RLE plots are simple and intuitive, for each expression value $y_{ij}$ we plot $y_{ij}-Median(y_{.j})$ where $y_{.j}$ represents the column $j$ of a $m \times n$ expression matrix of $m$ samples and $n$ genes.

Simulation strategy presented here is as in the original publication

In [1]:
%matplotlib inline
import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np
import scipy as sp
import pandas as pd
sns.set_style('whitegrid')
In [2]:
np.random.seed(42)
m = 30
n = 10000
m_u = 5
s2_u = 0.5
s2_0 = 0.5
alpha = 10
beta = 1
\begin{align*} y_{ij} &= \mu_j + \theta_i + \gamma_{ij} + \epsilon_{ij}\\ \mu_j &\sim N(m_\mu, s^2_\mu)\\ \theta_i &\sim N(m_\theta, s^2_\theta)\\ \gamma_{ij} &= \lambda (\theta_i-\bar{\theta})(\mu_j-\bar{\mu})\\ \epsilon_{ij} &= N(0, \sigma_j^2)\\ 1/\sigma^2_j &\sim Gamma(\alpha, \beta)\\ m_\mu &= 5\\ s^2_\mu &= 0.5\\ s^2_\theta &= 0.5\\ \end{align*}

Additive Effects only ($m_\theta=0, \lambda=0$)

In [12]:
# m (samples) rows, n (genes) cols
m_0 = 0
mu = np.random.normal(m_u, np.sqrt(s2_u), n)
theta = np.random.normal(m_0, np.sqrt(s2_0), m)

eps_sigma2 = 1/np.random.gamma(alpha, beta, (m,n))
epsilon = np.random.normal(0, np.sqrt(eps_sigma2))

theta_M = np.tile(theta, (n,1)).T
mu_M = np.tile(mu, (m,1))

Y = mu_M + theta_M + epsilon

df = pd.DataFrame(Y.T)
df.columns = map(lambda x: str(x), range(1, m+1))
df_median = df.sub(df.median(axis=1), axis=0)
In [13]:
fig = plt.figure(figsize=(25,8))
ax = plt.subplot(1, 2, 1)
sns.boxplot(data=df, color='#3498db', ax=ax)    
sns.despine(offset=10, trim=True)
ax.set_title('Additive Effects only ($m_{\\theta}=0, \lambda=0$) | Box')

ax = plt.subplot(1, 2, 2)
sns.boxplot(data=df_median, color='#3498db', ax=ax)    
plt.axhline(y=0, color='black', linestyle='--')
sns.despine(offset=10, trim=True)
ax.set_title('Additive Effects only ($m_{\\theta}=0, \lambda=0$) | RLE')
Out[13]:
<matplotlib.text.Text at 0x7f86d47a4860>

Additive effects only, in two batches: $m_{\theta} = 0$ for $i \in [1, 25]$, $m_\theta = 2$ for $i \in [26, 30]$ and $\lambda = 0$

In [14]:
# m (samples) rows, n (genes) cols
m_0 = 0
np.random.seed(42)
mu = np.random.normal(m_u, np.sqrt(s2_u), n)
theta = np.random.normal(m_0, np.sqrt(s2_0), m-5)

m_0 = 2
theta = np.append(theta, np.random.normal(m_0, np.sqrt(s2_0), 5))


eps_sigma2 = 1/np.random.gamma(alpha, beta, (m,n))
epsilon = np.random.normal(0, np.sqrt(eps_sigma2))

theta_M = np.tile(theta, (n,1)).T
mu_M = np.tile(mu, (m,1))

Y = mu_M+theta_M+epsilon
df = pd.DataFrame(Y.T)
df.columns = map(lambda x: str(x), range(1, m+1))
df_median = df.sub(df.median(axis=1), axis=0)
In [15]:
fig = plt.figure(figsize=(25,8))
ax = plt.subplot(1, 2, 1)
sns.boxplot(data=df, color='#3498db', ax=ax)    
sns.despine(offset=10, trim=True)
ax.set_title('Additive effects only, in two batches: $m_{\\theta} = 0$ for $i \in [1, 25]$, $m_\\theta = 2$ for $i \\in [26, 30]$ and $\\lambda = 0$) | Box')
for i in range(m-5,m):
    x = ax.artists[i]
    x.set_color('#2ecc71')

ax = plt.subplot(1, 2, 2)
sns.boxplot(data=df_median, color='#3498db', ax=ax)    
plt.axhline(y=0, color='black', linestyle='--')
sns.despine(offset=10, trim=True)
ax.set_title('Additive effects only, in two batches: $m_{\\theta} = 0$ for $i \in [1, 25]$, $m_\\theta = 2$ for $i \\in [26, 30]$ and $\\lambda = 0$)  | RLE')
for i in range(m-5,m):
    x = ax.artists[i]
    x.set_color('#2ecc71')

Additive and non-additive effects: $m_\theta = 0$ and $\lambda = 1$

In [7]:
# m (samples) rows, n (genes) cols
m_0 = 0
np.random.seed(42)
mu = np.random.normal(m_u, np.sqrt(s2_u), n)
mu = mu[np.newaxis]
theta = np.random.normal(m_0, np.sqrt(s2_0), m)
theta = theta[np.newaxis]
lambda_l = 1
gamma = lambda_l*(theta-np.mean(theta)).T*(mu-np.mean(mu))


eps_sigma2 = 1/np.random.gamma(alpha, beta, (m,n))
epsilon = np.random.normal(0, np.sqrt(eps_sigma2))

theta_M = np.tile(theta, (n,1)).T
mu_M = np.tile(mu, (m,1))

Y = mu_M+theta_M+epsilon+gamma
df = pd.DataFrame(Y.T)
df.columns = map(lambda x: str(x), range(1, m+1))
df_median = df.sub(df.median(axis=1), axis=0)
In [8]:
fig = plt.figure(figsize=(25,8))
ax = plt.subplot(1, 2, 1)
sns.boxplot(data=df, color='#3498db', ax=ax)    
sns.despine(offset=10, trim=True)
ax.set_title('Additive and non-additive effects: $m_\\theta = 0$ and $\\lambda = 1$ | Box')

ax = plt.subplot(1, 2, 2)
sns.boxplot(data=df_median, color='#3498db', ax=ax)    
plt.axhline(y=0, color='black', linestyle='--')
sns.despine(offset=10, trim=True)
ax.set_title('Additive and non-additive effects: $m_\\theta = 0$ and $\\lambda = 1$ | RLE')
Out[8]:
<matplotlib.text.Text at 0x7fb205fef4e0>

Additive and non-additive effects, in two batches: $m_{\theta} = 0$ for $i \in [1, 25]$, $m_\theta = 2$ for $i \in [26, 30]$ and $\lambda = 1$

In [9]:
# m (samples) rows, n (genes) cols
m_0 = 0
np.random.seed(42)
mu = np.random.normal(m_u, np.sqrt(s2_u), n)
mu = mu[np.newaxis]
theta = np.random.normal(m_0, np.sqrt(s2_0), m-5)
theta = np.append(theta, np.random.normal(2, np.sqrt(s2_0), 5))
theta = theta[np.newaxis]

lambda_l = 1
gamma = lambda_l*(theta-np.mean(theta)).T*(mu-np.mean(mu))

eps_sigma2 = 1/np.random.gamma(alpha, beta, (m,n))
epsilon = np.random.normal(0, np.sqrt(eps_sigma2))

theta_M = np.tile(theta, (n,1)).T
mu_M = np.tile(mu, (m,1))

Y = mu_M+theta_M+epsilon+gamma
df = pd.DataFrame(Y.T)
df.columns = map(lambda x: str(x), range(1, m+1))
df_median = df.sub(df.median(axis=1), axis=0)
In [10]:
fig = plt.figure(figsize=(25,8))
ax = plt.subplot(1, 2, 1)
sns.boxplot(data=df, color='#3498db', ax=ax)    
sns.despine(offset=10, trim=True)
ax.set_title('Additive and non-additive effects, in two batches: $m_{\\theta} = 0$ for $i \in [1, 25]$, $m_\\theta = 2$ for $i \\in [26, 30]$ and $\\lambda = 1$) | Box')
for i in range(m-5,m):
    x = ax.artists[i]
    x.set_color('#2ecc71')

ax = plt.subplot(1, 2, 2)
sns.boxplot(data=df_median, color='#3498db', ax=ax)    
plt.axhline(y=0, color='black', linestyle='--')
sns.despine(offset=10, trim=True)
ax.set_title('Additive and non-additive effects, in two batches: $m_{\\theta} = 0$ for $i \in [1, 25]$, $m_\\theta = 2$ for $i \\in [26, 30]$ and $\\lambda = 1$)  | RLE')
for i in range(m-5,m):
    x = ax.artists[i]
    x.set_color('#2ecc71')