In ipython Notebook, first create a pandas Series object, then by calling the instance method .hist(), the browser displays the figure.
I am wondering how to save this figure to a file (I mean not by right click and save as, but the commands needed in the script).
Use the Figure.savefig() method, like so:
ax = s.hist() # s is an instance of Series
fig = ax.get_figure()
fig.savefig('/path/to/figure.pdf')
It doesn't have to end in pdf, there are many options. Check out the documentation.
Alternatively, you can use the pyplot interface and just call the savefig as a function to save the most recently created figure:
import matplotlib.pyplot as plt
s.hist()
plt.savefig('path/to/figure.pdf') # saves the current figure
Plots from multiple columns
Added from a comment toto_tico made on 2018-05-11
If you are getting this error AttributeError: 'numpy.ndarray' object has no attribute 'get_figure', then it is likely that you are plotting multiple columns.
In this case, ax will be an array of all the axes.
ax = s.hist(columns=['colA', 'colB'])
# try one of the following
fig = ax[0].get_figure()
fig = ax[0][0].get_figure()
fig.savefig('figure.pdf')
You can use ax.figure.savefig():
import pandas as pd
s = pd.Series([0, 1])
ax = s.plot.hist()
ax.figure.savefig('demo-file.pdf')
This has no practical benefit over ax.get_figure().savefig() as suggested in Philip Cloud's answer, so you can pick the option you find the most aesthetically pleasing. In fact, get_figure() simply returns self.figure:
# Source from snippet linked above
def get_figure(self):
"""Return the `.Figure` instance the artist belongs to."""
return self.figure
You can simply save your (e.g. histogram) plot like this:
df.plot.hist().get_figure().savefig('name')
Just wanted to add that the default resolution is 100dpi, which is fine for screen but won't work if you want to enlarge or print it. You can pass a 'dpi' parameter to get a high-resolution file:
ax = s.hist() # s is an instance of Series
ax.figure.savefig('/path/to/figure.png', dpi=300)
Related
I'm getting a bit confused around the concepts of axes, and frankly - what modifies what when it comes to the matplotlib backend. I was told in this post that "whenever you first do something that requires an axes object, one is created for you and becomes the default object that all of your future actions will be applied to until you change the current axes to something else."
But why is it, then, that figsize doesn't seem to do anything when I use the following code in the same cells in a Jupyter notebook:
dataset[['TV','radio']].plot()
plt.figure(figsize=(5,10))
and also
dataset.hist()
plt.figure(figsize=(10,20))
Why don't either of these work? How can I tell which axes object I'm referencing? Thanks so much
The problem is that plt.figure creates a new figure.
If you want to resize the existing figure use this:
dataset[['TV','radio']].plot()
fig = plt.gcf() # gcf: get current figure
fig.set_size_inches(5,10)
Another way you could do it -- that's illustrative of how axes get created and later used -- is to start off with the figure size like this:
import numpy as np, pandas as pd
df = pd.DataFrame({'x':[np.random.randint(0,10) for i in range(10)]})
fig = plt.figure(figsize=(5,5))
ax = fig.gca() # gca: get current axes
df.plot(ax=ax)
Result:
I am using a function which spits out a figure object of validation data. My script calculates a few model parameters that I would like to plot on top of this existing figure object. How can I do this? Whenever I try to plot my modeled data, it does so in a new window. Here's what my code looks like:
datafig = plotting_function(args) #Returning a figure object
datafig.show()
plt.plot([modeled_x],[modeled_y]) #Plotting in a new window
I've tried using plt.hold() / plt.hold(True) but this doesn't do anything. Any ideas?
Edit:
MCVE:
import matplotlib.pyplot as plt
def fig_create():
fig_1, ax_1 = plt.subplots()
ax_1.plot([0,1],[0,1])
fig_2, ax_2 = plt.subplots()
ax_2.plot([0,1],[0,5])
return fig_1, ax_1, fig_2, ax_2
figure_1, axes_1, figure_2, axes_2 = fig_create()
plt.close("all") # Spyder plots even without a plt.show(), so running the function generates figures. I'm closing them here.
figure_2.show()
plt.figure(2)
plt.plot([0,1],[0,10])
Result of the MCVE: https://i.imgur.com/FiCJX33.png
You need to specify which axis to plot on. plt.figure(2) will make a figure with a number of 2, regardless of whether an existing figure has that number or not! axes_2.plot(), however will plot whatever data you input directly onto axes_2 and whatever was there already. If it doesn't immediately show up you should add plt.draw() after the plot function.
Try not to mix plt, notation and ax notation as this will create confusion later on! If you are using fig and ax, stick with those!
You can specify which figure to plot to by calling plt.figure(my_figure_index) before any plt.plot (or any other plt plotting function) call.
For example:
plt.figure(10) # creates new figure if doesn't exist yet
plt.plot(...) # plots in figure 10
plt.figure(2) # creates new figure if doesn't exist yet
plt.plot(...) # plots in this figure 2
plt.figure(10) # figure already exists, just makes it the active one
plt.plot(...) # plots in figure 10 (in addition to already existing stuff)
In ipython Notebook, first create a pandas Series object, then by calling the instance method .hist(), the browser displays the figure.
I am wondering how to save this figure to a file (I mean not by right click and save as, but the commands needed in the script).
Use the Figure.savefig() method, like so:
ax = s.hist() # s is an instance of Series
fig = ax.get_figure()
fig.savefig('/path/to/figure.pdf')
It doesn't have to end in pdf, there are many options. Check out the documentation.
Alternatively, you can use the pyplot interface and just call the savefig as a function to save the most recently created figure:
import matplotlib.pyplot as plt
s.hist()
plt.savefig('path/to/figure.pdf') # saves the current figure
Plots from multiple columns
Added from a comment toto_tico made on 2018-05-11
If you are getting this error AttributeError: 'numpy.ndarray' object has no attribute 'get_figure', then it is likely that you are plotting multiple columns.
In this case, ax will be an array of all the axes.
ax = s.hist(columns=['colA', 'colB'])
# try one of the following
fig = ax[0].get_figure()
fig = ax[0][0].get_figure()
fig.savefig('figure.pdf')
You can use ax.figure.savefig():
import pandas as pd
s = pd.Series([0, 1])
ax = s.plot.hist()
ax.figure.savefig('demo-file.pdf')
This has no practical benefit over ax.get_figure().savefig() as suggested in Philip Cloud's answer, so you can pick the option you find the most aesthetically pleasing. In fact, get_figure() simply returns self.figure:
# Source from snippet linked above
def get_figure(self):
"""Return the `.Figure` instance the artist belongs to."""
return self.figure
You can simply save your (e.g. histogram) plot like this:
df.plot.hist().get_figure().savefig('name')
Just wanted to add that the default resolution is 100dpi, which is fine for screen but won't work if you want to enlarge or print it. You can pass a 'dpi' parameter to get a high-resolution file:
ax = s.hist() # s is an instance of Series
ax.figure.savefig('/path/to/figure.png', dpi=300)
Often, I create a figure that I'd like to use in a published article as well as on powerpoint slides. What looks good in print doesn't always look good on a slide. I'd like to create a matplotlib figure, save it, then update the font and line thicknesses and save again. How can I push updated rcParams to a figure that's been made?
For example:
import numpy as np
import matplotlib.pylab as plt
x = np.arange(100)/99.*4.*np.pi
y = np.sin(x)
plt.plot(x,y)
plt.xlabel('x')
plt.ylabel('y')
plt.title('Nice title')
plt.savefig('default.pdf')
update_rcParams(font=20, thick=5)
plt.savefig('publish.pdf')
update_rcParams(font=30, thick=10)
plt.savefig('slide.pdf')
What would that update_rcParams look like?
I don't think you'll be able to make sweeping changes like that, because rcParams is used to instantiate a bunch of objects (line objects, text objects, etc. which all come together to make the plot), and after they are created they don't care at all what rcParams is. You can, however, modify the objects themselves ... for example, to change the font size for the axis labels you can get the actual text objects and modify them.
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
xlbl = ax.set_xlabel('X axis label')
xlbl.set_fontsize(20)
plt.show()
Or, if you didn't save the individual object (i.e. you just called ax.set_xlabel() or plt.xlabel()), you can grab it from the Axes hierarchy:
ax = plt.gca() # gets the current Axes object
xlbl = ax.xaxis.get_label() # gets the Text object for the x axis label
For the sweeping changes you want, you'll need to write your own function that goes and modifies the items of interest. Hopefully this will get you going in the right direction.
Matplotlib offers these functions:
cla() # Clear axis
clf() # Clear figure
close() # Close a figure window
When should I use each function and what exactly does it do?
They all do different things, since matplotlib uses a hierarchical order in which a figure window contains a figure which may consist of many axes. Additionally, there are functions from the pyplot interface and there are methods on the Figure class. I will discuss both cases below.
pyplot interface
pyplot is a module that collects a couple of functions that allow matplotlib to be used in a functional manner. I here assume that pyplot has been imported as import matplotlib.pyplot as plt.
In this case, there are three different commands that remove stuff:
See matplotlib.pyplot Functions:
plt.cla() clears an axis, i.e. the currently active axis in the current figure. It leaves the other axes untouched.
plt.clf() clears the entire current figure with all its axes, but leaves the window opened, such that it may be reused for other plots.
plt.close() closes a window, which will be the current window, if not specified otherwise.
Which functions suits you best depends thus on your use-case.
The close() function furthermore allows one to specify which window should be closed. The argument can either be a number or name given to a window when it was created using figure(number_or_name) or it can be a figure instance fig obtained, i.e., usingfig = figure(). If no argument is given to close(), the currently active window will be closed. Furthermore, there is the syntax close('all'), which closes all figures.
methods of the Figure class
Additionally, the Figure class provides methods for clearing figures.
I'll assume in the following that fig is an instance of a Figure:
fig.clf() clears the entire figure. This call is equivalent to plt.clf() only if fig is the current figure.
fig.clear() is a synonym for fig.clf()
Note that even del fig will not close the associated figure window. As far as I know the only way to close a figure window is using plt.close(fig) as described above.
There is just a caveat that I discovered today.
If you have a function that is calling a plot a lot of times you better use plt.close(fig) instead of fig.clf() somehow the first does not accumulate in memory. In short if memory is a concern use plt.close(fig) (Although it seems that there are better ways, go to the end of this comment for relevant links).
So the the following script will produce an empty list:
for i in range(5):
fig = plot_figure()
plt.close(fig)
# This returns a list with all figure numbers available
print(plt.get_fignums())
Whereas this one will produce a list with five figures on it.
for i in range(5):
fig = plot_figure()
fig.clf()
# This returns a list with all figure numbers available
print(plt.get_fignums())
From the documentation above is not clear to me what is the difference between closing a figure and closing a window. Maybe that will clarify.
If you want to try a complete script there you have:
import numpy as np
import matplotlib.pyplot as plt
x = np.arange(1000)
y = np.sin(x)
for i in range(5):
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
ax.plot(x, y)
plt.close(fig)
print(plt.get_fignums())
for i in range(5):
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
ax.plot(x, y)
fig.clf()
print(plt.get_fignums())
If memory is a concern somebody already posted a work-around in SO see:
Create a figure that is reference counted
plt.cla() means clear current axis
plt.clf() means clear current figure
also, there's plt.gca() (get current axis) and plt.gcf() (get current figure)
Read more here: Matplotlib, Pyplot, Pylab etc: What's the difference between these and when to use each?