"]]
  (kind/table
   (tc/dataset {:x (range 33)
                :y (map inc (range 33))}))

  [:hr]
  [:pre [:code "kind/vega-lite"]]
  (random-vega-lite-plot 9)

  [:hr]
  [:pre [:code "kind/vega-lite"]]
  (-> {:data {:values "x,y
1,1
2,4
3,9
-1,1
-2,4
-3,9"
              :format {:type :csv}},
       :mark "point"
       :encoding
       {:x {:field "x", :type "quantitative"}
        :y {:field "y", :type "quantitative"}}}
      kind/vega-lite)

  [:hr]
  [:pre [:code "kind/reagent"]]
  (kind/reagent
   ['(fn [numbers]
       [:p {:style {:background "#d4ebe9"}}
        (pr-str (map inc numbers))])
    (vec (range 40))])])

kind/md

some text some more text


kind/code
{:x (1 2 [3 4])}

kind/dataset

_unnamed [33 2]:

:x :y
0 1
1 2
2 3
3 4
4 5
5 6
6 7
7 8
8 9
9 10
... ...
22 23
23 24
24 25
25 26
26 27
27 28
28 29
29 30
30 31
31 32
32 33

kind/table
x y
0 1
1 2
2 3
3 4
4 5
5 6
6 7
7 8
8 9
9 10
10 11
11 12
12 13
13 14
14 15
15 16
16 17
17 18
18 19
19 20
20 21
21 22
22 23
23 24
24 25
25 26
26 27
27 28
28 29
29 30
30 31
31 32
32 33

kind/vega-lite

kind/vega-lite

kind/reagent

Nesting kinds in Tables

Kinds are treated recursively inside Tables:

(kind/table
{:column-names [(kind/hiccup
                 [:div {:style {:background-color "#ccaabb"}} [:big ":x"]])
                (kind/hiccup
                 [:div {:style {:background-color "#aabbcc"}} [:big ":y"]])]
 :row-vectors [[(kind/md "*some text* **some more text**")
                (kind/code "{:x (1 2 [3 4])}")]
               [(tc/dataset {:x (range 3)
                             :y (map inc (range 3))})
                (random-vega-lite-plot 9)]
               [(kind/hiccup [:div.clay-limit-image-width
                              clay-image])
                (kind/md "$x^2$")]]})
:x
:y
some text some more text
{:x (1 2 [3 4])}
_unnamed [3 2]:
:x:y
01
12
23
\(x^2\)
(kind/table
{:column-names ["size" "square"]
 :row-vectors (for [i (range 20)]
                (let [size (* i 10)
                      px (str size "px")]
                  [size
                   (kind/hiccup
                    [:div {:style {:height px
                                   :width px
                                   :background-color "purple"}}])]))}
{:use-datatables true})
sizesquare
0
10
20
30
40
50
60
70
80
90
100
110
120
130
140
150
160
170
180
190

More nesting examples

{:plot (random-vega-lite-plot 9)
 :dataset (tc/dataset {:x (range 3)
                       :y (repeatedly 3 rand)})}

{

:plot
:dataset

_unnamed [3 2]:

:x :y
0 0.56216231
1 0.50584193
2 0.02965696

}

[(random-vega-lite-plot 9)
 (tc/dataset {:x (range 3)
              :y (repeatedly 3 rand)})]

[

_unnamed [3 2]:

:x :y
0 0.68820540
1 0.04134803
2 0.45990875

]

Fragments

kind/fragment is a special kind. It expects a sequential value and generates multiple items, of potentially multiple kinds, from its elements.

(->> ["purple" "darkgreen" "brown"]
     (mapcat (fn [color]
               [(kind/md (str "### subsection: " color))
                (kind/hiccup [:div {:style {:background-color color
                                            :color "lightgrey"}}
                              [:big [:p color]]])]))
     kind/fragment)

subsection: purple

purple

subsection: darkgreen

darkgreen

subsection: brown

brown

(->> (range 3)
     kind/fragment)
0
1
2

Importantly, markdown subsections affect the Quarto table of contents.

Functions

kind/fn is a special kind. It is displayed by first evaluating the given function and arguments, then proceeding recursively with the resulting value.

(kind/fn
  [+ 1 2])
3
(kind/fn
  {:kindly/f (fn [{:keys [x y]}]
               (+ x y))
   :x 1
   :y 2})
3
(kind/fn
  [tc/dataset
   {:x (range 3)
    :y (repeatedly 3 rand)}])

_unnamed [3 2]:

:x :y
0 0.12683574
1 0.05460325
2 0.08112254
(kind/fn
  {:kindly/f tc/dataset
   :x (range 3)
   :y (repeatedly 3 rand)})

_unnamed [3 2]:

:x :y
0 0.95894133
1 0.19937508
2 0.77858145

Delays

Clojure Delays are a common way to define computations that do not take place immediately. The computation takes place when dereferencing the value for the first time.

Clay makes sure to dererence Delays when passing values for visualization.

This is handy for slow example snippets and explorations, that one would typically not like to slow down the evaluation of the whole namespace, but would like to visualize them on demand and also include in them in the final document.

(delay
  (Thread/sleep 500)
  (+ 1 2))
3

Referring to files

In data visualizations, one can directly refrer to files places under "notebooks/" or "src/". By default, all files except of these directories, except for Clojure files, are copied alongside the HTML target.

This default can be overridden using the :subdirs-to-sync config option. E.g., :subdirs-to-sync ["notebooks" "data"] will copy files from the "notebooks" and "data" directories, but not from "src".

(kind/hiccup
 [:img {:src "notebooks/images/Clay.svg.png"}])
(kind/vega-lite
 {:data {:url "notebooks/datasets/iris.csv"},
  :mark "rule",
  :encoding {:opacity {:value 0.2}
             :size {:value 3}
             :x {:field "sepal_width", :type "quantitative"},
             :x2 {:field "sepal_length", :type "quantitative"},
             :y {:field "petal_width", :type "quantitative"},
             :y2 {:field "petal_length", :type "quantitative"},
             :color {:field "species", :type "nominal"}}
  :background "floralwhite"})

Hiding code

By default, a Clay notebook shows both the code and the result of an evaluated form. Here are a few ways one may hide the code:

  1. Add the metadata :kindly/hide-code true to the form (e.g., by preceding it with ^:kindly/hide-code).
  2. Add the metadata :kindly/hide-code true to the value.
  3. Globally define certain kinds (e.g., :kind/md, :kind/hiccup) to always hide code (on project level or namespace level) by adding thme as a set to the project config or namespace config, e.g., :kindly/options {:kinds-that-hide-code #{:kind/md :kind/hiccup}}.

Test generation

(experimental 🛠)

(+ 1 2)
3

We generate tests checking whether this last value is greater than 2.9. We can do it in a few ways.

We include the test annotations in the markdown text, since the annotations themselves are invisible.

(kind/test-last [> 2.9])

^kind/test-last
[> 2.9]

(kindly/check > 2.9)

See the generated test/index_generated_test.clj.

For a detailed example using this mechanism, see the source of the ClojisR tutorial.

source: notebooks/index.clj