Python Plotting: Heatmap from dataframe with fixed colors in case of strings

Question

I'm trying to visualise a large (pandas) dataframe in Python as a heatmap. This dataframe has two types of variables: strings ("Absent" or "Unknown") and floats.

I want the heatmap to show cells with "Absent" in black and "Unknown" in red, and the rest of the dataframe as a normal heatmap, with the floats in a scale of greens.

I can do this easily in Excel with conditional formatting of cells, but I can't find any help online to do this with Python either with matplotlib, seaborn, ggplot. What am I missing?

Thank you for your time.

score 3 · Accepted Answer · edited May 23 '17 at 12:23

You could use cmap_custom.set_under('red') and cmap_custom.set_over('black') to apply custom colors to values below and above vmin and vmax (See 1, 2):

import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.axes_grid1 as axes_grid1
import pandas as pd

# make a random DataFrame
np.random.seed(1)
arr = np.random.choice(['Absent', 'Unknown']+list(range(10)), size=(5,7))
df = pd.DataFrame(arr)

# find the largest and smallest finite values
finite_values = pd.to_numeric(list(set(np.unique(df.values))
                                   .difference(['Absent', 'Unknown'])))
vmin, vmax = finite_values.min(), finite_values.max()

# change Absent and Unknown to numeric values
df2 = df.replace({'Absent': vmax+1, 'Unknown': vmin-1})
# make sure the values are numeric
for col in df2:
    df2[col] = pd.to_numeric(df2[col])

fig, ax = plt.subplots()
cmap_custom = plt.get_cmap('Greens')
cmap_custom.set_under('red')
cmap_custom.set_over('black')
im = plt.imshow(df2, interpolation='nearest', cmap = cmap_custom, 
           vmin=vmin, vmax=vmax)
# add a colorbar (https://stackoverflow.com/a/18195921/190597)
divider = axes_grid1.make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.05)
plt.colorbar(im, cax=cax, extend='both')
plt.show()

The DataFrame

In [117]: df
Out[117]: 
        0        1  2        3  4        5       6
0       3        9  6        7  9        3  Absent
1  Absent  Unknown  5        4  7        0       2
2       3        0  2        9  8        0       2
3       5        5  7  Unknown  5   Absent       4
4       7        7  5        4  7  Unknown  Absent

becomes

Thank you very much. Exactly what I needed, and worked out perfectly. — JRCX, Oct 17 '16 at 18:17

Python Plotting: Heatmap from dataframe with fixed colors in case of strings

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