Hoffman Lab Tech Talk

1. Plotting heatmap with
matplotlib/seaborn
February 2nd 2022

2. Method 1: matplotlib (auto)
import numpy as np
import matplotlib.pyplot as plt
data = np.random.random(( 12 , 12 ))
plt.imshow( data , cmap = 'autumn',interpolation = 'nearest' )
plt.title( "2-D Heat Map" )
plt.show()
https://www.geeksforgeeks.org/how-to-draw-2d-heatmap-using-matplotlib-in-python/

3. Method 2: seaborn (auto)
import numpy as np; np.random.seed(0)
import seaborn as sns; sns.set_theme()
uniform_data = np.random.rand(10, 12)
ax = sns.heatmap(uniform_data)
https://seaborn.pydata.org/generated/seaborn.heatmap.html

4. Method 2: seaborn (auto + label)
flights = sns.load_dataset("flights")
flights = flights.pivot("month", "year", "passengers")
ax = sns.heatmap(flights)
https://seaborn.pydata.org/generated/seaborn.heatmap.html

5. Method 2: seaborn (auto + label + annotation)
flights = sns.load_dataset("flights")
ax = sns.heatmap(flights, annot=True, fmt="d")
ax = sns.heatmap(flights)
https://seaborn.pydata.org/generated/seaborn.heatmap.html

6. Method 2: Two heatmaps
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib import gridspec
fig = plt.figure(figsize=(12, 10), dpi=300)
gs = gridspec.GridSpec(1, 2, width_ratios=[3, 1])
ax0 = plt.subplot(gs[0])
ax0 = sns.heatmap(terms, cmap=cmap, cbar=False)
ax1 = plt.subplot(gs[1])
ax1 = sns.heatmap(ground_truth, cmap=cmap, yticklabels=False,
cbar_kws={'shrink': 2.0, 'label': 'Quantile of term'})

7. Method 3: matplotlib (manual)
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon, Rectangle
from matplotlib.collections import PatchCollection
fig, ax = plt.subplots()
patch1 = []
for y_corr in reversed(range(11)):
for x_corr in range(11):
patch1.append(Rectangle((x_corr,y_corr),1,1))
p = PatchCollection(patch1, cmap='RdYlBu', alpha=0.6)
p.set_edgecolor('black')
# map color
color = df.values.flatten()
p.set_array(np.array(color))
ax.add_collection(p)
…
ax.set_yticklabels(...)
ax.set_ylabel('Query extension (bp)')
…
col = plt.colorbar(p, cax = cax, format=ticker.FuncFormatter(fmt))
col.ax.set_ylabel("Geometric mean of q-value")
…
ax.add_patch(Rectangle((5, 4), 1, 1, fill=False, edgecolor='lawngreen', lw=3))
Heatmap
Label
Color bar
Highlight rectangle

8. Method3: Heatmap with two colors

9. Heatmap with two colors
from matplotlib.patches import Polygon, Rectangle
for y_corr in reversed(range(10)):
for x_corr in range(10):
index1 = [[x_corr, y_corr], [x_corr + 1, y_corr + 1], [x_corr, y_corr + 1]]
patch1.append(plt.Polygon(index1))

10. Heatmap with two colors
added manually !!!