Say there are two datasets: a big "background" set, and much smaller "foreground" set. The foreground set comes from the background, but might be much smaller.
I am interested in showing the entire background distribution in an ordered sns.barplot, and have the foreground set a brighter contrasting color to draw attention to these samples.
The best solution I could find is to display one graph on top of the other, but what happens is the graph shrinks down to the smaller domain. Here's what I mean:
import matplotlib.pyplot as plt
import seaborn
# Load the example car crash dataset
crashes = sns.load_dataset("car_crashes").sort_values("total", ascending=False)
# states of interest
txcahi = crashes[crashes['abbrev'].isin(['TX','CA','HI'])]
# Plot the total crashes
f, ax = plt.subplots(figsize=(10, 5))
plt.xticks(rotation=90, fontsize=10)
sns.barplot(y="total", x="abbrev", data=crashes, label="Total", color="lightgray")
# overlay special states onto gray plot as red bars
sns.barplot(y="total", x="abbrev", data=txcahi, label="Total", color="red")
sns.despine(left=True, bottom=True)
This data produces:
But it should look like this (ignore stylistic differences):
Why doesn't this approach work, and what would be a better way to accomplish this?
A seaborn barplot just plots the its n data along the values of 0 to n-1. If instead you'd use a matplotlib bar plot, which is unit aware (from matplotlib 2.2 onwards), it'll work as expected.
import matplotlib.pyplot as plt
import seaborn as sns
# Load the example car crash dataset
crashes = sns.load_dataset("car_crashes").sort_values("total", ascending=False)
# states of interest
txcahi = crashes[crashes['abbrev'].isin(['TX','CA','HI'])]
# Plot the total crashes
f, ax = plt.subplots(figsize=(10, 5))
plt.xticks(rotation=90, fontsize=10)
plt.bar(height="total", x="abbrev", data=crashes, label="Total", color="lightgray")
plt.bar(height="total", x="abbrev", data=txcahi, label="Total", color="red")
sns.despine(left=True, bottom=True)
Related
I generate a graph like this, it measures the content of a transparent tube but the edges of the tube appear like that, you can see the peaks on the edges of the tube... Any suggestion on how to avoid this "extra" peaks? Any suggestion is welcome.
The image of the tube is this one
This is in fact not a matplotlib-specific question. From my understanding of your question, you would like to keep red peaks while remove blue ones. This task can be done by scipy.signal.find_peaks, you can specifiy a height value to control the peaks the algorithm finds. Here are some minimum code (adapted from scipy docs):
import matplotlib.pyplot as plt
from scipy.misc import electrocardiogram
from scipy.signal import find_peaks
x = electrocardiogram()[2000:4000]
peaks, _ = find_peaks(x, height=0.5)
fig, ax = plt.subplots(1, 1, figsize=(7.2, 7.2))
ax.plot(x)
ax.plot(peaks, x[peaks], "x")
ax.axhline(y=0.5, ls="--", color="gray")
Trying to plot a surface using matplotlib. However, the plotted surface has lower grid density than the meshgrid.
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
xgrid = np.arange(0,1,1/100)
ygrid = xgrid.copy()
xx, yy = np.meshgrid(xgrid,ygrid)
fig = plt.figure()
ax = fig.add_subplot(111,projection='3d')
ax.plot_surface(xx,yy,np.square(xx)+np.square(yy))
The meshgrid was defined to have 100 segments in each direction. However, the surface in the figure doesn't have 100 segments. Is there anyway to render the surface with the same density?
Don't worry, you don't have to count the number of segments, so I overlap the plot with a scatter plot with the same points
ax.scatter3D(xx,yy,np.square(xx)+np.square(yy))
Upon zooming in, you can see that each grid of the surface plot has a scatter point in the middle, which shows that the plot_surface changed the density of the points.
Usually it doesn't matter for smooth plots such as these, but I have singular points in my data which sometimes disappear in the surface plot because of this
I am trying to plot multiple rgb images with matplotlib
the code I am using is:
import numpy as np
import matplotlib.pyplot as plt
for i in range(0, images):
test = np.random.rand(1080, 720,3)
plt.subplot(images,2,i+1)
plt.imshow(test, interpolation='none')
the subplots appear tiny though as thumbnails
How can I make them bigger?
I have seen solutions using
fig, ax = plt.subplots()
syntax before but not with plt.subplot ?
plt.subplots initiates a subplot grid, while plt.subplot adds a subplot. So the difference is whether you want to initiate you plot right away or fill it over time. Since it seems, that you know how many images to plot beforehand, I would also recommend going with subplots.
Also notice, that the way you use plt.subplot you generate empy subplots in between the ones you are actually using, which is another reason they are so small.
import numpy as np
import matplotlib.pyplot as plt
images = 4
fig, axes = plt.subplots(images, 1, # Puts subplots in the axes variable
figsize=(4, 10), # Use figsize to set the size of the whole plot
dpi=200, # Further refine size with dpi setting
tight_layout=True) # Makes enough room between plots for labels
for i, ax in enumerate(axes):
y = np.random.randn(512, 512)
ax.imshow(y)
ax.set_title(str(i), fontweight='bold')
When I run the code below in a Jupyter Notebook,
I get a map of the world, colored in red.
There are fine white-ish lines between the countries.
Is there a way to plot the world so that all countries
are solid and there's no line in between?
I'm asking, because my real world usecase is a fine grid that
behaves just like the world map: Each grid shape has a fine outline
which I do not want to have in the plot. (Update, since this was asked: The grid shapes will not have the same fill color.
)
import geopandas as gpd
import geoplot as gplt
world = gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'))
world['total'] = 1
world.plot(column='total', cmap='Set1')
For the grid example, the grid files are at https://opendata-esri-de.opendata.arcgis.com/datasets/3c1f46241cbb4b669e18b002e4893711_0
A simplified example that shows the problem.
sf = 'Hexagone_125_km/Hexagone_125_km.shp'
shp = gpd.read_file(sf)
shp.crs = {'init': 'epsg:4326'}
shp['sum'] = 1 # for example, fill sum with something
shp.plot(figsize=(20,20), column='sum', cmap='gnuplot', alpha=1, legend=True)
The white lines are due to antialiasing. This usually makes the visual more smooth, but leads to white lines in between different shapes. You can turn off anialiasing via
antialiased=False
That has the inevitable drawback of the plot looking pixelated.
An alternative is to give the patches an edge with a certain linewidth. The edges should probably have the same color as the faces, so
edgecolor="face", linewidth=0.4
would be an option. This removes the white lines, but introduces a slight "searing" effect (You'll notice mainly looking at islands like Indonesia or Japan). This will be the more noticable, the smaller the features, so it may be irrelevant for showing a hexbin plot. Still, playing a bit with the linewidth might improve the result further.
Code for reproduction:
import numpy as np; np.random.seed(42)
import geopandas as gpd
import matplotlib.pyplot as plt
world = gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'))
world['total'] = np.random.randint(0,10, size=len(world))
fig, (ax1, ax2, ax3) = plt.subplots(nrows=3, figsize=(7,10))
world.plot(column='total', cmap='Set1', ax=ax1)
world.plot(column='total', cmap='Set1', ax=ax2, antialiased=False)
world.plot(column='total', cmap='Set1', ax=ax3, edgecolor="face", linewidth=0.4)
ax1.set_title("original")
ax2.set_title("antialiased=False")
ax3.set_title("edgecolor='face', linewidth=0.4")
plt.tight_layout()
plt.savefig("world.png")
plt.show()
The following code:
# in ipython notebook, enable inline plotting with:
# %pylab inline --no-import-all
import matplotlib.pyplot as plt
# create some circles
circle1 = plt.Circle((-.5,0), 1, color='r', alpha=.2)
circle2 = plt.Circle(( .5,0), 1, color='b', alpha=.2)
# add them to the plot (bad form to use ;, but saving space)
# and control the display a bit
ax = plt.gca()
ax.add_artist(circle1); ax.add_artist(circle2)
ax.set_xlim(-2, 2); ax.set_ylim(-2, 2)
ax.set_aspect('equal')
# display it
plt.plot()
Produces the following plot:
I would like to specify the colors of the four regions (1) the background (currently white), (2 and 3) each individual event (the non-overlapping areas, currently blue and red), and (4) the intersection event (currently blended to purple). For example, I might color them red, green, blue, yellow -or- I might give them four different, precisely specified grayscale values (the later is more likely). [The colors will be generated based on characteristics of the underlying data.]
I specifically do not want to use alpha blending to "infer" a color in the intersection. I need to explicitly control the colors of all four regions.
I can think of a few strategies to solve this:
Ask mpl to extract the "primitive" patch objects that make up the three distinctly colored graphical regions (and do something similar to operate on the background) and then color them.
Given the circles, manually compute their intersections and color that intersection (somehow). Going point by point seems ugly.
Thanks!
I'm not 100% sure but I think matplotlib does not have the functionality to intersect polygons. But you could use shapely:
import shapely.geometry as sg
import matplotlib.pyplot as plt
import descartes
# create the circles with shapely
a = sg.Point(-.5,0).buffer(1.)
b = sg.Point(0.5,0).buffer(1.)
# compute the 3 parts
left = a.difference(b)
right = b.difference(a)
middle = a.intersection(b)
# use descartes to create the matplotlib patches
ax = plt.gca()
ax.add_patch(descartes.PolygonPatch(left, fc='b', ec='k', alpha=0.2))
ax.add_patch(descartes.PolygonPatch(right, fc='r', ec='k', alpha=0.2))
ax.add_patch(descartes.PolygonPatch(middle, fc='g', ec='k', alpha=0.2))
# control display
ax.set_xlim(-2, 2); ax.set_ylim(-2, 2)
ax.set_aspect('equal')
plt.show()