init

README.md

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+### Assignment
+
+In this project, you will visualize and make calculations from medical examination data using matplotlib, seaborn, and pandas. The dataset values were collected during medical examinations.
+
+#### Data description
+
+The rows in the dataset represent patiets and the columns represent information like body measurements, results from various blood tests, and lifestyle choices. You will use the dataset to exploring the relationship between cardiac disease, body measurements, blood markers, and lifestyle choices.
+
+File name: medical_examination.csv
+
+| Feature | Variable Type | Variable      | Value Type |
+|:-------:|:------------:|:-------------:|:----------:|
+| Age | Objective Feature | age | int (days) |
+| Height | Objective Feature | height | int (cm) |
+| Weight | Objective Feature | weight | float (kg) |
+| Gender | Objective Feature | gender | categorical code |
+| Systolic blood pressure | Examination Feature | ap_hi | int |
+| Diastolic blood pressure | Examination Feature | ap_lo | int |
+| Cholesterol | Examination Feature | cholesterol | 1: normal, 2: above normal, 3: well above normal |
+| Glucose | Examination Feature | gluc | 1: normal, 2: above normal, 3: well above normal |
+| Smoking | Subjective Feature | smoke | binary |
+| Alcohol intake | Subjective Feature | alco | binary |
+| Physical activity | Subjective Feature | active | binary |
+| Presence or absence of cardiovascular disease | Target Variable | cardio | binary |
+
+#### Tasks
+
+Create a chart similar to `examples/Figure_1.png`, where we show the counts of good and bad outcomes for cholesterol, gluc, alco variable, active, and smoke for patients with cardio=1 and cardio=0 in different panels.
+
+Use the data to complete the following tasks in `medical_data_visualizer.py`:
+* Add an 'overweight' column to the data. To determine if a person is overweight, first calculate their BMI by dividing their weight in kilograms by the square of their height in meters. If that value is > 25 then the person is overweight. Use the value 0 for NOT overweight and the value 1 for overweight.
+* Normalize data by making 0 always good and 1 always bad. If the value of 'cholestorol' or 'gluc' is 1, make the value 0. If the value is more than 1, make the value 1.
+* Convert the data into long format and create a chart that shows the value counts of the categorical features using seaborn's `catplot()`. The dataset should be split by 'Cardio' so there is one chart for each 'cardio' value. The chart should look like "examples/Figure_1.png".
+* Clean the data. Filter out the following patient segments that represent incorrect data:
+  - diastolic pressure is higher then systolic (Keep the correct data with `df['ap_lo'] <= df['ap_hi'])`)
+  - height is less than the 2.5th percentile (Keep the correct data with `(df['height'] >= df['height'].quantile(0.025))`)
+  - height is more than the 97.5th percentile
+  - weight is less then the 2.5th percentile
+  - weight is more than the 97.5th percentile
+* Create a correlation matrix using the dataset. Plot the correlation matrix using seaborn's `heatmap()`. Mask the upper triangle. The chart should look like "examples/Figure_2.png".
+
+Any time a variable is set to 'None', make sure to set it to the correct code.
+
+Unit tests are written for you under `test_module.py`.
+
+### Development
+
+For development, you can use `main.py` to test your functions. Click the "run" button and `main.py` will run.
+
+### Testing 
+
+We imported the tests from `test_module.py` to `main.py` for your convenience. The tests will run automatically whenever you hit the "run" button.
+
+### Submitting
+
+Copy your project's URL and submit it to freeCodeCamp.

main.py

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+# This entrypoint file to be used in development. Start by reading README.md
+import medical_data_visualizer
+from unittest import main
+
+# Test your function by calling it here
+medical_data_visualizer.draw_cat_plot()
+medical_data_visualizer.draw_heat_map()
+
+# Run unit tests automatically
+main(module='test_module', exit=False)

medical_data_visualizer.py

@@ -0,0 +1,55 @@
+import pandas as pd
+import seaborn as sns
+import matplotlib.pyplot as plt
+import numpy as np
+
+# Import data
+df = None
+
+# Add 'overweight' column
+df['overweight'] = None
+
+# Normalize data by making 0 always good and 1 always bad. If the value of 'cholestorol' or 'gluc' is 1, make the value 0. If the value is more than 1, make the value 1.
+
+
+# Draw Categorical Plot
+def draw_cat_plot():
+    # Create DataFrame for cat plot using `pd.melt` using just the values from 'cholesterol', 'gluc', 'smoke', 'alco', 'active', and 'overweight'.
+    df_cat = None
+
+
+    # Group and reformat the data to split it by 'cardio'. Show the counts of each feature. You will have to rename one of the collumns for the catplot to work correctly.
+    df_cat = None
+
+    # Draw the catplot with 'sns.catplot()'
+
+
+
+    # Do not modify the next two lines
+    fig.savefig('catplot.png')
+    return fig
+
+
+# Draw Heat Map
+def draw_heat_map():
+    # Clean the data
+    df_heat = None
+
+    # Calculate the correlation matrix
+    corr = None
+
+    # Generate a mask for the upper triangle
+    mask = None
+
+
+
+    # Set up the matplotlib figure
+    fig, ax = None
+
+    # Draw the heatmap with 'sns.heatmap()'
+
+
+
+    # Do not modify the next two lines
+    fig.savefig('heatmap.png')
+    return fig

poetry.lock

@@ -0,0 +1,134 @@
+[[package]]
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+description = "Composable style cycles"
+name = "cycler"
+optional = false
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+[package.dependencies]
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+[[package]]
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+name = "kiwisolver"
+optional = false
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+[package.dependencies]
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+python-dateutil = ">=2.1"
+
+[[package]]
+category = "main"
+description = "NumPy is the fundamental package for array computing with Python."
+name = "numpy"
+optional = false
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+version = "1.17.4"
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+[[package]]
+category = "main"
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+version = "0.25.3"
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+[package.dependencies]
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+pytz = ">=2017.2"
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+[[package]]
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+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+version = "2.4.5"
+
+[[package]]
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+name = "python-dateutil"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+version = "2.8.1"
+
+[package.dependencies]
+six = ">=1.5"
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+[[package]]
+category = "main"
+description = "World timezone definitions, modern and historical"
+name = "pytz"
+optional = false
+python-versions = "*"
+version = "2019.3"
+
+[[package]]
+category = "main"
+description = "SciPy: Scientific Library for Python"
+name = "scipy"
+optional = false
+python-versions = ">=3.5"
+version = "1.3.3"
+
+[package.dependencies]
+numpy = ">=1.13.3"
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+[[package]]
+category = "main"
+description = "seaborn: statistical data visualization"
+name = "seaborn"
+optional = false
+python-versions = "*"
+version = "0.9.0"
+
+[package.dependencies]
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+scipy = ">=0.14.0"
+
+[[package]]
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+description = "Python 2 and 3 compatibility utilities"
+name = "six"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*"
+version = "1.13.0"
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+[metadata]
+content-hash = "4e8082311e9378f77d7a1accb8cd080faf04d14d5f7beba06a8e2f950698f9f3"
+python-versions = "^3.7"
+
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+python-dateutil = ["73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c", "75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a"]
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+seaborn = ["42e627b24e849c2d3bbfd059e00005f6afbc4a76e4895baf44ae23fe8a4b09a5", "76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f"]
+six = ["1f1b7d42e254082a9db6279deae68afb421ceba6158efa6131de7b3003ee93fd", "30f610279e8b2578cab6db20741130331735c781b56053c59c4076da27f06b66"]

pyproject.toml

@@ -0,0 +1,9 @@
+[tool]
+[tool.poetry]
+authors = ["Your Name <you@example.com>"]
+name = "root"
+version = "0.0.0"
+[tool.poetry.dependencies]
+pandas = "*"
+python = "^3.7"
+seaborn = "*"

test_module.py

@@ -0,0 +1,50 @@
+import unittest
+import medical_data_visualizer
+import matplotlib as mpl
+
+
+# the test case
+class CatPlotTestCase(unittest.TestCase):
+    def setUp(self):
+        self.fig = medical_data_visualizer.draw_cat_plot()
+        self.ax = self.fig.axes[0]
+    
+    def test_line_plot_labels(self):
+        actual = self.ax.get_xlabel()
+        expected = "variable"
+        self.assertEqual(actual, expected, "Expected line plot xlabel to be 'variable'")
+        actual = self.ax.get_ylabel()
+        expected = "total"
+        self.assertEqual(actual, expected, "Expected line plot ylabel to be 'total'")
+        actual = []
+        for label in self.ax.get_xaxis().get_majorticklabels():
+            actual.append(label.get_text())
+        expected = ['active', 'alco', 'cholesterol', 'gluc', 'overweight', 'smoke']
+        self.assertEqual(actual, expected, "Expected bar plot secondary x labels to be 'active', 'alco', 'cholesterol', 'gluc', 'overweight', 'smoke'")
+
+    def test_bar_plot_number_of_bars(self):
+        actual = len([rect for rect in self.ax.get_children() if isinstance(rect, mpl.patches.Rectangle)])
+        expected = 13
+        self.assertEqual(actual, expected, "Expected a different number of bars chart.")
+
+
+class HeatMapTestCase(unittest.TestCase):
+    def setUp(self):
+        self.fig = medical_data_visualizer.draw_heat_map()
+        self.ax = self.fig.axes[0]
+
+    def test_heat_map_labels(self):
+        actual = []
+        for label in self.ax.get_xticklabels():
+          actual.append(label.get_text())
+        expected = ['id', 'age', 'gender', 'height', 'weight', 'ap_hi', 'ap_lo', 'cholesterol', 'gluc', 'smoke', 'alco', 'active', 'cardio', 'overweight']
+        self.assertEqual(actual, expected, "Expected bar plot legend labels to be months of the year.")
+    
+    def test_heat_map_values(self):
+        actual = [text.get_text() for text in self.ax.get_default_bbox_extra_artists() if isinstance(text, mpl.text.Text)]
+        print(actual)
+        expected = ['0.0', '0.0', '-0.0', '0.0', '-0.1', '0.5', '0.0', '0.1', '0.1', '0.3', '0.0', '0.0', '0.0', '0.0', '0.0', '0.0', '0.2', '0.1', '0.0', '0.2', '0.1', '0.0', '0.1', '-0.0', '-0.1', '0.1', '0.0', '0.2', '0.0', '0.1', '-0.0', '-0.0', '0.1', '0.0', '0.1', '0.4', '-0.0', '-0.0', '0.3', '0.2', '0.1', '-0.0', '0.0', '0.0', '-0.0', '-0.0', '-0.0', '0.2', '0.1', '0.1', '0.0', '0.0', '0.0', '0.0', '0.3', '0.0', '-0.0', '0.0', '-0.0', '-0.0', '-0.0', '0.0', '0.0', '-0.0', '0.0', '0.0', '0.0', '0.2', '0.0', '-0.0', '0.2', '0.1', '0.3', '0.2', '0.1', '-0.0', '-0.0', '-0.0', '-0.0', '0.1', '-0.1', '-0.1', '0.7', '0.0', '0.2', '0.1', '0.1', '-0.0', '0.0', '-0.0', '0.1', '', '', '']
+        self.assertEqual(actual, expected, "Expected differnt values in heat map.")
+
+if __name__ == "__main__":
+    unittest.main()