fix bug in viz.

[cdsc_reddit.git] / visualization / tsne_vis.py

diff --git a/visualization/tsne_vis.py b/visualization/tsne_vis.py
index 915cd7e9019a095855b5c3bc512cee80acbef49c..a644ecf5ae7c77f9b1b753b94e83b2839bb17903 100644 (file)
--- a/visualization/tsne_vis.py
+++ b/visualization/tsne_vis.py
@@ -5,19 +5,42 @@ alt.data_transformers.enable('default')
 from sklearn.neighbors import NearestNeighbors
 import pandas as pd
 from numpy import random
 from sklearn.neighbors import NearestNeighbors
 import pandas as pd
 from numpy import random

+import fire

 import numpy as np
 
 def base_plot(plot_data):
 import numpy as np
 
 def base_plot(plot_data):

+
+#    base = base.encode(alt.Color(field='color',type='nominal',scale=alt.Scale(scheme='category10')))
+
+    cluster_dropdown = alt.binding_select(options=[str(c) for c in sorted(set(plot_data.cluster))])
+
+    subreddit_dropdown = alt.binding_select(options=sorted(plot_data.subreddit))
+
+    cluster_click_select = alt.selection_single(on='click',fields=['cluster'], bind=cluster_dropdown, name=' ')
+    # cluster_select = alt.selection_single(fields=['cluster'], bind=cluster_dropdown, name='cluster')
+    # cluster_select_and = cluster_click_select & cluster_select
+    #
+    #    subreddit_select = alt.selection_single(on='click',fields=['subreddit'],bind=subreddit_dropdown,name='subreddit_click')
+    
+    color = alt.condition(cluster_click_select ,
+                          alt.Color(field='color',type='nominal',scale=alt.Scale(scheme='category10')),
+                          alt.value("lightgray"))
+  
+    

     base = alt.Chart(plot_data).mark_text().encode(
         alt.X('x',axis=alt.Axis(grid=False),scale=alt.Scale(domain=(-65,65))),
         alt.Y('y',axis=alt.Axis(grid=False),scale=alt.Scale(domain=(-65,65))),
     base = alt.Chart(plot_data).mark_text().encode(
         alt.X('x',axis=alt.Axis(grid=False),scale=alt.Scale(domain=(-65,65))),
         alt.Y('y',axis=alt.Axis(grid=False),scale=alt.Scale(domain=(-65,65))),

+        color=color,

         text='subreddit')
 
         text='subreddit')
 

+    base = base.add_selection(cluster_click_select)
+ 
+

     return base
 
 def zoom_plot(plot_data):
     chart = base_plot(plot_data)
     return base
 
 def zoom_plot(plot_data):
     chart = base_plot(plot_data)

-    chart = chart.encode(alt.Color(field='color',type='nominal',scale=alt.Scale(scheme='category10')))
+

     chart = chart.interactive()
     chart = chart.properties(width=1275,height=1000)
 
     chart = chart.interactive()
     chart = chart.properties(width=1275,height=1000)
 


@@ -34,7 +57,7 @@ def viewport_plot(plot_data):
         alt.X('x',axis=alt.Axis(grid=False)),
         alt.Y('y',axis=alt.Axis(grid=False)),
     )
         alt.X('x',axis=alt.Axis(grid=False)),
         alt.Y('y',axis=alt.Axis(grid=False)),
     )

-
+   

     viewport = viewport.properties(width=600,height=400)
 
     viewport1 = viewport.add_selection(selector1)
     viewport = viewport.properties(width=600,height=400)
 
     viewport1 = viewport.add_selection(selector1)


@@ -51,7 +74,7 @@ def viewport_plot(plot_data):
                      alt.Y('y',axis=alt.Axis(grid=False),scale=alt.Scale(domain=selectory2))
     )
 
                      alt.Y('y',axis=alt.Axis(grid=False),scale=alt.Scale(domain=selectory2))
     )
 

-    sr = sr.encode(alt.Color(field='color',type='nominal',scale=alt.Scale(scheme='category10')))
+

     sr = sr.properties(width=1275,height=600)
 
 
     sr = sr.properties(width=1275,height=600)
 
 


@@ -70,15 +93,29 @@ def assign_cluster_colors(tsne_data, clusters, n_colors, n_neighbors = 4):
     distances = np.empty(shape=(centroids.shape[0],centroids.shape[0]))
 
     groups = tsne_data.groupby('cluster')
     distances = np.empty(shape=(centroids.shape[0],centroids.shape[0]))
 
     groups = tsne_data.groupby('cluster')

-    for centroid in centroids.itertuples():
-        c_dists = groups.apply(lambda r: min(np.sqrt(np.square(centroid.x - r.x) + np.square(centroid.y-r.y))))
-        distances[:,centroid.Index] = c_dists
+    
+    points = np.array(tsne_data.loc[:,['x','y']])
+    centers = np.array(centroids.loc[:,['x','y']])
+
+    # point x centroid
+    point_center_distances = np.linalg.norm((points[:,None,:] - centers[None,:,:]),axis=-1)
+    
+    # distances is cluster x point
+    for gid, group in groups:
+        c_dists = point_center_distances[group.index.values,:].min(axis=0)
+        distances[group.cluster.values[0],] = c_dists        

 
     # nbrs = NearestNeighbors(n_neighbors=n_neighbors).fit(centroids) 
     # distances, indices = nbrs.kneighbors()
 
 
     # nbrs = NearestNeighbors(n_neighbors=n_neighbors).fit(centroids) 
     # distances, indices = nbrs.kneighbors()
 

-    nbrs = NearestNeighbors(n_neighbors=n_neighbors,metric='precomputed').fit(distances) 
-    distances, indices = nbrs.kneighbors()
+    nearest = distances.argpartition(n_neighbors,0)
+    indices = nearest[:n_neighbors,:].T
+    # neighbor_distances = np.copy(distances)
+    # neighbor_distances.sort(0)
+    # neighbor_distances = neighbor_distances[0:n_neighbors,:]
+    
+    # nbrs = NearestNeighbors(n_neighbors=n_neighbors,metric='precomputed').fit(distances) 
+    # distances, indices = nbrs.kneighbors()

 
     color_assignments = np.repeat(-1,len(centroids))
 
 
     color_assignments = np.repeat(-1,len(centroids))
 


@@ -100,26 +137,31 @@ def assign_cluster_colors(tsne_data, clusters, n_colors, n_neighbors = 4):
     tsne_data = tsne_data.merge(colors,on='cluster')
     return(tsne_data)
 
     tsne_data = tsne_data.merge(colors,on='cluster')
     return(tsne_data)
 

-term_data = pd.read_feather("tsne_subreddit_fit.feather")
-clusters = pd.read_feather("term_3000_clusters.feather")
+def build_visualization(tsne_data, clusters, output):
+
+    tsne_data = pd.read_feather(tsne_data)
+    clusters = pd.read_feather(clusters)
+
+    tsne_data = assign_cluster_colors(tsne_data,clusters,10,8)

 
 

-tsne_data = assign_cluster_colors(term_data,clusters,10,8)
+    term_zoom_plot = zoom_plot(tsne_data)

 
 

-term_zoom_plot = zoom_plot(tsne_data)
+    term_zoom_plot.save(output)

 
 

-term_zoom_plot.save("subreddit_terms_tsne_3000.html")
+    term_viewport_plot = viewport_plot(tsne_data)

 
 

-term_viewport_plot = viewport_plot(tsne_data)
+    term_viewport_plot.save(output.replace(".html","_viewport.html"))

 
 

-term_viewport_plot.save("subreddit_terms_tsne_3000_viewport.html")
+if __name__ == "__main__":
+    fire.Fire(build_visualization)

 
 

-commenter_data = pd.read_feather("tsne_author_fit.feather")
-clusters = pd.read_feather('author_3000_clusters.feather')
-commenter_data = assign_cluster_colors(commenter_data,clusters,10,8)
-commenter_zoom_plot = zoom_plot(commenter_data)
-commenter_viewport_plot = viewport_plot(commenter_data)
-commenter_zoom_plot.save("subreddit_commenters_tsne_3000.html")
-commenter_viewport_plot.save("subreddit_commenters_tsne_3000_viewport.html")
+# commenter_data = pd.read_feather("tsne_author_fit.feather")
+# clusters = pd.read_feather('author_3000_clusters.feather')
+# commenter_data = assign_cluster_colors(commenter_data,clusters,10,8)
+# commenter_zoom_plot = zoom_plot(commenter_data)
+# commenter_viewport_plot = viewport_plot(commenter_data)
+# commenter_zoom_plot.save("subreddit_commenters_tsne_3000.html")
+# commenter_viewport_plot.save("subreddit_commenters_tsne_3000_viewport.html")

 
 # chart = chart.properties(width=10000,height=10000)
 # chart.save("test_tsne_whole.svg")
 
 # chart = chart.properties(width=10000,height=10000)
 # chart.save("test_tsne_whole.svg")