iris_pca.clj

(use '(incanter core stats charts datasets))
;; load the iris dataset
(def iris (to-matrix (get-dataset :iris)))
;; run the pca on the first four columns only
(def pca (principal-components (sel iris :cols (range 4))))
;; extract the first two principal components
(def pc1 (sel (:rotation pca) :cols 0))
(def pc2 (sel (:rotation pca) :cols 1))

;; project the first four dimension of the iris data onto the first
;; two principal components
(def x1 (mmult (sel iris :cols (range 4)) pc1)) 
(def x2 (mmult (sel iris :cols (range 4)) pc2)) 
   
;; now plot the transformed data, coloring each species a different color
(doto (scatter-plot (sel x1 :rows (range 50)) (sel x2 :rows (range 50))
                    :x-label "PC1" :y-label "PC2" :title "Iris PCA")
      (add-points (sel x1 :rows (range 50 100)) (sel x2 :rows (range 50 100)))
      (add-points (sel x1 :rows (range 100 150)) (sel x2 :rows (range 100 150)))
      view)