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Scaling a plot (matplotlib)

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.

Cannot set spine line style with matplotlib

I try to set the line style of matplotlib plot spines, but for some reason, it does not work. I can set them invisible or make them thinner, but I cannot change the line style.
My aim is to present one plot cut up into two to show outliers at the top. I would like to set the respective bottom/top spines to dotted so they clearly show that there is a break.
import numpy as np
import matplotlib.pyplot as plt
# Break ratio of the bottom/top plots respectively
ybreaks = [.25, .9]
figure, (ax1, ax2) = plt.subplots(
nrows=2, ncols=1,
sharex=True, figsize=(22, 10),
gridspec_kw = {'height_ratios':[1 - ybreaks[1], ybreaks[0]]}
)
d = np.random.random(100)
ax1.plot(d)
ax2.plot(d)
# Set the y axis limits
ori_ylim = ax1.get_ylim()
ax1.set_ylim(ori_ylim[1] * ybreaks[1], ori_ylim[1])
ax2.set_ylim(ori_ylim[0], ori_ylim[1] * ybreaks[0])
# Spine formatting
# ax1.spines['bottom'].set_visible(False) # This works
ax1.spines['bottom'].set_linewidth(.25) # This works
ax1.spines['bottom'].set_linestyle('dashed') # This does not work
ax2.spines['top'].set_linestyle('-') # Does not work
ax2.spines['top'].set_linewidth(.25) # Works
plt.subplots_adjust(hspace=0.05)
I would expect the above code to draw the top plot's bottom spine and the bottom plot's top spine dashed.
What do I miss?

First one should mention that if you do not change the linewidth, the dashed style shows fine.
ax1.spines['bottom'].set_linestyle("dashed")
However the spacing may be a bit too tight. This is due to the capstyle being set to "projecting" for spines by default.
One can hence set the capstyle to "butt" instead (which is also the default for normal lines in plots),
ax1.spines['bottom'].set_linestyle('dashed')
ax1.spines['bottom'].set_capstyle("butt")
Or, one can separate the dashes further. E.g.
ax1.spines['bottom'].set_linestyle((0,(4,4)))
Now, if you also set the linewidth so something smaller, then you would need proportionally more spacing. E.g.
ax1.spines['bottom'].set_linewidth(.2)
ax1.spines['bottom'].set_linestyle((0,(16,16)))
Note that the line does not actually become thinner on screen due to the antialiasing in use. It just washes out, such that it becomes lighter in color. So in total it may make sense to keep the lineswidth at some 0.72 points (0.72 points = 1 pixel at 100 dpi) and change the color to light gray instead.

Eliminate white space between subplots in a matplotlib figure

I am trying to create a nice plot which joins a 4x4 grid of subplots (placed with gridspec, each subplot is 8x8 pixels ). I constantly struggle getting the spacing between the plots to match what I am trying to tell it to do. I imagine the problem is arising from plotting a color bar on the right side of the figure, and adjusting the location of the plots in the figure to accommodate. However, it appears that this issue crops up even without the color bar included, which has further confused me. It may also have to do with the margin spacing. The images shown below are produced by the associated code. As you can see, I am trying to get the space between the plots to go to zero, but it doesn't seem to be working. Can anyone advise?
fig = plt.figure('W Heat Map', (18., 15.))
gs = gridspec.GridSpec(4,4)
gs.update(wspace=0., hspace=0.)
for index in indices:
loc = (i,j) #determined by the code
ax = plt.subplot(gs[loc])
c = ax.pcolor(physHeatArr[index,:,:], vmin=0, vmax=1500)
# take off axes
ax.axis('off')
ax.set_aspect('equal')
fig.subplots_adjust(right=0.8,top=0.9,bottom=0.1)
cbar_ax = heatFig.add_axes([0.85, 0.15, 0.05, 0.7])
cbar = heatFig.colorbar(c, cax=cbar_ax)
cbar_ax.tick_params(labelsize=16)
fig.savefig("heatMap.jpg")
Similarly, in making a square figure without the color bar:
fig = plt.figure('W Heat Map', (15., 15.))
gs = gridspec.GridSpec(4,4)
gs.update(wspace=0., hspace=0.)
for index in indices:
loc = (i,j) #determined by the code
ax = plt.subplot(gs[loc])
c = ax.pcolor(physHeatArr[index,:,:], vmin=0, vmax=400, cmap=plt.get_cmap("Reds_r"))
# take off axes
ax.axis('off')
ax.set_aspect('equal')
fig.savefig("heatMap.jpg")

When the axes aspect ratio is set to not automatically adjust (e.g. using set_aspect("equal") or a numeric aspect, or in general using imshow), there might be some white space between the subplots, even if wspace and hspaceare set to 0. In order to eliminate white space between figures, you may have a look at the following questions
How to remove gaps between *images* in matplotlib?
How to combine gridspec with plt.subplots() to eliminate space between rows of subplots
How to remove the space between subplots in matplotlib.pyplot?
You may first consider this answer to the first question, where the solution is to build a single array out of the individual arrays and then plot this single array using pcolor, pcolormesh or imshow. This makes it especially comfortable to add a colorbar later on.
Otherwise consider setting the figuresize and subplot parameters such that no whitespae will remain. Formulas for that calculation are found in this answer to the second question.
An adapted version with colorbar would look like this:
import matplotlib.pyplot as plt
import matplotlib.colors
import matplotlib.cm
import numpy as np
image = np.random.rand(16,8,8)
aspect = 1.
n = 4 # number of rows
m = 4 # numberof columns
bottom = 0.1; left=0.05
top=1.-bottom; right = 1.-0.18
fisasp = (1-bottom-(1-top))/float( 1-left-(1-right) )
#widthspace, relative to subplot size
wspace=0 # set to zero for no spacing
hspace=wspace/float(aspect)
#fix the figure height
figheight= 4 # inch
figwidth = (m + (m-1)*wspace)/float((n+(n-1)*hspace)*aspect)*figheight*fisasp
fig, axes = plt.subplots(nrows=n, ncols=m, figsize=(figwidth, figheight))
plt.subplots_adjust(top=top, bottom=bottom, left=left, right=right,
wspace=wspace, hspace=hspace)
#use a normalization to make sure the colormapping is the same for all subplots
norm=matplotlib.colors.Normalize(vmin=0, vmax=1 )
for i, ax in enumerate(axes.flatten()):
ax.imshow(image[i, :,:], cmap = "RdBu", norm=norm)
ax.axis('off')
# use a scalarmappable derived from the norm instance to create colorbar
sm = matplotlib.cm.ScalarMappable(cmap="RdBu", norm=norm)
sm.set_array([])
cax = fig.add_axes([right+0.035, bottom, 0.035, top-bottom])
fig.colorbar(sm, cax=cax)
plt.show()

inset imshow within figure matplotlib

I'm trying to have an imshow plot inset into another in matplotlib.
I have a figure that has an plot on top and an imshow on the bottom:
fig = plt.figure()
ax1 = fig.add_subplot(2,1,1)
plt.plot()
ax2 = fig.add_subplot(2,1,2)
plt.imshow()
and then I have another figure, which also is comprised of a plot on top and an imshow below. I want this second figure to be inset into the top plot on the first figure.
I tried follow this example. The code ran without an error but I had an empty axis in the position I wanted it.
My problem is just that I'm not sure where to put the plt.setp() command If that's what I am supposed to use.

First, I don't think you can put a figure into a figure in matplotlib. You will have to arrange your Axes objects (subplots) to achieve the look you want.
The example you provided uses absolute positioning to do that. setp there is not related to positioning, though — it just removes axis ticks from insets. An example of code that does what you want:
import numpy
import matplotlib.pyplot as plt
x = numpy.linspace(0, 1)
xx, yy = numpy.meshgrid(x, x)
im = numpy.sin(xx) + numpy.cos(yy)**2
fig = plt.figure()
ax1 = fig.add_subplot(2,1,1)
ax1.plot(x, x**2)
ax2 = fig.add_subplot(2,1,2)
ax2.imshow(im)
inset1 = fig.add_axes([.15, .72, .15, .15])
inset1.plot(x, x**2)
plt.setp(inset1, xticks=[], yticks=[])
inset2 = fig.add_axes([0.15, 0.55, .15, .15])
inset2.imshow(im)
plt.setp(inset2, xticks=[], yticks=[])
fig.savefig('tt.png')
Here the insets use explicit positioning with coordinates given in "figure units" (the whole figure has size 1 by 1).
Now, of course, there's plenty of room for improvement. You probably want the widths of your plots to be equal, so you'll have to:
specify the positioning of all subplots explicitly; or
play with aspect ratios; or
use two GridSpec objects (this way you'll have the least amount of magic numbers and manual adjustment)

Subplots: tight_layout changes figure size

Changing the vertical distance between two subplot using tight_layout(h_pad=-1) changes the total figuresize. How can I define the figuresize using tight_layout?
Here is the code:
#define figure
pl.figure(figsize=(10, 6.25))
ax1=subplot(211)
img=pl.imshow(np.random.random((10,50)), interpolation='none')
ax1.set_xticklabels(()) #hides the tickslabels of the first plot
subplot(212)
x=linspace(0,50)
pl.plot(x,x,'k-')
xlim( ax1.get_xlim() ) #same x-axis for both plots
And here is the results:
If I write
pl.tight_layout(h_pad=-2)
in the last line, then I get this:
As you can see, the figure is bigger...

You can use a GridSpec object to control precisely width and height ratios, as answered on this thread and documented here.
Experimenting with your code, I could produce something like what you want, by using a height_ratio that assigns twice the space to the upper subplot, and increasing the h_pad parameter to the tight_layout call. This does not sound completely right, but maybe you can adjust this further ...
import numpy as np
from matplotlib.pyplot import *
import matplotlib.pyplot as pl
import matplotlib.gridspec as gridspec
#define figure
fig = pl.figure(figsize=(10, 6.25))
gs = gridspec.GridSpec(2, 1, height_ratios=[2,1])
ax1=subplot(gs[0])
img=pl.imshow(np.random.random((10,50)), interpolation='none')
ax1.set_xticklabels(()) #hides the tickslabels of the first plot
ax2=subplot(gs[1])
x=np.linspace(0,50)
ax2.plot(x,x,'k-')
xlim( ax1.get_xlim() ) #same x-axis for both plots
fig.tight_layout(h_pad=-5)
show()
There were other issues, like correcting the imports, adding numpy, and plotting to ax2 instead of directly with pl. The output I see is this:

This case is peculiar because of the fact that the default aspect ratios of images and plots are not the same. So it is worth noting for people looking to remove the spaces in a grid of subplots consisting of images only or of plots only that you may find an appropriate solution among the answers to this question (and those linked to it): How to remove the space between subplots in matplotlib.pyplot?.
The aspect ratios of the subplots in this particular example are as follows:
# Default aspect ratio of images:
ax1.get_aspect()
# 1.0
# Which is as it is expected based on the default settings in rcParams file:
matplotlib.rcParams['image.aspect']
# 'equal'
# Default aspect ratio of plots:
ax2.get_aspect()
# 'auto'
The size of ax1 and the space beneath it are adjusted automatically based on the number of pixels along the x-axis (i.e. width) so as to preserve the 'equal' aspect ratio while fitting both subplots within the figure. As you mentioned, using fig.tight_layout(h_pad=xxx) or the similar fig.set_constrained_layout_pads(hspace=xxx) is not a good option as this makes the figure larger.
To remove the gap while preserving the original figure size, you can use fig.subplots_adjust(hspace=xxx) or the equivalent plt.subplots(gridspec_kw=dict(hspace=xxx)), as shown in the following example:
import numpy as np # v 1.19.2
import matplotlib.pyplot as plt # v 3.3.2
np.random.seed(1)
fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(10, 6.25),
gridspec_kw=dict(hspace=-0.206))
# For those not using plt.subplots, you can use this instead:
# fig.subplots_adjust(hspace=-0.206)
size = 50
ax1.imshow(np.random.random((10, size)))
ax1.xaxis.set_visible(False)
# Create plot of a line that is aligned with the image above
x = np.arange(0, size)
ax2.plot(x, x, 'k-')
ax2.set_xlim(ax1.get_xlim())
plt.show()
I am not aware of any way to define the appropriate hspace automatically so that the gap can be removed for any image width. As stated in the docstring for fig.subplots_adjust(), it corresponds to the height of the padding between subplots, as a fraction of the average axes height. So I attempted to compute hspace by dividing the gap between the subplots by the average height of both subplots like this:
# Extract axes positions in figure coordinates
ax1_x0, ax1_y0, ax1_x1, ax1_y1 = np.ravel(ax1.get_position())
ax2_x0, ax2_y0, ax2_x1, ax2_y1 = np.ravel(ax2.get_position())
# Compute negative hspace to close the vertical gap between subplots
ax1_h = ax1_y1-ax1_y0
ax2_h = ax2_y1-ax2_y0
avg_h = (ax1_h+ax2_h)/2
gap = ax1_y0-ax2_y1
hspace=-(gap/avg_h) # this divided by 2 also does not work
fig.subplots_adjust(hspace=hspace)
Unfortunately, this does not work. Maybe someone else has a solution for this.
It is also worth mentioning that I tried removing the gap between subplots by editing the y positions like in this example:
# Extract axes positions in figure coordinates
ax1_x0, ax1_y0, ax1_x1, ax1_y1 = np.ravel(ax1.get_position())
ax2_x0, ax2_y0, ax2_x1, ax2_y1 = np.ravel(ax2.get_position())
# Set new y positions: shift ax1 down over gap
gap = ax1_y0-ax2_y1
ax1.set_position([ax1_x0, ax1_y0-gap, ax1_x1, ax1_y1-gap])
ax2.set_position([ax2_x0, ax2_y0, ax2_x1, ax2_y1])
Unfortunately, this (and variations of this) produces seemingly unpredictable results, including a figure resizing similar to when using fig.tight_layout(). Maybe someone else has an explanation for what is happening here behind the scenes.