matplotlib - how to draw a new plot in a loop in the same window - matplotlib

I use the below code. This comes up with three different windows. I would like the plot to show up in the same window. Any ideas?
Thanks
--
ps: clarification. I would like to see the curve of y[0] vs x[0] first then it erased and see y[1] vs x[1] and then it erased and see y[2] vs x[2]. Right now it is showing all three with three different colors. See second chunk of code.
--
import numpy
from matplotlib import pyplot as plt
x = [1, 2, 3]
plt.ion() # turn on interactive mode, non-blocking `show`
for loop in range(0,3):
y = numpy.dot(x, loop)
plt.figure() # create a new figure
plt.plot(x,y) # plot the figure
plt.show() # show the figure, non-blocking
_ = input("Press [enter] to continue.") # wait for input from the
import numpy
import matplotlib.pyplot as plt
%matplotlib notebook
x = [[1, 2, 3], [4,5,6], [7,8,9]]
y = [[1,4,9], [16,25,36], [49,64,81]]
fig, ax = plt.subplots()
plt.ion()
plt.show()
for i in range(3):
ax.plot(x[i],y[i]) # plot the figure
plt.gcf().canvas.draw()
_ = input("Press [enter] to continue.") # wait for input from the

This should help you with the problem. Notice the use of plt.show() outside the loop. plt.show() starts an event loop, checks for the currently active figure objects, and opens a display window.
import numpy
%matplotlib notebook
import matplotlib.pyplot as plt
x = [1, 2, 3]
fig, ax = plt.subplots()
plt.ion()
plt.show()
for loop in range(0,3):
y = numpy.dot(x, loop)
line,=ax.plot(x,y) # plot the figure
plt.gcf().canvas.draw()
line.remove()
del line
_ = input("Press [enter] to continue.") # wait for input from the

Related

Grid appears in TeX output after tikzplotlib save

I am using matplotlib with tikzplotlib to plot (PGF/TikZ) figures.
I do not want a grid to be plotted, however the grid is always activated in the TeX output.
How can I get around this?
I don't want to edit the .tex
if possible.
Bonus question: Is there also a way to get the legend title?
Example:
import numpy as np
import matplotlib.pyplot as plt
import tikzplotlib as tikz
x = np.arange(0, 5, 1)
y = x
fig, ax = plt.subplots()
ax.plot(x, y, label='asdf')
ax.grid(False)
ax.legend(title='asdf')
ax.set(xlabel='x',
ylabel='y')
plt.show()
tikz.clean_figure()
tikz.save("asdf.tex", figure=fig)
matplotlib plot (without grid)
tikzplotlib plot (grid activated)

Is there a way to make a plot clickable so it will tell me what EEG channel I am looking at?

Note: This is a question relating to mouse EEG data plotting.
I made a plot showing the averaged trial signals for filtered EEG electrode channels. While plotting this I saw a few signals that I want to exclude from my plot, but I don't have a way to tell what channels were plotted. Is there a way to add something that would allow me to click on or hover over one of the plotted lines/channels and have my jupyter notebook tell me what channel I clicked/am hovering over?
This is the plot I am hoping to make clickable:
Here is the code I used to make the plots if that's helpful:
pick_stim = 'opto'
pick_param = '500ms'
pick_sweep = 0
prex = .1 # .2ms before stim to plot
postx = .1 # .6ms after stim to plot
auc_window = [-.04, .1]
fig, axs = plt.subplots(1,2, figsize=(9,5), sharex=True, sharey=True, constrained_layout=True)
run_timex = trial_running[pick_stim][pick_param][pick_sweep][0]
run_trials = trial_running[pick_stim][pick_param][pick_sweep][1] #running speed
ztimex = zscore_traces[pick_stim][pick_param][pick_sweep][0] #need for AUC
zscore_trials_all = zscore_not_mean_traces[pick_stim][pick_param][pick_sweep][1]
# Run trials #
mean_run_zscore = np.mean(zscore_trials_all[:,:,run_trial], axis=2)
run_zscore_inds = np.nonzero((ztimex >= auc_window[0]) & (ztimex <= auc_window[1]))[0]
run_zscore_trace = mean_run_zscore[run_zscore_inds,:]
axs[0].plot(ztimex[run_zscore_inds],run_zscore_trace, color='black', linewidth=0.6, alpha=0.8)
#axs[0].plot(run_timex, run_trials, color='k', linewidth=0.6)
axs[0].axvspan(-.001, .001, color='r', alpha=0.5)
#axs[0].set_xlim([-prex, postx])
axs[0].set_title('Run trials')
# No Run #
mean_no_run_zscore = np.mean(zscore_trials_all[:,:,no_run], axis=2)
no_run_zscore_inds = np.nonzero((ztimex >= auc_window[0]) & (ztimex <= auc_window[1]))[0]
no_run_zscore_trace = mean_no_run_zscore[no_run_zscore_inds,:]
axs[1].plot(ztimex[no_run_zscore_inds],no_run_zscore_trace, color='black', linewidth=0.6, alpha=0.8)
axs[1].axvspan(-.001, .001, color='r', alpha=0.5)
axs[1].set_title('No Run trials')
You can add a label to each of the curves and then use mplcursors to show an annotation while hovering (or when clicking with hover=False).
Note that to have an interactive plot in a Jupyter notebook, %matplotlib notebook (this might depend on how Jupyter is installed) is needed instead of just %matplotlib inline (which generates static images). See Docs.
Here is an example showing the general idea with some test data:
%matplotlib notebook
import matplotlib.pyplot as plt
import numpy as np
import mplcursors
np.random.seed(123)
x = np.arange(100)
y = np.random.randn(100, 20).cumsum(axis=0)
fig, ax = plt.subplots()
curves = plt.plot(x, y, color='black', alpha=0.3)
for ind, curv in enumerate(curves):
curv.set_label(f'curve nÂș{ind}')
cursor = mplcursors.cursor(curves, hover=True)
cursor.connect('add', lambda sel: sel.annotation.set_text(sel.artist.get_label()))
plt.show()

How to have only 1 shared colorbar for multiple plots [duplicate]

I've spent entirely too long researching how to get two subplots to share the same y-axis with a single colorbar shared between the two in Matplotlib.
What was happening was that when I called the colorbar() function in either subplot1 or subplot2, it would autoscale the plot such that the colorbar plus the plot would fit inside the 'subplot' bounding box, causing the two side-by-side plots to be two very different sizes.
To get around this, I tried to create a third subplot which I then hacked to render no plot with just a colorbar present.
The only problem is, now the heights and widths of the two plots are uneven, and I can't figure out how to make it look okay.
Here is my code:
from __future__ import division
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import patches
from matplotlib.ticker import NullFormatter
# SIS Functions
TE = 1 # Einstein radius
g1 = lambda x,y: (TE/2) * (y**2-x**2)/((x**2+y**2)**(3/2))
g2 = lambda x,y: -1*TE*x*y / ((x**2+y**2)**(3/2))
kappa = lambda x,y: TE / (2*np.sqrt(x**2+y**2))
coords = np.linspace(-2,2,400)
X,Y = np.meshgrid(coords,coords)
g1out = g1(X,Y)
g2out = g2(X,Y)
kappaout = kappa(X,Y)
for i in range(len(coords)):
for j in range(len(coords)):
if np.sqrt(coords[i]**2+coords[j]**2) <= TE:
g1out[i][j]=0
g2out[i][j]=0
fig = plt.figure()
fig.subplots_adjust(wspace=0,hspace=0)
# subplot number 1
ax1 = fig.add_subplot(1,2,1,aspect='equal',xlim=[-2,2],ylim=[-2,2])
plt.title(r"$\gamma_{1}$",fontsize="18")
plt.xlabel(r"x ($\theta_{E}$)",fontsize="15")
plt.ylabel(r"y ($\theta_{E}$)",rotation='horizontal',fontsize="15")
plt.xticks([-2.0,-1.5,-1.0,-0.5,0,0.5,1.0,1.5])
plt.xticks([-2.0,-1.5,-1.0,-0.5,0,0.5,1.0,1.5])
plt.imshow(g1out,extent=(-2,2,-2,2))
plt.axhline(y=0,linewidth=2,color='k',linestyle="--")
plt.axvline(x=0,linewidth=2,color='k',linestyle="--")
e1 = patches.Ellipse((0,0),2,2,color='white')
ax1.add_patch(e1)
# subplot number 2
ax2 = fig.add_subplot(1,2,2,sharey=ax1,xlim=[-2,2],ylim=[-2,2])
plt.title(r"$\gamma_{2}$",fontsize="18")
plt.xlabel(r"x ($\theta_{E}$)",fontsize="15")
ax2.yaxis.set_major_formatter( NullFormatter() )
plt.axhline(y=0,linewidth=2,color='k',linestyle="--")
plt.axvline(x=0,linewidth=2,color='k',linestyle="--")
plt.imshow(g2out,extent=(-2,2,-2,2))
e2 = patches.Ellipse((0,0),2,2,color='white')
ax2.add_patch(e2)
# subplot for colorbar
ax3 = fig.add_subplot(1,1,1)
ax3.axis('off')
cbar = plt.colorbar(ax=ax2)
plt.show()
Just place the colorbar in its own axis and use subplots_adjust to make room for it.
As a quick example:
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=2, ncols=2)
for ax in axes.flat:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
fig.subplots_adjust(right=0.8)
cbar_ax = fig.add_axes([0.85, 0.15, 0.05, 0.7])
fig.colorbar(im, cax=cbar_ax)
plt.show()
Note that the color range will be set by the last image plotted (that gave rise to im) even if the range of values is set by vmin and vmax. If another plot has, for example, a higher max value, points with higher values than the max of im will show in uniform color.
You can simplify Joe Kington's code using the axparameter of figure.colorbar() with a list of axes.
From the documentation:
ax
None | parent axes object(s) from which space for a new colorbar axes will be stolen. If a list of axes is given they will all be resized to make room for the colorbar axes.
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=2, ncols=2)
for ax in axes.flat:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
fig.colorbar(im, ax=axes.ravel().tolist())
plt.show()
This solution does not require manual tweaking of axes locations or colorbar size, works with multi-row and single-row layouts, and works with tight_layout(). It is adapted from a gallery example, using ImageGrid from matplotlib's AxesGrid Toolbox.
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import ImageGrid
# Set up figure and image grid
fig = plt.figure(figsize=(9.75, 3))
grid = ImageGrid(fig, 111, # as in plt.subplot(111)
nrows_ncols=(1,3),
axes_pad=0.15,
share_all=True,
cbar_location="right",
cbar_mode="single",
cbar_size="7%",
cbar_pad=0.15,
)
# Add data to image grid
for ax in grid:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
# Colorbar
ax.cax.colorbar(im)
ax.cax.toggle_label(True)
#plt.tight_layout() # Works, but may still require rect paramater to keep colorbar labels visible
plt.show()
Using make_axes is even easier and gives a better result. It also provides possibilities to customise the positioning of the colorbar.
Also note the option of subplots to share x and y axes.
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
fig, axes = plt.subplots(nrows=2, ncols=2, sharex=True, sharey=True)
for ax in axes.flat:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
cax,kw = mpl.colorbar.make_axes([ax for ax in axes.flat])
plt.colorbar(im, cax=cax, **kw)
plt.show()
As a beginner who stumbled across this thread, I'd like to add a python-for-dummies adaptation of abevieiramota's very neat answer (because I'm at the level that I had to look up 'ravel' to work out what their code was doing):
import numpy as np
import matplotlib.pyplot as plt
fig, ((ax1,ax2,ax3),(ax4,ax5,ax6)) = plt.subplots(2,3)
axlist = [ax1,ax2,ax3,ax4,ax5,ax6]
first = ax1.imshow(np.random.random((10,10)), vmin=0, vmax=1)
third = ax3.imshow(np.random.random((12,12)), vmin=0, vmax=1)
fig.colorbar(first, ax=axlist)
plt.show()
Much less pythonic, much easier for noobs like me to see what's actually happening here.
Shared colormap and colorbar
This is for the more complex case where the values are not just between 0 and 1; the cmap needs to be shared instead of just using the last one.
import numpy as np
from matplotlib.colors import Normalize
import matplotlib.pyplot as plt
import matplotlib.cm as cm
fig, axes = plt.subplots(nrows=2, ncols=2)
cmap=cm.get_cmap('viridis')
normalizer=Normalize(0,4)
im=cm.ScalarMappable(norm=normalizer)
for i,ax in enumerate(axes.flat):
ax.imshow(i+np.random.random((10,10)),cmap=cmap,norm=normalizer)
ax.set_title(str(i))
fig.colorbar(im, ax=axes.ravel().tolist())
plt.show()
As pointed out in other answers, the idea is usually to define an axes for the colorbar to reside in. There are various ways of doing so; one that hasn't been mentionned yet would be to directly specify the colorbar axes at subplot creation with plt.subplots(). The advantage is that the axes position does not need to be manually set and in all cases with automatic aspect the colorbar will be exactly the same height as the subplots. Even in many cases where images are used the result will be satisfying as shown below.
When using plt.subplots(), the use of gridspec_kw argument allows to make the colorbar axes much smaller than the other axes.
fig, (ax, ax2, cax) = plt.subplots(ncols=3,figsize=(5.5,3),
gridspec_kw={"width_ratios":[1,1, 0.05]})
Example:
import matplotlib.pyplot as plt
import numpy as np; np.random.seed(1)
fig, (ax, ax2, cax) = plt.subplots(ncols=3,figsize=(5.5,3),
gridspec_kw={"width_ratios":[1,1, 0.05]})
fig.subplots_adjust(wspace=0.3)
im = ax.imshow(np.random.rand(11,8), vmin=0, vmax=1)
im2 = ax2.imshow(np.random.rand(11,8), vmin=0, vmax=1)
ax.set_ylabel("y label")
fig.colorbar(im, cax=cax)
plt.show()
This works well, if the plots' aspect is autoscaled or the images are shrunk due to their aspect in the width direction (as in the above). If, however, the images are wider then high, the result would look as follows, which might be undesired.
A solution to fix the colorbar height to the subplot height would be to use mpl_toolkits.axes_grid1.inset_locator.InsetPosition to set the colorbar axes relative to the image subplot axes.
import matplotlib.pyplot as plt
import numpy as np; np.random.seed(1)
from mpl_toolkits.axes_grid1.inset_locator import InsetPosition
fig, (ax, ax2, cax) = plt.subplots(ncols=3,figsize=(7,3),
gridspec_kw={"width_ratios":[1,1, 0.05]})
fig.subplots_adjust(wspace=0.3)
im = ax.imshow(np.random.rand(11,16), vmin=0, vmax=1)
im2 = ax2.imshow(np.random.rand(11,16), vmin=0, vmax=1)
ax.set_ylabel("y label")
ip = InsetPosition(ax2, [1.05,0,0.05,1])
cax.set_axes_locator(ip)
fig.colorbar(im, cax=cax, ax=[ax,ax2])
plt.show()
New in matplotlib 3.4.0
Shared colorbars can now be implemented using subfigures:
New Figure.subfigures and Figure.add_subfigure allow ... localized figure artists (e.g., colorbars and suptitles) that only pertain to each subfigure.
The matplotlib gallery includes demos on how to plot subfigures.
Here is a minimal example with 2 subfigures, each with a shared colorbar:
fig = plt.figure(constrained_layout=True)
(subfig_l, subfig_r) = fig.subfigures(nrows=1, ncols=2)
axes_l = subfig_l.subplots(nrows=1, ncols=2, sharey=True)
for ax in axes_l:
im = ax.imshow(np.random.random((10, 10)), vmin=0, vmax=1)
# shared colorbar for left subfigure
subfig_l.colorbar(im, ax=axes_l, location='bottom')
axes_r = subfig_r.subplots(nrows=3, ncols=1, sharex=True)
for ax in axes_r:
mesh = ax.pcolormesh(np.random.randn(30, 30), vmin=-2.5, vmax=2.5)
# shared colorbar for right subfigure
subfig_r.colorbar(mesh, ax=axes_r)
The solution of using a list of axes by abevieiramota works very well until you use only one row of images, as pointed out in the comments. Using a reasonable aspect ratio for figsize helps, but is still far from perfect. For example:
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(9.75, 3))
for ax in axes.flat:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
fig.colorbar(im, ax=axes.ravel().tolist())
plt.show()
The colorbar function provides the shrink parameter which is a scaling factor for the size of the colorbar axes. It does require some manual trial and error. For example:
fig.colorbar(im, ax=axes.ravel().tolist(), shrink=0.75)
To add to #abevieiramota's excellent answer, you can get the euqivalent of tight_layout with constrained_layout. You will still get large horizontal gaps if you use imshow instead of pcolormesh because of the 1:1 aspect ratio imposed by imshow.
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=2, ncols=2, constrained_layout=True)
for ax in axes.flat:
im = ax.pcolormesh(np.random.random((10,10)), vmin=0, vmax=1)
fig.colorbar(im, ax=axes.flat)
plt.show()
I noticed that almost every solution posted involved ax.imshow(im, ...) and did not normalize the colors displayed to the colorbar for the multiple subfigures. The im mappable is taken from the last instance, but what if the values of the multiple im-s are different? (I'm assuming these mappables are treated in the same way that the contour-sets and surface-sets are treated.) I have an example using a 3d surface plot below that creates two colorbars for a 2x2 subplot (one colorbar per one row). Although the question asks explicitly for a different arrangement, I think the example helps clarify some things. I haven't found a way to do this using plt.subplots(...) yet because of the 3D axes unfortunately.
If only I could position the colorbars in a better way... (There is probably a much better way to do this, but at least it should be not too difficult to follow.)
import matplotlib
from matplotlib import cm
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
cmap = 'plasma'
ncontours = 5
def get_data(row, col):
""" get X, Y, Z, and plot number of subplot
Z > 0 for top row, Z < 0 for bottom row """
if row == 0:
x = np.linspace(1, 10, 10, dtype=int)
X, Y = np.meshgrid(x, x)
Z = np.sqrt(X**2 + Y**2)
if col == 0:
pnum = 1
else:
pnum = 2
elif row == 1:
x = np.linspace(1, 10, 10, dtype=int)
X, Y = np.meshgrid(x, x)
Z = -np.sqrt(X**2 + Y**2)
if col == 0:
pnum = 3
else:
pnum = 4
print("\nPNUM: {}, Zmin = {}, Zmax = {}\n".format(pnum, np.min(Z), np.max(Z)))
return X, Y, Z, pnum
fig = plt.figure()
nrows, ncols = 2, 2
zz = []
axes = []
for row in range(nrows):
for col in range(ncols):
X, Y, Z, pnum = get_data(row, col)
ax = fig.add_subplot(nrows, ncols, pnum, projection='3d')
ax.set_title('row = {}, col = {}'.format(row, col))
fhandle = ax.plot_surface(X, Y, Z, cmap=cmap)
zz.append(Z)
axes.append(ax)
## get full range of Z data as flat list for top and bottom rows
zz_top = zz[0].reshape(-1).tolist() + zz[1].reshape(-1).tolist()
zz_btm = zz[2].reshape(-1).tolist() + zz[3].reshape(-1).tolist()
## get top and bottom axes
ax_top = [axes[0], axes[1]]
ax_btm = [axes[2], axes[3]]
## normalize colors to minimum and maximum values of dataset
norm_top = matplotlib.colors.Normalize(vmin=min(zz_top), vmax=max(zz_top))
norm_btm = matplotlib.colors.Normalize(vmin=min(zz_btm), vmax=max(zz_btm))
cmap = cm.get_cmap(cmap, ncontours) # number of colors on colorbar
mtop = cm.ScalarMappable(cmap=cmap, norm=norm_top)
mbtm = cm.ScalarMappable(cmap=cmap, norm=norm_btm)
for m in (mtop, mbtm):
m.set_array([])
# ## create cax to draw colorbar in
# cax_top = fig.add_axes([0.9, 0.55, 0.05, 0.4])
# cax_btm = fig.add_axes([0.9, 0.05, 0.05, 0.4])
cbar_top = fig.colorbar(mtop, ax=ax_top, orientation='vertical', shrink=0.75, pad=0.2) #, cax=cax_top)
cbar_top.set_ticks(np.linspace(min(zz_top), max(zz_top), ncontours))
cbar_btm = fig.colorbar(mbtm, ax=ax_btm, orientation='vertical', shrink=0.75, pad=0.2) #, cax=cax_btm)
cbar_btm.set_ticks(np.linspace(min(zz_btm), max(zz_btm), ncontours))
plt.show()
plt.close(fig)
## orientation of colorbar = 'horizontal' if done by column
This topic is well covered but I still would like to propose another approach in a slightly different philosophy.
It is a bit more complex to set-up but it allow (in my opinion) a bit more flexibility. For example, one can play with the respective ratios of each subplots / colorbar:
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.gridspec import GridSpec
# Define number of rows and columns you want in your figure
nrow = 2
ncol = 3
# Make a new figure
fig = plt.figure(constrained_layout=True)
# Design your figure properties
widths = [3,4,5,1]
gs = GridSpec(nrow, ncol + 1, figure=fig, width_ratios=widths)
# Fill your figure with desired plots
axes = []
for i in range(nrow):
for j in range(ncol):
axes.append(fig.add_subplot(gs[i, j]))
im = axes[-1].pcolormesh(np.random.random((10,10)))
# Shared colorbar
axes.append(fig.add_subplot(gs[:, ncol]))
fig.colorbar(im, cax=axes[-1])
plt.show()
The answers above are great, but most of them use the fig.colobar() method applied to a fig object. This example shows how to use the plt.colobar() function, applied directly to pyplot:
def shared_colorbar_example():
fig, axs = plt.subplots(nrows=3, ncols=3)
for ax in axs.flat:
plt.sca(ax)
color = np.random.random((10))
plt.scatter(range(10), range(10), c=color, cmap='viridis', vmin=0, vmax=1)
plt.colorbar(ax=axs.ravel().tolist(), shrink=0.6)
plt.show()
shared_colorbar_example()
Since most answers above demonstrated usage on 2D matrices, I went with a simple scatter plot. The shrink keyword is optional and resizes the colorbar.
If vmin and vmax are not specified this approach will automatically analyze all of the subplots for the minimum and maximum value to be used on the colorbar. The above approaches when using fig.colorbar(im) scan only the image passed as argument for min and max values of the colorbar.
Result:

updated graphs through iteration, matplotlib

I'm trying to graph features of a data-set one by one by, via iteration.
So I want the graph to continuously update as I proceed through the loop.
I refered to this thread,real-time plotting in while loop with matplotlib but the answers are all over the place, and despite incorporating some of their suggestions as shown below, I still can't seem to get the code working. I'm using Jupyter Notebook.
import matplotlib.pyplot as plt
%matplotlib inline
import numpy as np
colors = ["darkblue", "darkgreen"]
f, (ax1, ax2) = plt.subplots(1, 2, sharey=True, sharex = True)
for i in range(X.shape[-1]-1):
idx = np.where(y == 1)[0]
ax1.scatter(X[idx, i], X[idx, i+1], color=colors[0], label=1)
idx = np.where(y == 0)[0]
ax2.scatter(X[idx, i], X[idx, i+1], color=colors[1], label=0)
plt.draw()
plt.pause(0.0001)
Any suggestions?
Thank you.
This is an example for real-time plotting in a Jupyter Notebook
%matplotlib inline
%load_ext autoreload #Reload all modules every time before executing the Python code typed.
%autoreload 2
%matplotlib notebook
import matplotlib.pyplot as plt
import numpy as np
import time
colors = ["darkblue", "darkgreen"]
# initialise the graph and settings
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax2 = fig.add_subplot(211)
plt.ion() # interactive mode
fig.show()
fig.canvas.draw() # matplotlib canvas drawing
# plotting loop
for i in range(X.shape[-1]-1):
ax1.clear()
ax2.clear()
idx = np.where(y == 1)[0]
ax1.scatter(X[idx, i], X[idx, i+1], color=colors[0], label=1)
idx = np.where(y == 0)[0]
ax2.scatter(X[idx, i], X[idx, i+1], color=colors[1], label=0)
fig.canvas.draw() # draw
time.sleep(0.5) # sleep
For an animation you need an interactive backend. %matplotlib inline is no interactive backend (it essentially shows a printed version of the figure).
You may decide not to run you code in jupyter but as a script. In this case you would need to put plt.ion() to put interactive mode on.
Another option would be to use a FuncAnimation, as e.g in this example. To run such a FuncAnimation in Jupyter you will still need some interactive backend, either %matplotlib tk or %matplotlib notebook.
From matplotlib 2.1 on, we can also create an animation using JavaScript.
from IPython.display import HTML
HTML(ani.to_jshtml())
Some complete example:
import matplotlib.pyplot as plt
import matplotlib.animation
import numpy as np
t = np.linspace(0,2*np.pi)
x = np.sin(t)
fig, ax = plt.subplots()
ax.axis([0,2*np.pi,-1,1])
l, = ax.plot([],[])
def animate(i):
l.set_data(t[:i], x[:i])
ani = matplotlib.animation.FuncAnimation(fig, animate, frames=len(t))
from IPython.display import HTML
HTML(ani.to_jshtml())

How can I have each plot in matplotlib's `subplots` use a different axes?

So when I try to graph multiple subplots using pyplot.subplots I get something like:
How can I have:
Multiple independent axes for every subplot
Axes for every subplot
Overlay plots in every subplot axes using subplots. I tried to do ((ax1,ax2),(ax3,ax4)) = subplots and then do ax1.plot twice, but as a result, neither of the two showed.
Code for the picture:
import string
import matplotlib
matplotlib.use('WX')
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import numpy as np
from itertools import izip,chain
f,((ax1,ax2),(ax3,ax4)) = plt.subplots(2,2,sharex='col',sharey='row')
ax1.plot(range(10),2*np.arange(10))
ax2.plot(range(10),range(10))
ax3.plot(range(5),np.arange(5)*1000)
#pyplot.yscale('log')
#ax2.set_autoscaley_on(False)
#ax2.set_ylim([0,10])
plt.show()
Questions 1 & 2:
To accomplish this, explicitly set the subplots options sharex and sharey=False.
replace this line in the code for the desired results.
f, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2, sharex=False, sharey=False)
Alternatively, those two options can be omitted altogether, as False is the default. (as noted by rubenvb below)
Question 3:
Here are two examples of adding secondary plots to two of the subplots:
(add this snippet before plt.show())
# add an additional line to the lower left subplot
ax3.plot(range(5), -1*np.arange(5)*1000)
# add a bar chart to the upper right subplot
width = 0.75 # the width of the bars
x = np.arange(2, 10, 2)
y = [3, 7, 2, 9]
rects1 = ax2.bar(x, y, width, color='r')
Don't tell it to share axes:
f, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2)
ax1.plot(range(10),2*np.arange(10))
ax2.plot(range(10),range(10))
ax3.plot(range(5),np.arange(5)*1000)
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