I'm using matplotlib to plot data (using plot and errorbar functions) from Python. I have to plot a set of totally separate and independent plots, and then adjust their ylim values so they can be easily visually compared.
How can I retrieve the ylim values from each plot, so that I can take the min and max of the lower and upper ylim values, respectively, and adjust the plots so they can be visually compared?
Of course, I could just analyze the data and come up with my own custom ylim values... but I'd like to use matplotlib to do that for me. Any suggestions on how to easily (and efficiently) do this?
Here's my Python function that plots using matplotlib:
import matplotlib.pyplot as plt
def myplotfunction(title, values, errors, plot_file_name):
# plot errorbars
indices = range(0, len(values))
fig = plt.figure()
plt.errorbar(tuple(indices), tuple(values), tuple(errors), marker='.')
# axes
axes = plt.gca()
axes.set_xlim([-0.5, len(values) - 0.5])
axes.set_xlabel('My x-axis title')
axes.set_ylabel('My y-axis title')
# title
plt.title(title)
# save as file
plt.savefig(plot_file_name)
# close figure
plt.close(fig)
Just use axes.get_ylim(), it is very similar to set_ylim. From the docs:
get_ylim()
Get the y-axis range [bottom, top]
ymin, ymax = axes.get_ylim()
If you are using the plt api directly, you can avoid calls to axes altogether:
def myplotfunction(title, values, errors, plot_file_name):
# plot errorbars
indices = range(0, len(values))
fig = plt.figure()
plt.errorbar(tuple(indices), tuple(values), tuple(errors), marker='.')
plt.ylim([-0.5, len(values) - 0.5])
plt.xlabel('My x-axis title')
plt.ylabel('My y-axis title')
# title
plt.title(title)
# save as file
plt.savefig(plot_file_name)
# close figure
plt.close(fig)
Leveraging from the good answers above and assuming you were only using plt as in
import matplotlib.pyplot as plt
then you can get all four plot limits using plt.axis() as in the following example.
import matplotlib.pyplot as plt
x = [1, 2, 3, 4, 5, 6, 7, 8] # fake data
y = [1, 2, 3, 4, 3, 2, 5, 6]
plt.plot(x, y, 'k')
xmin, xmax, ymin, ymax = plt.axis()
s = 'xmin = ' + str(round(xmin, 2)) + ', ' + \
'xmax = ' + str(xmax) + '\n' + \
'ymin = ' + str(ymin) + ', ' + \
'ymax = ' + str(ymax) + ' '
plt.annotate(s, (1, 5))
plt.show()
The above code should produce the following output plot.
Just use plt.ylim(), it can be used to set or get the min and max limit
ymin, ymax = plt.ylim()
I put above-mentioned methods together using ax instead of plt
import numpy as np
import matplotlib.pyplot as plt
x = range(100)
y = x
fig, ax = plt.subplots(1, 1, figsize=(7.2, 7.2))
ax.plot(x, y);
# method 1
print(ax.get_xlim())
print(ax.get_xlim())
# method 2
print(ax.axis())
It's an old question, but I don't see mentioned that, depending on the details, the sharey option may be able to do all of this for you, instead of digging up axis limits, margins, etc. There's a demo in the docs that shows how to use sharex, but the same can be done with y-axes.
Related
I want to make this type of graph you see below.
I get that I can make a matrix graph with matplotlib
like so
cmap = colors.ListedColormap(['white','red'])
data = [
[0,0,0,0,0,1,1,1,1,],
[0,0,0,0,0,1,0,0,1,],
]
plt.figure(figsize=(9,5))
plt.pcolor(data[::-1],cmap=cmap,edgecolors='k', linewidths=3)
plt.xlabel('Problem')
plt.ylabel('Particpant')
plt.show()
But how would I go about adding percentages to be included in this graph?
You can add a secondary x-axis (ax.twiny()), using the top axis for the numbering and the bottom axis to show the percentages.
Calling pcolor with a list of x and y positions that are 0.5 shifted will put the ticks and tick labels at integer positions. clip_on=False makes sure the outer cell borders have the same thickness as the rest. ax.invert_yaxis() lets you invert the y axis (so you can use data instead of data[::-1]).
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
import numpy as np
cmap = ListedColormap(['white', 'orangered'])
data = np.random.randint(0, 3, size=(28, 30)) % 2
data[:, 9] = 1 # one full column to simulate 100%
data[:, 11] = 0 # one empty column to simulate 0%
fig, ax = plt.subplots(figsize=(9, 5))
ax.pcolor(np.arange(data.shape[1] + 1) + 0.5, np.arange(data.shape[0] + 1) + 0.5, data,
cmap=cmap, edgecolors='k', linewidths=3, clip_on=False)
ax.set_yticks(range(1, data.shape[0] + 1))
ax.set_xticks(range(1, data.shape[1] + 1))
ax.set_xticklabels([f'{p:.0f}' for p in data.mean(axis=0) * 100])
ax.invert_yaxis()
ax2 = ax.twiny()
ax2.set_xlim(ax.get_xlim())
ax2.set_xticks(range(1, data.shape[1] + 1))
ax2.set_xlabel('Problem')
ax.tick_params(length=0)
ax2.tick_params(length=0)
ax.set_ylabel('Particpant')
plt.tight_layout()
plt.show()
Decreasing the fontsize (or increasing the figsize) allows to also show the percentage sign:
ax.set_xticklabels([f'{p:.0f}%' for p in data.mean(axis=0) * 100], fontsize=8)
I am using matplotlib in Python and want to use the same plot but with several different axes that are all functions of the first one, but that do not linearly depend on the first y value.
As an example, let's assume a plot that shows a simple line y=x.
Now I have a random function like f(y)=5y^2 + 2.
My ideal output graph should now still be a line, but the equidistant ticks should not be y=1, 2, 3, 4, but f(y)=7, 22, 47, 82, so that I can overlay the two graphs with 2 different axes.
Is this even possible, as the distance between the ticks is not even nor can it be expressed in a log plot? Therefore I simply want to put a function on each tick value, without changing the graph nor the ticks' positions.
In a graphics program this would be straightforward, by simply using the same plot and manually rewriting each tick.
https://drive.google.com/file/d/1fp2vrFvlz-9xdJPmqdQjyMQK7gzPX24G/view?usp=sharing
Thank you in advance! The example code is not really helpful, as it is just the standard matplotlib code but the most important scaling part is missing.
I know that I can set the ticks manually with yticks, but this does not solve the scaling problem and all ticks would appear very close together.
plt.plot(["time_max_axis"], ["position_max_axis"])
plt.xlabel("Time (ms)")
plt.ylabel("Max position (mm)")
plt.ylim(0, z0_mm)
plt.show()
plt.plot(["time_max_axis"], ["frequency_axis"])
plt.xlabel("Oscillation frequency (kHz)")
plt.ylabel("Max position (mm)")
plt.ylim(fion_kHz, fion_kHz * (1 + (f_shift4 + f_shift6) / 100))
plt.show()
import matplotlib.pyplot as plt
from matplotlib.ticker import (MultipleLocator, AutoMinorLocator)
x = np.arange(50)
y = x/10 + np.random.rand(50)
fig, axs = plt.subplots(1,2, gridspec_kw={'width_ratios': [1, 20]})
plt.subplots_adjust(wspace=0, hspace=0)
axs[1].plot(x, y)
axs[1].plot(x, 2*y)
axs[1].plot(x, 3*y)
axs[1].grid()
axs[1].set_ylim(0)
axs[1].set_xlim(0)
axs[1].set_ylabel('max displacement $z_{max}$ (mm)')
ymin, ymax = axs[1].get_ylim()
majorlocator = ymax // 8 # 8 horizontal grid lines
ytickloc = np.arange(0, int(ymax), majorlocator)
axs[1].yaxis.set_major_locator(MultipleLocator(majorlocator))
ax1 = axs[1].twinx() # ghost axis of axs[1]
ax1.yaxis.set_ticks_position('left')
ax1.set_yticks([ymin, ymax])
ax1.set_yticklabels(['', f'$z_0$ = {round(ymax,2)}'])
axs[0].spines['top'].set_visible(False)
axs[0].spines['right'].set_visible(False)
axs[0].spines['bottom'].set_visible(False)
axs[0].spines['left'].set_visible(False)
axs[0].set_xticks([])
axs[0].set_yticks(ytickloc)
ytick2 = 5 * ytickloc**2 + 2 # f = 5y^2 + 2
ytick2 = list(ytick2)
ymin2 = ytick2[0]
ytick2[0] = ''
axs[0].set_yticklabels(ytick2)
axs[0].set_ylim(ymin, ymax)
axs[0].set_ylim(0)
axs[0].set_ylabel('Oscillation frequency $f_{osc}$ (kHz)')
ymax2 = 5 * ymax**2 + 2 # f = 5y^2 + 2
ax0 = axs[0].twinx() # ghost axis of axs[0]
ax0.yaxis.set_ticks_position('left')
ax0.spines['top'].set_visible(False)
ax0.spines['right'].set_visible(False)
ax0.spines['bottom'].set_visible(False)
ax0.spines['left'].set_visible(False)
ax0.set_yticks([ymin, ymax])
ax0.set_yticklabels([f'$\\bf{{f_{{ion}}}} = {round(ymin2, 2)}$', f'$f_{{max}}$ = {round(ymax2,2)}'])
plt.tight_layout()
Output:
Current version of matplotlib do not allow box-forced anymore, how should I do the same thing as the answer?
I am using matplotlib 3.1.0. After I ploted another set of data on the same plot with twinx() function, I want to change the aspect ratio of the actual plot area to 1.
Normally I do this and it works for non-twinx axis
ratio = 1
xleft, xright = ax.get_xlim()
ybottom, ytop = ax.get_ylim()
ax.set_aspect(abs((xright - xleft) / (ybottom - ytop)) * ratio)
For twinx axis, the above code do not work, but will not raise any error either.
Then I found an answer here
The code basically used the same method to set aspect ratio to 1, only with box-forced option.
import numpy as np
import matplotlib.pyplot as plt
x = np.linspace(0, 1.6, 50) + 50.0
fig, ax = plt.subplots()
ax2 = ax.twinx()
XLIM = [50.0, 51.6]
YLIM = [0.0, 1.1, 0.0, 11.0]
ax.plot(x, np.sin(x - 50.0), 'b')
ax2.plot(x, np.cos(x - 50.0) * 10., 'r')
# set aspect to 1
ax.set(adjustable='box-forced',
xlim=XLIM, ylim=YLIM[:2],
xticks=np.arange(XLIM[0], XLIM[1], 0.2),
yticks=np.arange(YLIM[0], YLIM[1] + 0.1, 0.1)[:-1],
aspect=(XLIM[1] - XLIM[0]) / (YLIM[1] - YLIM[0]))
ax2.set(adjustable='box-forced',
ylim=YLIM[2:],
yticks=np.arange(YLIM[2], YLIM[3] + 1.0, 1.0),
aspect=(XLIM[1] - XLIM[0]) / (YLIM[3] - YLIM[2]))
ax.grid(True, which='major', linestyle='solid')
plt.show()
This code in my python don't work, raises
ValueError: 'box-forced' is not a valid value for adjustable; supported values are 'box', 'datalim'
And if I change that to 'box', it gives
RuntimeError: Adjustable 'box' is not allowed in a twinned Axes. Use 'datalim' instead.
I am not sure from when the box-forced was removed.
Now how should we set the aspect ratio in a 'box' manner?
Thanks!
For reference: matplotlib.axes.Axes.set_adjustable
As I just commented on a respective matplotlib issue,
"aspect" in matplotlib always refers to the data, not the axes box. Therefore setting the aspect for twinned or shared axes and letting the box be adjustable actually only makes sense when the scales are the same - or differ by an offset (as opposed to any other linear or nonlinear function). Matplotlib does not perform any check on this, so it disallows for adjustable='box' in such case.
It seems to me that using aspect here is merely a workaround for getting a fixed ratio for the axes box. Matplotlib does not provide any clear codepath for that as of now, but one could e.g. force the axes box into a square space by adjusting the subplot parameters
import numpy as np
import matplotlib.pyplot as plt
def squarify(fig):
w, h = fig.get_size_inches()
if w > h:
t = fig.subplotpars.top
b = fig.subplotpars.bottom
axs = h*(t-b)
l = (1.-axs/w)/2
fig.subplots_adjust(left=l, right=1-l)
else:
t = fig.subplotpars.right
b = fig.subplotpars.left
axs = w*(t-b)
l = (1.-axs/h)/2
fig.subplots_adjust(bottom=l, top=1-l)
x = np.linspace(0,1.6,50) + 50.0
fig, ax = plt.subplots()
ax2 = ax.twinx()
ax.set(xlim = [50.0, 51.6], ylim = [0.0, 1.1])
ax2.set(ylim = [0.0, 11.0])
ax.plot(x,np.sin(x-50.0),'b')
ax2.plot(x,np.cos(x-50.0)*10.,'r')
ax.grid(True, which='major',linestyle='solid')
squarify(fig)
fig.canvas.mpl_connect("resize_event", lambda evt: squarify(fig))
plt.show()
Also see this answer for more than one subplot.
If you want to use mpl_toolkits and make your hands dirty, this answer would be a good read.
Thanks to #ImportanceOfBeingErnest, but to make this work in several subplots, I found another way inspired by your answer:
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import Divider, Size
from mpl_toolkits.axes_grid1.axes_divider import AxesDivider
def make_patch_spines_invisible(ax):
ax.set_frame_on(True)
ax.patch.set_visible(False)
for sp in ax.spines.values():
sp.set_visible(False)
def demo_fixed_size_axes():
fig, axs = plt.subplots(1, 2, figsize=(12, 9))
axs[0].plot([1, 2, 3])
axs[1].plot([1, 2, 3.5])
ax3 = axs[1].twinx()
ax3.plot([1, 2, 3], [1, 25, 30])
axs[1].spines['right'].set_visible(False)
make_patch_spines_invisible(ax4Alt)
ax4Alt.spines['right'].set_visible(True)
for ax in fig.get_axes():
figPos = AxesDivider(ax).get_position()
h = [Size.Fixed(4)] # has to be fixed
v = h
divider = Divider(fig, figPos, h, v, aspect=False)
ax.set_axes_locator(divider.new_locator(nx=0, ny=0))
if __name__ == "__main__":
demo_fixed_size_axes()
plt.show()
The disadvantage is that one has to decide which size to use in inches.
I do not fully understand my code though...
i'm plotting subplots in matplotlib/seaborn using:
plt.figure()
s1 = plt.subplot(2, 1, 1)
# plot 1
# call seaborn here
s2 = plt.subplot(2, 1, 2)
# plot 2
plt.tight_layout()
plt.show()
i am running into the common issue of marker being hidden by the axis (Add margin when plots run against the edge of the graph). when i try to adjust margins it doesn't work:
s1 = plt.subplot(2, 1, 1)
s1.margins(0.05)
it gives no error but doesn't set margins either.
here is a complete example:
gammas = sns.load_dataset("gammas")
s = plt.subplot(1, 1, 1)
# this does not change the x margins
s.get_axes().margins(x=0.05, y=0.01)
ax = sns.tsplot(time="timepoint", value="BOLD signal",
unit="subject", condition="ROI",
err_style="ci_bars",
interpolate=False,
data=gammas)
plt.show()
in the above, i am trying to make the x-margins bigger, but the x argument to margins() seems to have no effect. how can this be done?
You can define a function to add a given fraction of the x and y ranges to the margin, which makes use of get_xlim, get_ylim, set_xlim and set_ylim. Using your minimal example:
import matplotlib.pyplot as plt
import seaborn as sns
def add_margin(ax,x=0.05,y=0.05):
# This will, by default, add 5% to the x and y margins. You
# can customise this using the x and y arguments when you call it.
xlim = ax.get_xlim()
ylim = ax.get_ylim()
xmargin = (xlim[1]-xlim[0])*x
ymargin = (ylim[1]-ylim[0])*y
ax.set_xlim(xlim[0]-xmargin,xlim[1]+xmargin)
ax.set_ylim(ylim[0]-ymargin,ylim[1]+ymargin)
gammas = sns.load_dataset("gammas")
s = plt.subplot(1, 1, 1)
ax = sns.tsplot(time="timepoint", value="BOLD signal",
unit="subject", condition="ROI",
err_style="ci_bars",
interpolate=False,
data=gammas)
# Check what the original limits were
x0,y0=s.get_xlim(),s.get_ylim()
# Update the limits using set_xlim and set_ylim
add_margin(s,x=0.05,y=0.01) ### Call this after tsplot
# Check the new limits
x1,y1=s.get_xlim(),s.get_ylim()
# Print the old and new limits
print x0,y0
print x1,y1
plt.show()
Which prints:
# The original limits
(-0.10101010101010099, 10.1010101010101) (-2.0, 3.0)
# The updated limits
(-0.61111111111111105, 10.611111111111111) (-2.0499999999999998, 3.0499999999999998)
And here's the figure this produces:
Which, when compared to the original figure, clearly has added margins:
I've got a bunch of regularly distributed points (θ = n*π/6, r=1...8), each having a value in [0, 1]. I can plot them with their values in matplotlib using
polar(thetas, rs, c=values)
But rather then having just a meagre little dot I'd like to shade the corresponding 'cell' (ie. everything until halfway to the adjacent points) with the colour corresponding to the point's value:
(Note that here my values are just [0, .5, 1], in really they will be everything between 0 and 1. Is there any straight-forward way of realising this (or something close enough) with matplotlib? Maybe it's easier to think about it as a 2D-histogram?
This can be done quite nicely by treating it as a polar stacked barchart:
import matplotlib.pyplot as plt
import numpy as np
from random import choice
fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8], polar=True)
for i in xrange(12*8):
color = choice(['navy','maroon','lightgreen'])
ax.bar(i * 2 * np.pi / 12, 1, width=2 * np.pi / 12, bottom=i / 12,
color=color, edgecolor = color)
plt.ylim(0,10)
ax.set_yticks([])
plt.show()
Produces:
Sure! Just use pcolormesh on a polar axes.
E.g.
import matplotlib.pyplot as plt
import numpy as np
# Generate some data...
# Note that all of these are _2D_ arrays, so that we can use meshgrid
# You'll need to "grid" your data to use pcolormesh if it's un-ordered points
theta, r = np.mgrid[0:2*np.pi:20j, 0:1:10j]
z = np.random.random(theta.size).reshape(theta.shape)
fig, (ax1, ax2) = plt.subplots(ncols=2, subplot_kw=dict(projection='polar'))
ax1.scatter(theta.flatten(), r.flatten(), c=z.flatten())
ax1.set_title('Scattered Points')
ax2.pcolormesh(theta, r, z)
ax2.set_title('Cells')
for ax in [ax1, ax2]:
ax.set_ylim([0, 1])
ax.set_yticklabels([])
plt.show()
If your data isn't already on a regular grid, then you'll need to grid it to use pcolormesh.
It looks like it's on a regular grid from your plot, though. In that case, gridding it is quite simple. If it's already ordered, it may be as simple as calling reshape. Otherwise, a simple loop or exploiting numpy.histogram2d with your z values as weights will do what you need.
Well, it's fairly unpolished overall, but here's a version that rounds out the sections.
from matplotlib.pylab import *
ax = subplot(111, projection='polar')
# starts grid and colors
th = array([pi/6 * n for n in range(13)]) # so n = 0..12, allowing for full wrapping
r = array(range(9)) # r = 0..8
c = array([[random_integers(0, 10)/10 for y in range(th.size)] for x in range(r.size)])
# The smoothing
TH = cbook.simple_linear_interpolation(th, 10)
# Properly padding out C so the colors go with the right sectors (can't remember the proper word for such segments of wedges)
# A much more elegant version could probably be created using stuff from itertools or functools
C = zeros((r.size, TH.size))
oldfill = 0
TH_ = TH.tolist()
for i in range(th.size):
fillto = TH_.index(th[i])
for j, x in enumerate(c[:,i]):
C[j, oldfill:fillto].fill(x)
oldfill = fillto
# The plotting
th, r = meshgrid(TH, r)
ax.pcolormesh(th, r, C)
show()