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blacktwin/botulism.json

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Mapping Infant Botulism Cases in the US from 1975-2017
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botulism.json
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}, {
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, [ "row-d73h~vhan_77ct", "00000000-0000-0000-3BC1-B976BB6C950B", 0, 1558625993, null, 1558625993, null, "{ }", "California", "2005", "Wound", "A", "21" ]
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, [ "row-pycu~zcdy-ct6v", "00000000-0000-0000-589B-584836E4B058", 0, 1558625993, null, 1558625993, null, "{ }", "California", "2007", "Wound", "A", "16" ]
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, [ "row-mexp-xg6x-9qpz", "00000000-0000-0000-1694-0666C1415E53", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2007", "Wound", "A", "2" ]
, [ "row-gfi8_kdr4_9yng", "00000000-0000-0000-A65A-A17B01E815C1", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2008", "Infant", "A", "1" ]
, [ "row-h9ks.pzzn-ex5a", "00000000-0000-0000-72BB-CFEA265959DE", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2008", "Wound", "A", "2" ]
, [ "row-kc4w.ukf3_x2s7", "00000000-0000-0000-FE19-3623F6121D89", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2009", "Foodborne", "A", "4" ]
, [ "row-vxkw-cc2q-ss44", "00000000-0000-0000-EB11-1EEEF2ADEA32", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2009", "Infant", "A", "2" ]
, [ "row-y6yn_vfpj-4pm6", "00000000-0000-0000-420A-98E189165EDA", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2009", "Wound", "A", "4" ]
, [ "row-vivu~9f2d_mzug", "00000000-0000-0000-555C-2ADC59B3E2C8", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2010", "Infant", "A", "2" ]
, [ "row-mcpc-32n3_ingv", "00000000-0000-0000-3928-566A4C43F387", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2010", "Infant", "B", "1" ]
, [ "row-f3ub_qewd.emyr", "00000000-0000-0000-3602-993BEAEDBE97", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2010", "Wound", "A", "1" ]
, [ "row-xiph.2e2q-9rmb", "00000000-0000-0000-1141-CB86809FDD10", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2011", "Infant", "A", "3" ]
, [ "row-ftt8_7c6z-fr7p", "00000000-0000-0000-AF48-995512C9E361", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2011", "Wound", "A", "2" ]
, [ "row-mfku~5c9d.edh9", "00000000-0000-0000-76F9-890F09CBD772", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2012", "Infant", "A", "4" ]
, [ "row-z5a7-aqz5.3ccs", "00000000-0000-0000-5E25-11F5EA4CA1DE", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2012", "Wound", "A", "1" ]
, [ "row-hsb3.65ai_ijcx", "00000000-0000-0000-79BC-428D21CC5C54", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2013", "Infant", "A", "4" ]
, [ "row-vjnh.v3ab~t66v", "00000000-0000-0000-42FF-0718FDA9AF4C", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2014", "Infant", "A", "3" ]
, [ "row-pkb5_iiij~dtxt", "00000000-0000-0000-5EC8-F2D1B0DCD8E3", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2015", "Infant", "A", "6" ]
, [ "row-9kra.apwj-d2n6", "00000000-0000-0000-0AE7-7B3BB3FC9D81", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2016", "Foodborne", "A", "2" ]
, [ "row-sx24~awmz-bkew", "00000000-0000-0000-C517-8830ED25EB36", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2016", "Infant", "A", "1" ]
, [ "row-84pz_tha3~5v69", "00000000-0000-0000-5CB0-EB47A4CECC8B", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2017", "Infant", "A", "5" ]
, [ "row-tuzz.j56a~9zss", "00000000-0000-0000-1DCD-59BD50A8712D", 0, 1558625993, null, 1558625993, null, "{ }", "Washington", "2017", "Wound", "A", "1" ]
, [ "row-svgv~6hvx-r737", "00000000-0000-0000-03DB-8F6416DEC1E4", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1919", "Foodborne", "Unknown", "3" ]
, [ "row-sm57~psjp-yvxi", "00000000-0000-0000-05A3-3C631D9FA792", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1929", "Foodborne", "Unknown", "2" ]
, [ "row-udxy.4xsb-gf87", "00000000-0000-0000-6A06-DAFC6F3CF634", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1939", "Foodborne", "Unknown", "1" ]
, [ "row-t9hs~7zur-bi6e", "00000000-0000-0000-55F4-3F698F7AC677", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1976", "Foodborne", "A", "1" ]
, [ "row-j4px.sknm_ry78", "00000000-0000-0000-0754-B4F4B14EAA21", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1977", "Infant", "B", "1" ]
, [ "row-t5fg_5x85.czf2", "00000000-0000-0000-B314-35C66FFAE6BA", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1978", "Foodborne", "B", "1" ]
, [ "row-r6ma-adzk.g3hc", "00000000-0000-0000-3E75-2261673C3165", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1980", "Foodborne", "A", "2" ]
, [ "row-2678-ke2u~paer", "00000000-0000-0000-5ADA-7E61F3205640", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1981", "Infant", "A", "1" ]
, [ "row-u9tt-pap7-wigg", "00000000-0000-0000-ACEE-0F72C15903AF", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1982", "Foodborne", "A", "1" ]
, [ "row-u8nx.7k7i.j7e2", "00000000-0000-0000-FBE6-C9B4F5419EC2", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1984", "Foodborne", "Unknown", "1" ]
, [ "row-zytf-u9nf_tx2h", "00000000-0000-0000-4989-F29144687135", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1987", "Foodborne", "A", "1" ]
, [ "row-kmu4.93qb.pbhj", "00000000-0000-0000-1528-58811327D442", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1989", "Infant", "F", "1" ]
, [ "row-dd6b_7kby.7553", "00000000-0000-0000-D243-9FB67E3AAFFA", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1991", "Foodborne", "B", "1" ]
, [ "row-xwqz_uq2a~mgz9", "00000000-0000-0000-3F9F-652090A60359", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1995", "Infant", "B", "1" ]
, [ "row-ihzf_paeg~hsiy", "00000000-0000-0000-97AB-ED013B83E68E", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1997", "Infant", "A", "2" ]
, [ "row-viq8-ng9d.ywrq", "00000000-0000-0000-DC01-F1631D5F692C", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1997", "Infant", "B", "1" ]
, [ "row-qnvz_99c9.ie8e", "00000000-0000-0000-43B2-E1557A595E42", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1998", "Infant", "B", "1" ]
, [ "row-p6x8_2hwm.td7b", "00000000-0000-0000-6042-58F1AA50EFAC", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1999", "Infant", "A", "1" ]
, [ "row-fuay-n4nq_gkbu", "00000000-0000-0000-184B-5150941BF63D", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "2000", "Other", "A", "1" ]
, [ "row-xg25-pndj_5y9t", "00000000-0000-0000-FC40-D21EE2D3CF0E", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "2007", "Foodborne", "A", "1" ]
, [ "row-n993_xbbu~gj9z", "00000000-0000-0000-0399-46EC932CB96E", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "2009", "Infant", "B", "1" ]
, [ "row-b9hs_2y8s.rwvb", "00000000-0000-0000-7529-6E91D7CF875F", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "2014", "Infant", "B", "1" ]
, [ "row-9xwz.dmjg_zs2g", "00000000-0000-0000-6DEF-D79758327F89", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1940", "Foodborne", "Unknown", "3" ]
, [ "row-sya8~rs8q-4vnb", "00000000-0000-0000-6505-A69B7003F2CF", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1963", "Foodborne", "B", "1" ]
, [ "row-493t.jibj-gygh", "00000000-0000-0000-C387-13E9393E951E", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1972", "Wound", "Unknown", "1" ]
, [ "row-f544~xk44_hw9f", "00000000-0000-0000-F996-E7382F860FAB", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1973", "Foodborne", "B", "6" ]
, [ "row-ni6v_cv39.8qrx", "00000000-0000-0000-731D-7AA4AFFB127B", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1981", "Infant", "B", "2" ]
, [ "row-9xbn.7cvj.54z5", "00000000-0000-0000-068F-C9BF65D67112", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1982", "Foodborne", "B", "1" ]
, [ "row-8p49.dbwm_7skg", "00000000-0000-0000-0838-D08BD6E4EBE6", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1984", "Infant", "B", "1" ]
, [ "row-q7ja-m5mh.ibve", "00000000-0000-0000-704D-79842FE64BE5", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1991", "Infant", "B", "1" ]
, [ "row-bdiy~9fdf_irrc", "00000000-0000-0000-D752-DD33D89C2272", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1997", "Infant", "A", "1" ]
, [ "row-ixvk-ugpp~xrfa", "00000000-0000-0000-8B80-DB85E30BE8A8", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1997", "Infant", "B", "1" ]
, [ "row-5vuf_7hkr.qwjb", "00000000-0000-0000-3556-5A8BB6437234", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2001", "Infant", "B", "1" ]
, [ "row-sr7r~3ix9~jwx3", "00000000-0000-0000-30CA-3E10A60B2F99", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2004", "Infant", "B", "2" ]
, [ "row-y7h8.vh7u_sjjp", "00000000-0000-0000-F507-767E6E78BCFC", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2006", "Infant", "B", "1" ]
, [ "row-c96k.fwak-vfnu", "00000000-0000-0000-728D-84DC85A27F60", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2007", "Infant", "A", "1" ]
, [ "row-k9p9~6wh6-j5zd", "00000000-0000-0000-8E21-A595C5AD6CC0", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2008", "Foodborne", "A", "1" ]
, [ "row-76f5_3etf.khmg", "00000000-0000-0000-1462-D40142340D7F", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2008", "Infant", "B", "1" ]
, [ "row-558f~3s3i~swew", "00000000-0000-0000-E71F-33D4FDAA436F", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2010", "Infant", "A", "1" ]
, [ "row-mxfh.ppdg-vqst", "00000000-0000-0000-8ABD-CFF6870D1602", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2010", "Infant", "B", "2" ]
, [ "row-4a48.ukt4_5ehu", "00000000-0000-0000-8D12-70E61C2B39E6", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2013", "Infant", "B", "1" ]
, [ "row-h6e5-hkqw~a7y2", "00000000-0000-0000-A0BF-2920E6BB340F", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2015", "Infant", "B", "1" ]
, [ "row-8v3i_zz9a-dmbk", "00000000-0000-0000-87CB-DD6F71AE075F", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2016", "Infant", "B", "2" ]
, [ "row-54zi_677w_6t98", "00000000-0000-0000-D1B1-94A9AB56E07A", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1924", "Foodborne", "A", "7" ]
, [ "row-96xz~giwm-xcpi", "00000000-0000-0000-547C-DCFB7641E54C", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1925", "Foodborne", "B", "4" ]
, [ "row-j85n.4ndn-st8u", "00000000-0000-0000-A7FC-A7ED21594450", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1926", "Foodborne", "Unknown", "3" ]
, [ "row-st2q~s6bj~xw3g", "00000000-0000-0000-D0D9-6E96B9A33A13", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1929", "Foodborne", "A", "6" ]
, [ "row-bji5~d5nb_mpyy", "00000000-0000-0000-7376-EA9F60272A59", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1936", "Foodborne", "A", "3" ]
, [ "row-tgnk-jec8.g923", "00000000-0000-0000-2263-A3C45AE7DDDB", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1936", "Foodborne", "Unknown", "5" ]
, [ "row-p6i7_9ysn~3a5v", "00000000-0000-0000-D827-A236FE109FDC", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1975", "Foodborne", "A", "1" ]
, [ "row-gza9.k2vf_msna", "00000000-0000-0000-97DD-726E8DEDC90B", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1982", "Foodborne", "A", "1" ]
, [ "row-v3ft-5hun.a4wk", "00000000-0000-0000-9599-21AC1FD98D02", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1984", "Infant", "A", "1" ]
, [ "row-tfw9~r9kc~jump", "00000000-0000-0000-5130-3656E0E0CA2D", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1986", "Wound", "Unknown", "1" ]
, [ "row-hmpb-ejpu_mkkh", "00000000-0000-0000-1840-23D8F330B9C2", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1990", "Foodborne", "A", "1" ]
, [ "row-zkuq.khjr_8tm3", "00000000-0000-0000-1B1B-344F55CD96E4", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2006", "Infant", "A", "1" ]
, [ "row-kp45-p65a_pk5a", "00000000-0000-0000-3E10-37DFCBF93812", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2008", "Infant", "A", "1" ]
, [ "row-97dy.efpn_p399", "00000000-0000-0000-F31C-F9ACFDCAAE11", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2012", "Infant", "A", "2" ]
, [ "row-4jn5.zbyj_e7b5", "00000000-0000-0000-CFED-417272A70C53", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2015", "Infant", "A", "1" ]
, [ "row-ddyu_e8zf~iczt", "00000000-0000-0000-EDE1-D95C542445C9", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2016", "Infant", "A", "1" ]
]
}
Raw
infant_botulism.py
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as ani
from matplotlib.collections import PatchCollection
from mpl_toolkits.basemap import Basemap
from matplotlib.patches import Polygon
import json
COLOR_COUNT = 5
def divide_chunks(l, n):
# looping till length l
for i in range(0, len(l), n):
yield l[i:i + n]
# Get data from exported json from CDC site
# https://data.cdc.gov/Foodborne-Waterborne-and-Related-Diseases/Botulism/66i6-hisz/data
with open("".join("botulism.json")) as file:
json_data = json.load(file)
# Sort by year
json_data = sorted(json_data["data"], key=lambda k: k[9])
year_data = {}
counts = []
# Pull data to be worked
for row in json_data:
if row[10].lower() == "infant" and row[8] != "NA":
if not year_data.get(row[9]):
year_data[row[9]] = {}
year_data[row[9]].update({row[8]: int(row[12])})
else:
if year_data[row[9]].get(row[8]):
year_data[row[9]][row[8]] += int(row[12])
else:
year_data[row[9]].update({row[8]: int(row[12])})
# Find year range from data
years = [year for year in year_data.keys()]
first_last = years[::len(years)-1]
# Create figure
fig = plt.figure(figsize=(10, 12))
plt.suptitle("Infant Botulism Cases in the US from {}".format("-".join(first_last)), x=0.475,
size=25)
# Create subplots
map_ax = plt.subplot2grid((2, 3), (0, 0), colspan=3)
# Draw map before creating bargraph subplot
bmap = Basemap(llcrnrlon=-119,llcrnrlat=22,urcrnrlon=-64,urcrnrlat=49,
projection='lcc',lat_1=33,lat_2=45,lon_0=-95)
bmap.drawcoastlines()
# Load the shapefile, use the name 'states'
bmap.readshapefile('st99_d00', name='states', drawbounds=True)
# Create list of State names
state_names = []
for shape_dict in bmap.states_info:
state_names.append(shape_dict['NAME'])
# Set color map to red
patches = []
reds = plt.get_cmap('Reds', COLOR_COUNT)
# Work through data collect to create state polygon and red mappings
year_totals = {}
year_poly = {}
for year, data in year_data.items():
yearly_counts = []
year_poly.update({year: []})
for state, count in data.items():
seg = bmap.states[state_names.index(state)]
color = reds(float(count / (10 * COLOR_COUNT)))
poly = Polygon(seg, facecolor=color, edgecolor=color)
patches.append(poly)
counts.append(count)
yearly_counts.append(count)
year_poly[year].append({"state": state,
"count": count,
"poly": poly,
"color": color})
year_totals[year] = sum(yearly_counts)
# Gether information for colorbar for map legend
clean_counts = list(set(counts))
count_max = clean_counts[-1]
clean_range = list(range(count_max))
range_array = np.array(clean_range)
# Compute the indices to split on for colorbar for map legend
splits = np.array_split(range_array, COLOR_COUNT)
clean_labels = ["> {}".format(splits[0][-1])]
for chunk in splits[1:-1]:
clean_labels.append("{}-{}".format(chunk[0], chunk[-1]))
clean_labels.append("< {}".format(splits[-1][0]))
# Create colorbar for map legend
pathcollection = PatchCollection(patches, cmap=reds)
pathcollection.set_array(np.array(clean_counts))
pathcollection.set_clim(-0.5, COLOR_COUNT+0.5)
colorbar = fig.colorbar(pathcollection, ax=map_ax, orientation='vertical')
colorbar.set_ticks(np.linspace(0, COLOR_COUNT, COLOR_COUNT))
colorbar.set_ticklabels(range(COLOR_COUNT))
colorbar.ax.tick_params(labelsize=15)
colorbar.ax.set_yticklabels(clean_labels)
map_ax.set_aspect('auto')
# Create bar chart for top states
bar_ax = plt.subplot2grid((2, 3), (1, 0))
bar_ax.set_xlim(0, count_max + 5)
# Create line graph for yearly occurrences
line_ax = plt.subplot2grid((2, 3), (1, 1), colspan=2)
xlim = [int(x) for x in first_last]
ylim = [0, max(year_totals.values())]
xlim[1] += 2
ylim[1] += 5
year_dates = [int(year)for year in years]
line_ax.set_xticks(year_dates)
# Create writer for creating gif
ImageWriter = ani.writers['imagemagick']
metadata = dict(title='Ani CDC Infant Botulism', artist='Matplotlib',
comment='Gif support!')
writer = ImageWriter(fps=1, metadata=metadata)
counts_lst = []
years_lst = []
# Start writing
with writer.saving(fig, 'infant_botulism_results.gif', 60):
for year, data in year_poly.items():
state_totals = {}
state_colors = {}
# Update states map
for d in data:
map_ax.add_patch(d["poly"])
state_totals.update({d["state"]: d["count"]})
state_colors.update({d["state"]: d["color"]})
# Find top 3 states with most cases
top_counts = sorted(state_totals.items(), key=lambda kv: kv[1], reverse=True)
top_list = list(top_counts)[:3]
top_counts = []
top_states = []
top_colors = []
for state, count in top_list:
top_states.append(state)
top_counts.append(count)
top_colors.append(state_colors.get(state))
x_pos = list(reversed([i for i, _ in enumerate(top_states)]))
# Clear bar chart each year and create
bar_ax.cla()
bar_ax.barh(x_pos, count_max, align='center', color="white", edgecolor="white", height=0.9)
rects = bar_ax.barh(x_pos, top_counts, align='center', color=top_colors, edgecolor="black")
bar_ax.set_yticklabels(top_states)
bar_ax.set_yticks(x_pos)
plt.cla()
year_total = sum(state_totals.values())
years_lst.append(int(year))
counts_lst.append(year_total)
# Plot to line graph
line_ax.plot(years_lst, counts_lst, color="r")
line_ax.set_xlim(xlim)
line_ax.set_ylim(ylim)
# Set updating yearly totals
bar_ax.set_title('Top 3 States', size=20, loc='left')
line_ax.set_title("{} Total: {}".format(year, year_total), size=20, loc='left')
# plt.show()
writer.grab_frame()
writer.grab_frame()
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