In Matplotlib I need to draw a graph with points on the x-axis on each integer between 1 and 5000 and on the y-axis only in a very limited range.
Matplotlib automatically compacts everything to let all the data fit on a (landscape) page. In my case I would like the x-axis to be as large as possible so that all points are clearly visible. Right now there's just a thick coloured line as opposed to scattered points.
How can I do this?
(I'm saving to pdf, if that helps)
You can always try to specify the dimensions (in inches) of the figure you are creating. Something along the following line might help:
fig = plt.figure(figsize=(20, 2))
ax = fig.add_subplot(111)
ax.plot(x, y)
The figsize takes a tuple of width, height in inches.
Related
I want to plot a graph with pyplot. The graph is quite big, so in order to not only see many overlapping dots indicating the nodes, I have to scale the output picture.
I used:
f,ax = plt.subplots(1,1)
ax.set_aspect('equal')
zoom=30
w, h = f.get_size_inches()
f.set_size_inches(w * zoom, h * zoom)
But now I have the problem, that I have big white spaces at the edges of the picture. There nothing is drawn and it is caused because the picture is much higher than wide.
How can I avoid this?
Instead of zooming a figure, you can use figsize argument to plt.subplots. You might also be interested in plt.tight_layout.
So you can do something like:
f,ax = plt.subplots(figsize=(10, 10)) # figure size in inches
ax.set_aspect('equal')
plt.tight_layout() # fill empty space
I also removed 1,1 from call to subplots as it's not necessary when you make only one plot.
I am starting to play around with creating polar plots in Matplotlib that do NOT encompass an entire circle - i.e. a "wedge" plot - by setting the thetamin and thetamax properties. This is something I was waiting for for a long time, and I am glad they have it done :)
However, I have noticed that the figure location inside the axes seem to change in a strange manner when using this feature; depending on the wedge angular aperture, it can be difficult to fine tune the figure so it looks nice.
Here's an example:
import numpy as np
import matplotlib.pyplot as plt
# get 4 polar axes in a row
fig, axes = plt.subplots(2, 2, subplot_kw={'projection': 'polar'},
figsize=(8, 8))
# set facecolor to better display the boundaries
# (as suggested by ImportanceOfBeingErnest)
fig.set_facecolor('paleturquoise')
for i, theta_max in enumerate([2*np.pi, np.pi, 2*np.pi/3, np.pi/3]):
# define theta vector with varying end point and some data to plot
theta = np.linspace(0, theta_max, 181)
data = (1/6)*np.abs(np.sin(3*theta)/np.sin(theta/2))
# set 'thetamin' and 'thetamax' according to data
axes[i//2, i%2].set_thetamin(0)
axes[i//2, i%2].set_thetamax(theta_max*180/np.pi)
# actually plot the data, fine tune radius limits and add labels
axes[i//2, i%2].plot(theta, data)
axes[i//2, i%2].set_ylim([0, 1])
axes[i//2, i%2].set_xlabel('Magnitude', fontsize=15)
axes[i//2, i%2].set_ylabel('Angles', fontsize=15)
fig.set_tight_layout(True)
#fig.savefig('fig.png', facecolor='skyblue')
The labels are in awkward locations and over the tick labels, but can be moved closer or further away from the axes by adding an extra labelpad parameter to set_xlabel, set_ylabel commands, so it's not a big issue.
Unfortunately, I have the impression that the plot is adjusted to fit inside the existing axes dimensions, which in turn lead to a very awkward white space above and below the half circle plot (which of course is the one I need to use).
It sounds like something that should be reasonably easy to get rid of - I mean, the wedge plots are doing it automatically - but I can't seem to figure it out how to do it for the half circle. Can anyone shed a light on this?
EDIT: Apologies, my question was not very clear; I want to create a half circle polar plot, but it seems that using set_thetamin() you end up with large amounts of white space around the image (especially above and below) which I would rather have removed, if possible.
It's the kind of stuff that normally tight_layout() takes care of, but it doesn't seem to be doing the trick here. I tried manually changing the figure window size after plotting, but the white space simply scales with the changes. Below is a minimum working example; I can get the xlabel closer to the image if I want to, but saved image file still contains tons of white space around it.
Does anyone knows how to remove this white space?
import numpy as np
import matplotlib.pyplot as plt
# get a half circle polar plot
fig1, ax1 = plt.subplots(1, 1, subplot_kw={'projection': 'polar'})
# set facecolor to better display the boundaries
# (as suggested by ImportanceOfBeingErnest)
fig1.set_facecolor('skyblue')
theta_min = 0
theta_max = np.pi
theta = np.linspace(theta_min, theta_max, 181)
data = (1/6)*np.abs(np.sin(3*theta)/np.sin(theta/2))
# set 'thetamin' and 'thetamax' according to data
ax1.set_thetamin(0)
ax1.set_thetamax(theta_max*180/np.pi)
# actually plot the data, fine tune radius limits and add labels
ax1.plot(theta, data)
ax1.set_ylim([0, 1])
ax1.set_xlabel('Magnitude', fontsize=15)
ax1.set_ylabel('Angles', fontsize=15)
fig1.set_tight_layout(True)
#fig1.savefig('fig1.png', facecolor='skyblue')
EDIT 2: Added background color to figures to better show the boundaries, as suggested in ImportanteOfBeingErnest's answer.
It seems the wedge of the "truncated" polar axes is placed such that it sits in the middle of the original axes. There seems so be some constructs called LockedBBox and _WedgeBbox in the game, which I have never seen before and do not fully understand. Those seem to be created at draw time, such that manipulating them from the outside seems somewhere between hard and impossible.
One hack can be to manipulate the original axes such that the resulting wedge turns up at the desired position. This is not really deterministic, but rather looking for some good values by trial and error.
The parameters to adjust in this case are the figure size (figsize), the padding of the labels (labelpad, as already pointed out in the question) and finally the axes' position (ax.set_position([left, bottom, width, height])).
The result could then look like
import numpy as np
import matplotlib.pyplot as plt
# get a half circle polar plot
fig1, ax1 = plt.subplots(1, 1, figsize=(6,3.4), subplot_kw={'projection': 'polar'})
theta_min = 1.e-9
theta_max = np.pi
theta = np.linspace(theta_min, theta_max, 181)
data = (1/6.)*np.abs(np.sin(3*theta)/np.sin(theta/2.))
# set 'thetamin' and 'thetamax' according to data
ax1.set_thetamin(0)
ax1.set_thetamax(theta_max*180./np.pi)
# actually plot the data, fine tune radius limits and add labels
ax1.plot(theta, data)
ax1.set_ylim([0, 1])
ax1.set_xlabel('Magnitude', fontsize=15, labelpad=-60)
ax1.set_ylabel('Angles', fontsize=15)
ax1.set_position( [0.1, -0.45, 0.8, 2])
plt.show()
Here I've set some color to the background of the figure to better see the boundary.
I have made a error-bar plot using matplotlib but it is too crowded to see everything without zooming in. I can of course do this but when I save the plot I can only save the zoomed in bit and lose the rest of the data.
Is there a way to get a scrollable plot with matplotlib so that when I save it as a png everything is included or any other format such that no data is lost? Essentially I would like the length of the plot to be much greater than the width.
The code I used to plot is:
plot1_dataerr = get_plot_data_errbars(processed_answers[0][plot_low:]) #the data to be plotted, the zeroth element of this is the labels, the first is the means and the second is the errorbar size
fig, axs = plt.subplots()
fig.subplots_adjust(left=0.2)
axs.set_xlim([1,5])
axs.grid()
axs.errorbar(plot1_dataerr[1],range(len(plot1_dataerr[1])),xerr = plot1_dataerr[2], fmt = 'k o')
axs.yaxis.set_ticks(np.arange(len(plot1_dataerr[1])))
axs.set_yticklabels(plot1_dataerr[0])
And here is the plot I am getting, as you can see it is very crowded and unclear:
You may increase the size of the plot
plt.subplots(figsize=(18,10))
This of course has a limitation for showing the plot on the screen. So you may as well or additionally, decrease the dots per inch,
plt.subplots(figsize=(36,20), dpi=50)
Then saving the plot in a vector format like pdf will allow you not to loose any details in the saved figure.
You may also keep the dpi, increase the figuresize and finally show your plot in a window with scrollbars. This is shown e.g. in the question Scrollbar on Matplotlib showing page
You can specify a bigger figure size in the subplots() constructor.
fig, axs = plt.subplots(figsize=(w, h))
Where w and h are the width and height in inches.
I have created a series of simple greyscale images which I have plotted in a grid (unfortunately, can't upload an image because I don't have a high enough reputation :( ).
The pseudo-code is
# Define matplotlib PyPlot object
nrow = 8
ncol = 12
fig, axes = plt.subplots(nrow, ncol, subplot_kw={'xticks': [], 'yticks': []})
fig.subplots_adjust(hspace=0.05, wspace=0.05)
# Sample the fine scale model at random well locations
for ax in axes.flat:
plot_data = # some Python code here to create 2D grey scale array...
# ... create sub-plot
img = ax.imshow(plot_data, interpolation='none')
img.set_cmap('gray')
# Display the plot
plt.show()
I want to change the aspect ratio so that the plots are squashed vertically and stretched horizontally. I have tried using ax.set_aspect and passing 'aspect' as a subplot_kw argument but to no avail. I also switched 'autoscale' off but I can then only see a handful of pixels. All suggestions welcome!
Thanks in advance!!
#JoeKington - thank you! That was a great reply!! Still trying to get my head around it all. Thanks also to the other posters for their suggestions. So, the original plot looked like this: http://imgur.com/Wi6v4cs
When I set' aspect='auto'' the plot looks like this: http://imgur.com/eRBO6MZ
which is a big improvement. All I need to do now is adjust the subplot size so that sub-plots are plotted in a portrait aspect ratio of eg 2:1, but with the plot filling the entire sub-plot. I guess 'colspan' would do this?
The Short Answer
You're probably wanting to call:
ax.imshow(..., aspect='auto')
imshow will set the aspect ratio of the axes to 1 when it is called, by default. This will override any aspect you specify when you create the axes.
However, this is a common source of confusion in matplotlib. Let me back up and explain what's going on in detail.
Matplotlib's Layout Model
aspect in matplotlib refers to the ratio of the xscale and yscale in data coordinates. It doesn't directly control the ratio of the width and height of the axes.
There are three things that control the size and shape of the "outside box" of a matplotlib axes:
The size/shape of the Figure (shown in red in figures below)
The specified extent of the Axes in figure coordinates (e.g. the subplot location, shown in green in figures below)
The mechanism that the Axes uses to accommodate a fixed aspect ratio (the adjustable parameter).
Axes are always placed in figure coordinates in other words, their shape/size is always a ratio of the figure's shape/size. (Note: Some things such as axes_grid will change this at draw time to get around this limitation.)
However, the extent the axes is given (either from its subplot location or explicitly set extent) isn't necessarily the size it will take up. Depending on the aspect and adjustable parameters, the Axes will shrink inside of its given extent.
To understand how everything interacts, let's plot a circle in lots of different cases.
No Fixed Aspect
In the basic case (no fixed aspect ratio set for the axes), the axes will fill up the entire space allocated to it in figure coordinates (shown by the green box).
The x and y scales (as set by aspect) will be free to change independently, distorting the circle:
When we resize the figure (interactively or at figure creation), the axes will "squish" with it:
Fixed Aspect Ratio, adjustable='box'
However, if the aspect ratio of the plot is set (imshow will force the aspect ratio to 1, by default), the Axes will adjust the size of the outside of the axes to keep the x and y data ratios at the specified aspect.
A key point to understand here, though, is that the aspect of the plot is the aspect of the x and y data scales. It's not the aspect of the width and height of the plot. Therefore, if the aspect is 1, the circle will always be a circle.
As an example, let's say we had done something like:
fig, ax = plt.subplots()
# Plot circle, etc, then:
ax.set(xlim=[0, 10], ylim=[0, 20], aspect=1)
By default, adjustable will be "box". Let's see what happens:
The maximum space the Axes can take up is shown by the green box. However, it has to maintain the same x and y scales. There are two ways this could be accomplished: Change the x and y limits or change the shape/size of the Axes bounding box. Because the adjustable parameter of the Axes is set to the default "box", the Axes shrinks inside of its maximum space.
And as we resize the figure, it will keep shrinking, but maintain the x and y scales by making the Axes use up less of the maximum space allocated to the axes (green box):
Two quick side-notes:
If you're using shared axes, and want to have adjustable="box", use adjustable="box-forced" instead.
If you'd like to control where the axes is positioned inside of the "green box" set the anchor of the axes. E.g. ax.set_anchor('NE') to have it remain "pinned" to the upper right corner of the "green box" as it adjusts its size to maintain the aspect ratio.
Fixed Aspect, adjustable="datalim"
The other main option for adjustable is "datalim".
In this case, matplotlib will keep the x and y scales in data space by changing one of the axes limits. The Axes will fill up the entire space allocated to it. However, if you manually set the x or y limits, they may be overridden to allow the axes to both fill up the full space allocated to it and keep the x/y scale ratio to the specified aspect.
In this case, the x limits were set to 0-10 and the y-limits to 0-20, with aspect=1, adjustable='datalim'. Note that the y-limit was not honored:
And as we resize the figure, the aspect ratio says the same, but the data limits change (in this case, the x-limit is not honored).
On a side note, the code to generate all of the above figures is at: https://gist.github.com/joferkington/4fe0d9164b5e4fe1e247
What does this have to do with imshow?
When imshow is called, it calls ax.set_aspect(1.0), by default. Because adjustable="box" by default, any plot with imshow will behave like the 3rd/4th images above.
For example:
However, if we specify imshow(..., aspect='auto'), the aspect ratio of the plot won't be overridden, and the image will "squish" to take up the full space allocated to the Axes:
On the other hand, if you wanted the pixels to remain "square" (note: they may not be square depending on what's specified by the extent kwarg), you can leave out the aspect='auto' and set the adjustable parameter of the axes to "datalim" instead.
E.g.
ax.imshow(data, cmap='gist_earth', interpolation='none')
ax.set(adjustable="datalim")
Axes Shape is Controlled by Figure Shape
The final part to remember is that the axes shape/size is defined as a percentage of the figure's shape/size.
Therefore, if you want to preserve the aspect ratio of the axes and have a fixed spacing between adjacent subplots, you'll need to define the shape of the figure to match. plt.figaspect is extremely handy for this. It simply generates a tuple of width, height based on a specified aspect ratio or a 2D array (it will take the aspect ratio from the array's shape, not contents).
For your example of a grid of subplots, each with a constant 2x1 aspect ratio, you might consider something like the following (note that I'm not using aspect="auto" here, as we want the pixels in the images to remain square):
import numpy as np
import matplotlib.pyplot as plt
nrows, ncols = 8, 12
dx, dy = 1, 2
figsize = plt.figaspect(float(dy * nrows) / float(dx * ncols))
fig, axes = plt.subplots(nrows, ncols, figsize=figsize)
for ax in axes.flat:
data = np.random.random((10*dy, 10*dx))
ax.imshow(data, interpolation='none', cmap='gray')
ax.set(xticks=[], yticks=[])
pad = 0.05 # Padding around the edge of the figure
xpad, ypad = dx * pad, dy * pad
fig.subplots_adjust(left=xpad, right=1-xpad, top=1-ypad, bottom=ypad)
plt.show()
How can I use yaxis and xaxis, which I want and that are not correlated with data in the plot?
For example, I want to plot the world map as an image using the code below:
import matplotlib.pyplot as plt
fig = plt.figure()
plt.imshow(world_map)
As a result, I got xaxis: 0...image_size_x from the left to the rigth and yaxis: 0...image_size_y from top to bottom.
What do I need to to do to change its axis range into latitude and longitude formats? Thus the figure axis should contain degrees (from 90 to -90) on the both fields (x and y) regardless of what its real data plotted in the figure.
Setting
pylab.ylim([90,-90])
will shift the image to the bottom by 90 pixels and reduced the y-dimension of the image into the scale of image_size_y/90. So it'll not work because xlim/ylim works with data, plotted in the figure.
In short: Use the extent keyword with imshow.
In code:
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subaxis(111)
ax.imshow(world_map, extent=[-180,180,-90,90], aspect='auto')
If your map is then upside down, add the keyword argument origin='lower' to the imshow. That aspect='auto' is needed to make the map scalable in both dimensions independently. (The rest of the extra rows with add_subaxis are just to make the code more object-oriented, the real beef is in the keyword arguments.)
If imshow is not given the extents of the image, it thinks that you'll want to have each pixel centered at positions (0,0), (0,1), ..., (Nx-1, Ny-1), and then the image extents will start from (-.5, -.5).
Assuming (based on your post) the image is fine but the axis labels are off, try playing around with this, which will manually implement the axis labels:
plt.figure(1)
ax = plt.subplot(111)
#... do your stuff
#need to figure out your image size divided by the number of labels you want
#FOR EXample, if image size was 180, and you wanted every second coordinate labeled:
ax.set_xticks([i for i in range(0,180,2)]) #python3 code to create 90 tick marks
ax.set_xticklabels([-i for i in range(-90,90,2)]) #python3 code to create 90 labels
#DO SAME FOR Y
The trick im using is to figure out how many labels you want (here, its 90: 180/2), add the tickmarks evenly in the range (0,imagesize), then manually do the labels. Here is a general formula:
ax.set_xticks([i for i in range(0,IMAGE_SIZE,_EVERY_XTH_COORD_LABELED)]) #python3 code to create 90 tick marks
ax.set_xticklabels([-i for i in range(-90,90,EVERY_XTH_COORD_LABELED)]) #python3 code to create 90 labels