piton, dotplots and box-dotplot kind of working

Author: Mike Travers

src/data_visualization/violin.clj

@@ -12,61 +12,248 @@
 (ns scicloj.data-visualization.violin
   (:require
    [clojure.data.json :as json]
+   [tablecloth.api :as tc]
    [scicloj.kindly.v4.api :as kindly]
    [scicloj.kindly.v4.kind :as kind]
    ))
 
+;;; I can't stand writing long text in ;;; comments, so import it from actual .md files
+^{:kind/md true :kindly/hide-code true}
+(slurp "src/data_visualization/violin1.md")
+
+;;; # Get some data
+
+;;; ## Movie Dataset
 
 ;;; Get the movie dataset
 (def movie-data
-  (json/read-str (slurp  "https://vega.github.io/editor/data/movies.json") ))
+  (json/read-str (slurp "https://vega.github.io/editor/data/movies.json") ))
 
+;;; Here we'll take a look at a sample of the data (selected columns and just a few rows).
+(kind/table
+ {:row-maps (take 10 movie-data)
+  :column-names ["Title" "IMDB Rating" "US Gross" "Distributor" "Production Budget" "MPAA Rating" "Major Genre"]})
 
-;;; Make a simple boxplot showing US Gross by Genre
-(kind/vega-lite
- {:mark {:type "boxplot" :tooltip {:content "data"}},
-  :data {:values  movie-data}
+
+;;; ## Penguin dataset
+
+(def penguin-data-url "https://raw.githubusercontent.com/ttimbers/palmerpenguins/refs/heads/file-variants/inst/extdata/penguins.tsv")
+
+(def penguin-data
+  (tc/dataset penguin-data-url {:key-fn keyword}))
+
+(kind/table (tc/random penguin-data 10))
+
+;;; # Boxplot
+
+
+;;; A basic boxplot shows the distribution of a single varianle. Here we look at the distribution of US gross profits:
+^:kind/vega-lite
+ {:mark {:type "boxplot"}
+  :data {:values movie-data}
   :encoding
-  {"color" {:field "Major Genre", :type "nominal" :legend false},
-   "y" {:field "Major Genre",
-        :type "nominal"},
-   "x" {:field "US Gross",
+  {"x" {:field "US Gross"
         :type "quantitative"}
-   :tooltip {:field "Title"
-             ;; :type "quantitative"
-             }},
+   :tooltip {:field "Title"}}
   :width 800
-  })
+  }
+
+
+
+
+
+
+;;; But boxplots are more useful when you compare distributions given a second variable. Here we see the different distributions for specific genres of movie.
+
+^:kind/vega-lite
+ {:mark {:type "boxplot"}
+  :data {:values movie-data}
+  :encoding
+  {"x" {:field "US Gross"
+        :type "quantitative"}
+   "y" {:field "Major Genre"
+        :type "nominal"}
+   "color" {:field "Major Genre" :type "nominal" :legend false}
+   :tooltip {:field "Title"}}
+  :width 800
+  }
+
+;;; This shows us the median (white line)
+
+;;; # Violins
 
 
-;; That's nice, but how can we add violins to this?
 (kind/vega-lite
- {:mark {:type "area"},
+ {:mark {:type "area"}
   :data {:values movie-data}
   :transform [{:density "US Gross"
                :groupby ["Major Genre"]
-               :extent [0, 200000000]}]
+               :extent [0 200000000]}]
+  :height 50                            ;this is the height of each row (facet)
   :encoding
-  {"color" {:field "Major Genre", :type "nominal" :legend false},
-   "y" {:field "density",
+  {"color" {:field "Major Genre" :type "nominal" :legend false}
+   "y" {:field "density"
         :type "quantitative"
         :stack "center"
         :axis false
-        },               ;this reflect-doubles the area plot to produce the violin shape
-   "x" {:field "value",
+        }               ;this reflect-doubles the area plot to produce the violin shape
+   "x" {:field "value"
         :type "quantitative"}
-   "facet" {:field "Major Genre"
-            :type "nominal"
-            :columns 1
-            :spacing 0
-            :legend :left
-            }
-   },
+   "row" {:field "Major Genre"
+          :type "nominal"
+          :columns 1
+          :spacing 0
+          :header {:labelAngle 0 :labelAlign "left"}
+          }
+   }
   :width 800
   })
 
 
+(defn violin-plot
+  [data value-field group-field min max]
+  {:mark {:type "area"}
+   :data data
+   :transform [{:filter (format "datum['%s'] != 'NA'" value-field)}
+               {:density value-field
+                :groupby [group-field]
+                ;; :bandwidth 1.0
+                :extent [min max]}]
+   :height 50                            ;this is the height of each row (facet)
+   :encoding
+   {:color {:field group-field :type "nominal" :legend false}
+    :y {:field "density"
+        :type "quantitative"
+        :stack "center"
+        :axis false
+        }               ;this reflect-doubles the area plot to produce the violin shape
+    :x {:field "value"
+        :type "quantitative"}
+    :row {:field group-field
+          :type "nominal"
+          :columns 1
+          :spacing 0
+          :header {:labelAngle 0 :labelAlign "left"}
+          }
+    }
+   :width 800
+   })
+
+;;; TODO show box, whiskers, points
+;;; TODO need a better dataset, this is boring
+
+;;; # Here's a more scientific example
+
+(def iris 
+  (json/read-str (slurp "https://storage.googleapis.com/kagglesdsdata/datasets/20079/26025/iris.json?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=gcp-kaggle-com%40kaggle-161607.iam.gserviceaccount.com%2F20251129%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20251129T050349Z&X-Goog-Expires=259200&X-Goog-SignedHeaders=host&X-Goog-Signature=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")))
+
+^:kind/vega-lite
+(violin-plot {:values iris} "petalWidth" "species" 0 4)
+
+^:kind/vega-lite
+(violin-plot {:url penguin-data-url
+              :format {:type "tsv"}
+              }
+             "flipper_length_mm" "species island"
+             150 250)
+
+
+;;; # Dotplot
+
+(defn dot-plot
+  [data value-field group-field min max]
+  {:mark {:type "point" :tooltip {:content :data}}
+   :data data
+   :transform [{:filter (format "datum['%s'] != 'NA'" value-field)}
+               {:calculate "random()" :as "jitter"}]
+   :height 50                            ;this is the height of each row (facet)
+   :encoding
+   {:color {:field group-field :type "nominal" :legend false}
+    :x {:field value-field
+        :type "quantitative"
+        :scale {:domain [min max]}}
+    :y {:field "jitter"
+        :type "quantitative"
+        :axis false}
+    :row {:field group-field
+          :type "nominal"
+          :columns 1
+          :spacing 0
+          :header {:labelAngle 0 :labelAlign "left"}
+          }
+    }
+   :width 800
+   })
+
+^:kind/vega-lite
+(dot-plot {:url penguin-data-url
+           :format {:type "tsv"}
+           }
+          "flipper_length_mm" "species island"
+          150 250
+          )
+
+;;; TODO vertical violins
+;;; TODO controls
+;;; TODO layering
+;;; TODO more options
+;;; TODO merge
+
+
+;;; # Combining layers
+
+
+(defn box-dot-plot
+  [data value-field group-field min max]
+  {
+   ;; Data is in common
+   :data data
+
+   :facet
+   {:row {:field group-field
+          :type "nominal"
+          :spacing 0                    ;??? not working
+          :header {:labelAngle 0 :labelAlign "left"}
+          }}
+
+   :spec
+   {
+    :height 50                            ;this is the height of each row (facet)
+    :encoding 
+    {:x {:field value-field
+         :type "quantitative"
+         :scale {:domain [min max]}}
+     }    
+    
+    :layer
+    [{:mark {:type "point" :tooltip {:content :data}}
+      :transform [{:filter (format "datum['%s'] != 'NA'" value-field)}
+                  {:calculate "random()" :as "jitter"}]
+
+      :encoding
+      {:color {:value "gray"}
+       :y {:field "jitter"
+           :type "quantitative"
+           :axis false}
+       }}
+
+     ;; box layer
+     ;; TODO turn off outliers, widen box
+     {:mark {:type "boxplot" :outliers false}
+      :encoding
+      {:color {:field group-field :type "nominal" :legend false}
+       }}]
+   :width 800
+    }
 
+   })
 
 
 
+^:kind/vega-lite
+(box-dot-plot {:url penguin-data-url
+           :format {:type "tsv"}
+           }
+          "flipper_length_mm" "species island"
+          150 250
+          )