How to create a density plot in matplotlib?


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In R I can create the desired output by doing:

data = c(rep(1.5, 7), rep(2.5, 2), rep(3.5, 8),
         rep(4.5, 3), rep(5.5, 1), rep(6.5, 8))
plot(density(data, bw=0.5))

Density plot in R

In python (with matplotlib) the closest I got was with a simple histogram:

import matplotlib.pyplot as plt
data = [1.5]*7 + [2.5]*2 + [3.5]*8 + [4.5]*3 + [5.5]*1 + [6.5]*8
plt.hist(data, bins=6)

Histogram in matplotlib

I also tried the normed=True parameter but couldn"t get anything other than trying to fit a gaussian to the histogram.

My latest attempts were around scipy.stats and gaussian_kde, following examples on the web, but I"ve been unsuccessful so far.

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How to create a density plot in matplotlib? around: Questions

Removing white space around a saved image in matplotlib

2 answers

I need to take an image and save it after some process. The figure looks fine when I display it, but after saving the figure, I got some white space around the saved image. I have tried the "tight" option for savefig method, did not work either. The code:

  import matplotlib.image as mpimg
  import matplotlib.pyplot as plt

  fig = plt.figure(1)
  img = mpimg.imread(path)

  extent = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted())
  plt.savefig("1.png", bbox_inches=extent)


I am trying to draw a basic graph by using NetworkX on a figure and save it. I realized that without a graph it works, but when added a graph I get white space around the saved image;

import matplotlib.image as mpimg
import matplotlib.pyplot as plt
import networkx as nx

G = nx.Graph()
pos = {1:[100,120], 2:[200,300], 3:[50,75]}

fig = plt.figure(1)
img = mpimg.imread("image.jpg")

nx.draw(G, pos=pos)

extent = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted())
plt.savefig("1.png", bbox_inches = extent)


Answer #1

You can remove the white space padding by setting bbox_inches="tight" in savefig:


You"ll have to put the argument to bbox_inches as a string, perhaps this is why it didn"t work earlier for you.

Possible duplicates:

Matplotlib plots: removing axis, legends and white spaces

How to set the margins for a matplotlib figure?

Reduce left and right margins in matplotlib plot


Answer #2

I cannot claim I know exactly why or how my “solution” works, but this is what I had to do when I wanted to plot the outline of a couple of aerofoil sections — without white margins — to a PDF file. (Note that I used matplotlib inside an IPython notebook, with the -pylab flag.)

plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0, 
            hspace = 0, wspace = 0)
plt.savefig("filename.pdf", bbox_inches = "tight",
    pad_inches = 0)

I have tried to deactivate different parts of this, but this always lead to a white margin somewhere. You may even have modify this to keep fat lines near the limits of the figure from being shaved by the lack of margins.


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