How I turned a csv into a binified shapefile and then a JSON file. Uses ogr2ogr (http://www.gdal.org/ogr2ogr.html) and binify (https://github.com/kevinschaul/binify)

csv_binify.sh

# We start with a CSV called "crime_master_wloo_violent.csv" that has violent crime reports in Waterloo.
# Included in csv are columns for latitude ("lat") and longitude ("long"):
https://github.com/csessig86/crime_map2013/blob/master/csv/crime_master_wloo_violent.csv

# Command to turn CSV into DBF with the same name
ogr2ogr -f "ESRI Shapefile" crime_master_wloo_violent.dbf crime_master_wloo_violent.csv

# Create a file called "crime_master_wloo_violent.vrt"
# Change "SrcLayer" to the name of the source
# Change OGRVRTLayer name to "wloo_violent"
# Add name of lat, long columns to "GeometryField"
<OGRVRTDataSource>
  <OGRVRTLayer name="wloo_violent">
    <SrcDataSource relativeToVRT="1">./</SrcDataSource>
    <SrcLayer>crime_master_wloo_violent</SrcLayer>
    <GeometryType>wkbPoint</GeometryType>
    <LayerSRS>WGS84</LayerSRS>
    <GeometryField encoding="PointFromColumns" x="long" y="lat"/>
  </OGRVRTLayer>
</OGRVRTDataSource>

# Create "violent" folder to stash shp file
mkdir violent

# Convert "vrt" file into shp and put it in our "violent" folder
ogr2ogr -f "ESRI Shapefile" violent crime_master_wloo_property.vrt

# Binify the "wloo_violent" shp into a shp called "wloo_violent_binify" with three options
# The first sets the number of hexagons across to 45
# The second sets the custom extent to a box around Waterloo
# Custom extent is basically the extent of the area that the overlay of hexagons will cover
# The third tells binify to ignore hexagons that have zero points
binify wloo_violent.shp wloo_violent_binify.shp -n 45 -E -92.431873 -92.260867 42.4097259 42.558403 --exclude-empty

# Convert binified shp into JSON file called "crime_data_review_violent"
ogr2ogr -f "GeoJSON" crime_data_review_violent.json wloo_violent_binify.shp

# Add this variable to JSON file
var crime_data_review_violent

# Here's the final files:
https://github.com/csessig86/crime_map2013/tree/master/shps/wloo_shps

# And our JSON file:
https://github.com/csessig86/crime_map2013/blob/master/JSON/crime_data_review_violent.json

# And the Javascript file that is used with Leaflet to run the map.
# Lines 113 through 291 are the ones related to pulling the data from the JSON files,
# coloring them, setting the legend and setting a mouseover for each hexagon
https://github.com/csessig86/crime_map2013/blob/master/js/script_map_review.js

# And the map online:
http://wcfcourier.com/app/crime_map2013/index_wloo.php