introduction to biostatistics and bioinformatics exploring data and descriptive statistics

Introduction to Biostatistics and Bioinformatics

Exploring Data and Descriptive Statistics

Learning Objectives

Python matplotlib library to visualize data:• Scatter plot• Histogram• Kernel density estimate• Box plots

Descriptive statistics:• Mean and median• Standard deviation and inter quartile range• Central limit theorem

An Example Data Set

0.022-0.0830.048-0.010-0.1250.195-0.071-0.1470.0330.0800.0730.0160.1480.1350.006-0.0890.165-0.088-0.1370.094

Scatter Plot

0.022-0.0830.048-0.010-0.1250.195-0.071-0.1470.0330.0800.0730.0160.1480.1350.006-0.0890.165-0.088-0.1370.094

Order or Measurement

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Histogram


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Measurement Measurement Measurement

Bin size = 0.1 Bin size = 0.05 Bin size = 0.025

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Cumulative Distributions


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Kernel Density Estimate


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Original Distribution


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Histogram

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Exercise 1

Download ibb2015_7_exercise1.py

(a) Draw 20 points from a normal distribution with mean=0 and standard deviation=0.1.

import numpy as np

y=0.1*np.random.normal(size=20)print y

[-0.09946073 -0.19612617 0.03442682 0.02622746 -0.28418124 -0.04245968 0.05922837 0.01199874 0.13454915 -0.07482707 -0.11688758 0.01714036 0.03280043 0.01356022 0.09128649 -0.18923468 0.14536047 -0.07764629 -0.0349553 0.04300367]

Exercise 1

(b) Make scatter plot of the 20 points.

import matplotlib.pyplot as plt

x=range(1,points+1)fig, (ax1) = plt.subplots(1,figsize=(6,6))ax1.scatter(x,y,color='red',lw=0,s=40)ax1.set_xlim([0,points+1])ax1.set_ylim([-1,1])fig.savefig('ibb2015_7_exercise1_scatter_points'+str(poi

nts)+'.png',dpi=300,bbox_inches='tight')plt.close(fig)

Exercise 1

(c) Plot histograms.

for bin in [20,40,80]:fig, (ax1) = plt.subplots(1,figsize=(6,6))

ax1.hist(y,bins=bin,histtype='step',color='black', range=[-1,1], lw=2, normed=True)ax1.set_xlim([-1,1])fig.savefig('ibb2015_7_exercise1_bin'+str(bin)+'_points'+str(points)+'.png',dpi=300,bbox_inches='tight')plt.close(fig)

Exercise 1

(d) Plot cumulative distribution.

y_cumulative=np.linspace(0,1,points)x_cumulative=np.sort(y)fig, (ax1) = plt.subplots(1,figsize=(6,6))ax1.plot(x_cumulative,y_cumulative,color='black', lw=2)ax1.set_xlim([-1,1])ax1.set_ylim([0,1])fig.savefig('ibb2015_7_exercise1_cumulative_points'+

str(points)+'.png',dpi=300,bbox_inches='tight')plt.close(fig)

Exercise 1

(e) Plot kernel density estimate.

import scipy.stats as stats

kde_points=1000kde_x = np.linspace(-1,1,kde_points)fig, (ax1) = plt.subplots(1,figsize=(6,6))kde_y=stats.gaussian_kde(y)ax1.plot(kde_x,kde_y(kde_x),color='black', lw=2)ax1.set_xlim([-1,1])fig.savefig('ibb2015_7_exercise1_kde_points'+str(points)

+'.png',dpi=300,bbox_inches='tight')plt.close(fig)

Comparing Measurements

Comparing Measurements – Cumulative distributions

Systematic Shifts

Exercise 2


(a) Generate 5 data sets with 20 data points each from normal distributions with means = 0, 0, 0.1, 0.5 and 0.3 and standard deviation=0.1.

y=[]for j in range(5):

y.append(0.1*np.random.normal(size=20))y[2]+=0.1y[3]+=0.5y[4]+=0.3print y

Exercise 2

(b) Make scatter plots for the 5 data sets.

sixcolors=['#D4C6DF','#8968AC','#3D6570','#91732B','#963725','#4D0132']

fig, (ax1) = plt.subplots(1,figsize=(6,6))for j in range(5):

ax1.scatter(np.linspace(j+1-0.2,j+1+0.2,20), y[j],color=sixcolors[6-(j+1)], lw=0, alpha=1)

ax1.set_xlim([0,6])ax1.set_ylim([-1,1])

fig.savefig('ibb2015_7_exercise2_scatter_sample'+str(20),dpi=300,bbox_inches='tight')

plt.close(fig)

Correlation Between Two Variables

Data Visualization

http://blogs.nature.com/methagora/2013/07/data-visualization-points-of-view.html

Process of Statistical Analysis

Population

Random Sample

Sample Statistics

Describe

MakeInferences

DistributionsComplex Normal Skewed Long tails

n=3

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Mean

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Normal Distribution

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Mode, Maximum and Minimum

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Median, Quartiles and Percentiles

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Percentiles

Median and Mean – Sample SizeComplex Normal Skewed Long tails

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Variance

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Inter Quartile Range and Standard Deviation

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Central Limit Theorem

The sum of a large number of values drawn from many distributions converge normal if:

• The values are drawn independently;• The values are from the one distribution; and • The distribution has to have a finite mean and

variance.

Uncertainty in Determining the MeanComplex Normal Skewed Long tails

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Exercise 3


(a) Generate skewed data sets.

sample_size=10x_test=np.random.uniform(-1.0,1.0,size=30*sample_size)y_test=np.random.uniform(0.0,1.0,size=30*sample_size)y_test2=skew(x_test,-0.1,0.2,10)y_test2/=max(y_test2)x_test2=x_test[y_test<y_test2]x_sample=x_test2[:sample_size]

1. Generate a pair of random numbers within the range.2. Assign them to x and y3. Keep x if the point (x,y) is within the distribution.4. Repeat 1-3 until the desired sample size is obtained.5. The values x obtained in this was will be distributed according to

the original distribution.

Exercise 3(b) Calculate the mean of samples drawn from the skewed data set and the

standard error of the mean, and plot the distribution of averages.

for repeat in range(1000):…average.append(np.mean(x_sample))

sem=np.std(average)fig, (ax1) = plt.subplots(1,figsize=(6,6))ax1.set_title('Sample size = '+str(sample_size)+', SEM = '

+str(sem))ax1.hist(average,bins=100,histtype='step',color='red',range=

[-0.5,0.5],normed=True,lw=2)ax1.set_xlim([-0.5,0.5])

Box Plot

M. Krzywinski & N. Altman, Visualizing samples with box plots, Nature Methods 11 (2014) 119

n=5

Box PlotsComplex Normal Skewed Long tails

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Box Plots with All the Data PointsComplex Normal Skewed Long tails

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Box Plots, Scatter Plots and Bar GraphsNormal Distribution

Error bars: standard deviation error bars: standard deviation

error bars: standard error error bars: standard error

Box Plots, Scatter Plots and Bar GraphsSkewed Distribution

Error bars: standard deviation error bars: standard deviation

error bars: standard errorerror bars: standard error

Exercise 4

Download ibb2015_7_exercise4.py and plot box plots for a skewed data set.

fig, (ax1) = plt.subplots(1,figsize=(6,6))ax1.scatter(np.linspace(1-0.1, 1+0.1,sample_size),

x_sample, facecolors='none', edgecolor=thiscolor, lw=1)

bp=ax1.boxplot(x_samples, notch=False, sym='')plt.setp(bp['boxes'], color=thiscolor, lw=2)plt.setp(bp['whiskers'], color=thiscolor, lw=2)plt.setp(bp['medians'], color='black', lw=2)plt.setp(bp['caps'], color=thiscolor, lw=2)plt.setp(bp['fliers'], color=thiscolor, marker='o', lw=0)

fig.savefig(…)

Descriptive Statistics - Summary

• Example distribution: • Normal distribution• Skewed distribution• Distribution with long tails• Complex distribution with several peaks

• Mean, median, quartiles, percentiles

• Variance, Standard deviation, Inter Quartile Range (IQR), error bars

• Box plots, bar graphs, and scatter plots

Descriptive Statistics – Recommended Reading

http://blogs.nature.com/methagora/2013/08/giving_statistics_the_attention_it_deserves.html

Homework

Plot the ratio of the standard error of the mean and the standard deviation as a function of sample size (use sample sizes of 3, 10, 30, 100, 300, 1000) for the skewed distribution in Exercise 3. Modify ibb2015_7_exercise3.py to generate this plot and email both the script and the plot.

Next Lecture: Sequence Alignment Concepts

introduction to biostatistics and bioinformatics exploring data and descriptive statistics

Documents

data order

points strpoints

exercise strpoints

stats kde

color lw

print y

dplot cumulative distribution

data sets