Python – How to convert numbers to a color scale in matplotlib

colorsmatplotlibpython

I'm making a bar plot and I want the colors of the bars to vary from red to blue according to a color gradient. I have a dimension of the data frame that tells me where on the red-blue scale each bar should be. My current method is to manually convert these values to RGB colors by linearly interpolating between the RGB red and blue colors but I want an automatic way of converting my numeric values to a color scale. I also need to be able to have a colorbar legend to help interpret it.

Best Answer

It's pretty straight forward to create a barchart and set the bar colors according to a value from the dataframe. A colormap and a normalization instance help converting the values to colors, which are understood by the color argument of matplotlib.Axes.bar. The colorbar is then created from a ScalarMappable using the same normalization and colormap as the bars.

import matplotlib.pyplot as plt
import matplotlib.colors
import numpy as np; np.random.seed(0)
import pandas as pd

x = np.arange(12)
y = np.random.rand(len(x))*51
c = np.random.rand(len(x))*3+1.5
df = pd.DataFrame({"x":x,"y":y,"c":c})

cmap = plt.cm.rainbow
norm = matplotlib.colors.Normalize(vmin=1.5, vmax=4.5)

fig, ax = plt.subplots()
ax.bar(df.x, df.y, color=cmap(norm(df.c.values)))
ax.set_xticks(df.x)

sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
sm.set_array([])  # only needed for matplotlib < 3.1
fig.colorbar(sm)

plt.show()

For using a custom colormap with bar plots see Barplot colored according a colormap?

Related Solutions

Python – How to safely create a nested directory in Python

On Python ≥ 3.5, use pathlib.Path.mkdir:

from pathlib import Path
Path("/my/directory").mkdir(parents=True, exist_ok=True)

For older versions of Python, I see two answers with good qualities, each with a small flaw, so I will give my take on it:

Try os.path.exists, and consider os.makedirs for the creation.

import os
if not os.path.exists(directory):
    os.makedirs(directory)

As noted in comments and elsewhere, there's a race condition – if the directory is created between the os.path.exists and the os.makedirs calls, the os.makedirs will fail with an OSError. Unfortunately, blanket-catching OSError and continuing is not foolproof, as it will ignore a failure to create the directory due to other factors, such as insufficient permissions, full disk, etc.

One option would be to trap the OSError and examine the embedded error code (see Is there a cross-platform way of getting information from Python’s OSError):

import os, errno

try:
    os.makedirs(directory)
except OSError as e:
    if e.errno != errno.EEXIST:
        raise

Alternatively, there could be a second os.path.exists, but suppose another created the directory after the first check, then removed it before the second one – we could still be fooled.

Depending on the application, the danger of concurrent operations may be more or less than the danger posed by other factors such as file permissions. The developer would have to know more about the particular application being developed and its expected environment before choosing an implementation.

Modern versions of Python improve this code quite a bit, both by exposing FileExistsError (in 3.3+)...

try:
    os.makedirs("path/to/directory")
except FileExistsError:
    # directory already exists
    pass

...and by allowing a keyword argument to os.makedirs called exist_ok (in 3.2+).

os.makedirs("path/to/directory", exist_ok=True)  # succeeds even if directory exists.

Python – How to remove a trailing newline

Try the method rstrip() (see doc Python 2 and Python 3)

>>> 'test string\n'.rstrip()
'test string'

Python's rstrip() method strips all kinds of trailing whitespace by default, not just one newline as Perl does with chomp.

>>> 'test string \n \r\n\n\r \n\n'.rstrip()
'test string'

To strip only newlines:

>>> 'test string \n \r\n\n\r \n\n'.rstrip('\n')
'test string \n \r\n\n\r '

In addition to rstrip(), there are also the methods strip() and lstrip(). Here is an example with the three of them:

>>> s = "   \n\r\n  \n  abc   def \n\r\n  \n  "
>>> s.strip()
'abc   def'
>>> s.lstrip()
'abc   def \n\r\n  \n  '
>>> s.rstrip()
'   \n\r\n  \n  abc   def'

Best Answer

Related Solutions

Python – How to safely create a nested directory in Python

Python – How to remove a trailing newline

Related Topic