Vertical line at the end of a CDF histogram using matplotlib
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I'm trying to create a CDF but at the end of the graph, there is a vertical line, shown below:
I've read that his is because matplotlib uses the end of the bins to draw the vertical lines, which makes sense, so I added into my code as:
bins = sorted(X) + [np.inf]
where X is the data set I'm using and set the bin size to this when plotting:
plt.hist(X, bins = bins, cumulative = True, histtype = 'step', color = 'b')
This does remove the line at the end and produce the desired effect, however when I normalise this graph now it produces an error:
ymin = max(ymin*0.9, minimum) if not input_empty else minimum UnboundLocalError: local variable 'ymin' referenced before assignment
Is there anyway to either normalise the data with
bins = sorted(X) + [np.inf]
in my code or is there another way to remove the line on the graph?
An alternative way to plot a CDF would be as follows (in my example,
X is a bunch of samples drawn from the unit normal):
import numpy as np import matplotlib.pyplot as plt X = np.random.randn(10000) n = np.arange(1,len(X)+1) / np.float(len(X)) Xs = np.sort(X) fig, ax = plt.subplots() ax.step(Xs,n)
Matplotlib cumulative histogram, If you do not set the bins parameter yourself, plt.hist will choose (by default, 10) bins for you: In : n, bins, patches = plt.hist(X, normed=False,� Using histograms to plot a cumulative distribution¶ This shows how to plot a cumulative, normalized histogram as a step function in order to visualize the empirical cumulative distribution function (CDF) of a sample. We also show the theoretical CDF. A couple of other options to the hist function are demonstrated.
I needed a solution where I would not need to alter the rest of my code (using
plt.hist(...) or, with pandas,
dataframe.plot.hist(...)) and that I could reuse easily many times in the same jupyter notebook.
I now use this little helper function to do so:
def fix_hist_step_vertical_line_at_end(ax): axpolygons = [poly for poly in ax.get_children() if isinstance(poly, mpl.patches.Polygon)] for poly in axpolygons: poly.set_xy(poly.get_xy()[:-1])
Which can be used like this (without pandas):
import numpy as np import matplotlib as mpl import matplotlib.pyplot as plt X = np.sort(np.random.randn(1000)) fig, ax = plt.subplots() plt.hist(X, bins=100, cumulative=True, density=True, histtype='step') fix_hist_step_vertical_line_at_end(ax)
Or like this (with pandas):
import numpy as np import pandas as pd import matplotlib as mpl import matplotlib.pyplot as plt df = pd.DataFrame(np.random.randn(1000)) fig, ax = plt.subplots() ax = df.plot.hist(ax=ax, bins=100, cumulative=True, density=True, histtype='step', legend=False) fix_hist_step_vertical_line_at_end(ax)
This works well even if you have multiple cumulative density histograms on the same axes.
Warning: this may not lead to the wanted results if your axes contain other patches falling under the
mpl.patches.Polygon category. That was not my case so I prefer using this little helper function in my plots.
Using histograms to plot a cumulative distribution — Matplotlib 3.1.0 , Conversely, setting, cumulative to -1 as is done in the last series for this example, creates a "exceedance" curve. Selecting different bin counts and sizes can� Parameters: x: scalar or 1D array_like. x-indexes where to plot the lines. ymin, ymax: scalar or 1D array_like. Respective beginning and end of each line. If scalars are provided, all lines will have same length.
Assuming that your intentions are pure aesthetic, add a vertical line, of the same color as your plot background:
ax.axvline(y = value, color = 'white', linewidth = 2)
Where "value" stands for the right extreme of the rightmost bin.
matplotlib.pyplot.hist — Matplotlib 3.1.0 documentation, matplotlib.pyplot. hist (x, bins=None, range=None, density=None, weights=None, cumulative=False, bottom=None, histtype='bar', align='mid', orientation='vertical', rwidth=None, log=False, color=None, With Numpy 1.11 or newer, you can alternatively provide a string describing a binning strategy, such as 'auto', 'sturges ',� At the end of this guide, I’ll show you another way to derive the bins. Step 4: Plot the histogram in Python using matplotlib. You’ll now be able to plot the histogram based on the template that you saw at the beginning of this guide: import matplotlib.pyplot as plt x = [value1, value2, value3,.] plt.hist(x, bins = number of bins) plt.show()
matplotlib.axes.Axes.hist — Matplotlib 3.3.0 documentation, Axes. hist (self, x, bins=None, range=None, density=False, weights=None, bottom=None, histtype='bar', align='mid', orientation='vertical', rwidth=None, log= False, or as a 2-D ndarray in which each column is a dataset. cumulativebool or -1, default: False If multiple data are given the bars are arranged side by side. You can use the plot or vlines to draw a vertical line, but to draw a vertical line from the bottom to the top of the y axis, axvline is the probably the simplest function to use.
python, i'm trying create cdf @ end of graph, there vertical line, shown below: plot. i've read because matplotlib uses end of bins draw vertical lines,� Bases: matplotlib.axes._base._AxesBase The Axes contains most of the figure elements: Axis , Tick , Line2D , Text , Polygon , etc., and sets the coordinate system. The Axes instance supports callbacks through a callbacks attribute which is a CallbackRegistry instance.
Python Histogram Plotting: NumPy, Matplotlib, Pandas & Seaborn , A histogram is a great tool for quickly assessing a probability distribution that is intuitively Building histograms in pure Python, without use of third party libraries def ascii_histogram(seq) -> None: """A horizontal frequency-table/ histogram plot. The last line contains some LaTex, which integrates nicely with Matplotlib. Plotting Histogram using only Matplotlib. Plotting histogram using matplotlib is a piece of cake. All you have to do is use plt.hist() function of matplotlib and pass in the data along with the number of bins and a few optional parameters. In plt.hist(), passing bins='auto' gives you the “ideal” number of bins. The idea is to select a bin
- Not sure why this got down-voted. This is an artifact of how hist + step works. You may be better off computing the cumulative histogram and then using
- Do you want a CDF or a histogram? If it's a CDF, which one?
- This is a brilliant and beautiful alternative!
- The problem that appears is that plot will be linearly interpolated inbetween dots, but the true cumulative function should have these "jumps".
- Yes, that's probably a fair point - although it won't make much difference for large samples of data. Nonetheless, I have updated my answer to use
- Thanks! That worked for me. I have a complementary CDF, so I just needed to change