Plot variant abundance vs. time (e,g, of mutant strains) in python

Question

Given [absolute] numbers for each of a number of variants over time, I would like to produce a plot like the following:

Is there a function for this in Python (preferably, but not necesarily, in matplotlib)? In general, do these sort of plots have a name? I had a hard time googling it even though Iv'e seen them many times in the past.

Answer 1

This type of plot is called a "time stack plot" matplotlib has a built in function for building time stack plots. The syntax is:

matplotlib.pyplot.stackplot(x, y1, y2, ..., yn, colors=None, ...)

In your case x would be time (e.g. in months), y1,...,yn would be the abundance of each strain, and colors denotes a color map for y1,...,yn. (There are other optional arguments as well.) Here is an example of use:

import matplotlib.pyplot as plt

days = [1,2,3,4,5]

sleep = [6,7,5,8,6]
eat =   [2,2,1,2,1]
work =  [5,7,10,8,6]
exercise=  [3,3,0,1,3]


plt.plot([],[],color='green', label='sleep', linewidth=3)
plt.plot([],[],color='blue', label='eat', linewidth=3)
plt.plot([],[],color='red', label='work', linewidth=3)
plt.plot([],[],color='black', label='play', linewidth=3)

plt.stackplot(days, sleep, eat, work, exercise, colors=['green','blue','red','black'])

plt.xlabel('days')
plt.ylabel('activities')
plt.title('5 DAY ROUTINE')
plt.legend()
plt.show()

Which produces this plot:

See this page for more info: https://www.educative.io/edpresso/how-to-create-a-stack-plot-using-matplotlib

Answer 2

Density Plot from seaborn package seems to be your case

import seaborn as sns
sns.kdeplot(...)

Stacked Chart from pygal

import pygal
pygal.StackedLine(...)

StackPlot from matplotlib

import matplotlib.pyplot as plt
plt.stackplot(...)