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I would like to use varying degrees of red color to represent the different importance of each time element and fill in that region.
The example code is shown below.
import matplotlib.pyplot as plt
X_example = np.random.rand(400)
importance_values = np.random.rand(400)
plt.figure(figsize=(13,7))
plt.plot(X_example)
for j in range(len(X_example)):
plt.axvspan(xmin=j, xmax=j+1,facecolor="r",alpha=importance_values[j])
It generates a graph like:
Now I would like to add a colormap in this figure to show that, e.g. the light red means low importance and the dark red means high importance, just like this:
How could I achieve that in my case?
One solution would be to create a LinearSegmentedColormap which takes a list of colors and turns it into a matplotlib colorbar object. Then you can set the "alpha channel":
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.colors import LinearSegmentedColormap, ListedColormap
from matplotlib.colorbar import ColorbarBase
X_example = np.random.rand(400)
importance_values = np.random.rand(400)
fig, (ax, cax) = plt.subplots(ncols=2, figsize=(8,5), gridspec_kw={'width_ratios': [1, 0.05]})
ax.plot(X_example, color='b')
for j in range(len(X_example)):
ax.axvspan(xmin=j, xmax=j+1,facecolor="r",alpha=importance_values[j])
N = 20 # the number of colors/alpha-values in the colorbar
cmap = LinearSegmentedColormap.from_list(None, ['r' for i in range(N)], N=N)
alpha_cmap = cmap(np.arange(N))
alpha_cmap[:,-1] = np.linspace(0, 1, N)
alpha_cmap = ListedColormap(alpha_cmap, N=N)
cbar = ColorbarBase(cax, cmap=alpha_cmap, ticks=[0., 1],)
cbar.ax.set_yticklabels(["low importance", "high importance"])
This gives the following plot, where the two colors of the colorbar have custom labels:
You could create a colormap mixing the red color with a range of alpha values:
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap, to_rgba
from matplotlib.cm import ScalarMappable
import numpy as np
X_example = np.random.rand(400)
importance_values = np.random.rand(400)
fig, ax = plt.subplots(figsize=(12, 5))
ax.plot(X_example)
for j in range(len(X_example)):
ax.axvspan(xmin=j, xmax=j + 1, facecolor="r", alpha=importance_values[j])
ax.margins(x=0)
cmap = LinearSegmentedColormap.from_list(None, [to_rgba('r', 0), 'r'])
cbar = plt.colorbar(ScalarMappable(cmap=cmap), ticks=[0, 1], pad=0.02)
cbar.ax.set_yticklabels(["low", "high"], fontsize=20)
cbar.ax.set_ylabel("importance", labelpad=-30, fontsize=20)
plt.tight_layout()
plt.show()
An example of a horizontal colorbar:
cbar = plt.colorbar(ScalarMappable(cmap=cmap), ticks=[0, 1], orientation='horizontal')
cbar.ax.set_xticklabels(["low", "high"], fontsize=20)
cbar.ax.set_xlabel("importance", labelpad=-15, fontsize=20)
I am trying to plot a circle over a plot. Using the Anatomy of a Figure for inspiration, I've created a short test code :
import numpy as np
from matplotlib import pyplot as plt
from matplotlib.patches import Circle
from matplotlib.patheffects import withStroke
fig = plt.figure()
x = np.arange(1,10,.1)
y3 = np.sin(x)
gs = fig.add_gridspec(1,1) # 2x2 grid
ax=fig.add_subplot(gs[0,0])
ax.plot(x,y3)
Xc = 6
Yc = 0.5
### This produces an ellipse
circle = Circle((Xc, Yc), 0.25, clip_on=False, zorder=10, linewidth=1,
edgecolor='black', facecolor=(0, 0, 0, .0125),
path_effects=[withStroke(linewidth=5, foreground='w')])
ax.add_artist(circle)
plt.show()
which generates the below plot
Question :
Why is the displayed 'circle' really an ellipse?
The help page for Circle, defines a resolution order, but it isn't obvious how this 'resolution' order is decided. Given that my circle is following the format of the above Anatomy of a Figure, I don't understand how this happens.
For your circle to look like a circle, you have to set the aspect ratio of your plot to 1.
In your link, that is done in this line:
ax = fig.add_subplot(1, 1, 1, aspect=1)
In your example:
import numpy as np
from matplotlib import pyplot as plt
from matplotlib.patches import Circle
from matplotlib.patheffects import withStroke
fig = plt.figure()
x = np.arange(1,10,.1)
y3 = np.sin(x)
gs = fig.add_gridspec(1,1) # 2x2 grid
ax=fig.add_subplot(gs[0,0], aspect=1)
ax.plot(x,y3)
Xc = 6
Yc = 0.5
### This produces an ellipse
circle = Circle((Xc, Yc), 0.25, clip_on=False, zorder=10, linewidth=1,
edgecolor='black', facecolor=(0, 0, 0, .0125),
path_effects=[withStroke(linewidth=5, foreground='w')])
ax.add_artist(circle)
plt.show()
It seems like some of the methods that work for matplotlib 2D might not be working for matplotlib 3D. I'm not sure.
I'd like to remove the tick marks from all axes, and extend the edge color from the bottom and sides to the top as well. The farthest I have gotten is being able to draw the ticks as white, which looks bad as they are rendered on top of the edge lines.
Below is a big chunk of self-contained code that results in the following image. Any help is much appreciated!
import numpy as np
import matplotlib as mpl
from matplotlib import pyplot as plt
from matplotlib import animation
from mpl_toolkits.mplot3d import Axes3D
mpl.rcParams['ytick.color'] = 'white'
#mpl.rcParams['ytick.left'] = False
sample = np.random.random_integers(low=1,high=5, size=(10,3))
# Create a figure and a 3D Axes
fig = plt.figure(figsize=(5,5))
ax = Axes3D(fig)
#ax.w_xaxis.set_tick_params(color='white')
#ax.axes.tick_params
ax.axes.tick_params(bottom=False, color='blue')
##['size', 'width', 'color', 'tickdir', 'pad', 'labelsize',
##'labelcolor', 'zorder', 'gridOn', 'tick1On', 'tick2On',
##'label1On', 'label2On', 'length', 'direction', 'left', 'bottom',
##'right', 'top', 'labelleft', 'labelbottom',
##'labelright', 'labeltop', 'labelrotation']
colors = np.mean(sample[:, :], axis=1)
ax.scatter(sample[:,0], sample[:,1], sample[:,2],
marker='o', s=20, c=colors, alpha=1)
ax.tick_params(color='red')
frame1 = plt.gca()
frame1.axes.xaxis.set_ticklabels([])
frame1.axes.yaxis.set_ticklabels([])
frame1.axes.zaxis.set_ticklabels([])
#frame1.axes.yaxis.set_tick_params(color='white')
To answer the first bit of the question, about tick removal,
it's probably easiest to just disable the tick lines:
for line in ax.xaxis.get_ticklines():
line.set_visible(False)
for line in ax.yaxis.get_ticklines():
line.set_visible(False)
for line in ax.zaxis.get_ticklines():
line.set_visible(False)
E.g.:
import numpy as np
import matplotlib as mpl
from matplotlib import pyplot as plt
from matplotlib import animation
from mpl_toolkits.mplot3d import Axes3D
sample = np.random.random_integers(low=1,high=5, size=(10,3))
# Create a figure and a 3D Axes
fig = plt.figure(figsize=(5,5))
ax = Axes3D(fig)
colors = np.mean(sample[:, :], axis=1)
ax.scatter(sample[:,0], sample[:,1], sample[:,2],
marker='o', s=20, c=colors, alpha=1)
ax = plt.gca()
ax.xaxis.set_ticklabels([])
ax.yaxis.set_ticklabels([])
ax.zaxis.set_ticklabels([])
for line in ax.xaxis.get_ticklines():
line.set_visible(False)
for line in ax.yaxis.get_ticklines():
line.set_visible(False)
for line in ax.zaxis.get_ticklines():
line.set_visible(False)
For newer versions (e.g. matplotlib 3.5.1) a lot of formatting can be done via mpl_toolkits.mplot3d.axis3d._axinfo:
import numpy as np
from matplotlib import pyplot as plt
sample = np.random.randint(low=1,high=5, size=(10,3))
# Create a figure and a 3D Axes
fig = plt.figure(figsize=(5,5))
ax = fig.add_subplot(projection='3d')
colors = np.mean(sample[:, :], axis=1)
ax.scatter(sample[:,0], sample[:,1], sample[:,2],
marker='o', s=20, c=colors, alpha=1)
for axis in [ax.xaxis, ax.yaxis, ax.zaxis]:
axis.set_ticklabels([])
axis._axinfo['axisline']['linewidth'] = 1
axis._axinfo['axisline']['color'] = (0, 0, 0)
axis._axinfo['grid']['linewidth'] = 0.5
axis._axinfo['grid']['linestyle'] = "-"
axis._axinfo['grid']['color'] = (0, 0, 0)
axis._axinfo['tick']['inward_factor'] = 0.0
axis._axinfo['tick']['outward_factor'] = 0.0
axis.set_pane_color((0.95, 0.95, 0.95))
plt.show()
I was unsuccessful browsing web for a solution for the following simple question:
How to draw 3D polygon (say a filled rectangle or triangle) using vertices values?
I have tried many ideas but all failed, see:
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.collections import PolyCollection
import matplotlib.pyplot as plt
fig = plt.figure()
ax = Axes3D(fig)
x = [0,1,1,0]
y = [0,0,1,1]
z = [0,1,0,1]
verts = [zip(x, y,z)]
ax.add_collection3d(PolyCollection(verts),zs=z)
plt.show()
I appreciate in advance any idea/comment.
Updates based on the accepted answer:
import mpl_toolkits.mplot3d as a3
import matplotlib.colors as colors
import pylab as pl
import numpy as np
ax = a3.Axes3D(pl.figure())
for i in range(10000):
vtx = np.random.rand(3,3)
tri = a3.art3d.Poly3DCollection([vtx])
tri.set_color(colors.rgb2hex(np.random.rand(3)))
tri.set_edgecolor('k')
ax.add_collection3d(tri)
pl.show()
Here is the result:
I think you've almost got it. Is this what you want?
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
import matplotlib.pyplot as plt
fig = plt.figure()
ax = Axes3D(fig, auto_add_to_figure=False)
fig.add_axes(ax)
x = [0,1,1,0]
y = [0,0,1,1]
z = [0,1,0,1]
verts = [list(zip(x,y,z))]
ax.add_collection3d(Poly3DCollection(verts))
plt.show()
You might also be interested in art3d.pathpatch_2d_to_3d.
The above solution is for Python 2, and gives an error 'TypeError: object of type 'zip' has no len()' when run with python 3.
See Plotting 3D Polygons in Python 3 for discussion on updating this to Python 3.
Here's some working code from there:
from mpl_toolkits.mplot3d import Axes3D
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
import matplotlib.pyplot as plt
fig = plt.figure()
ax = Axes3D(fig)
x = [0, 1, 1, 0]
y = [0, 0, 1, 1]
z = [0, 1, 0, 1]
verts = [list(zip(x, y, z))]
print(verts)
ax.add_collection3d(Poly3DCollection(verts), zs='z')
plt.show()
I want to add a 2nd axes at the top right corner of a 1st axes. After googling, I found two ways to do things like this: fig.add_axes(), and mpl_toolkits.axes_grid.inset_locator.inset_axes. But the fig.add_axes() doesn't accept transform arg. So the following code throws an error. So the position can't be under the parent axes coordinates but the figure coordinates.
import matplotlib.pyplot as plt
import cartopy.crs as ccrs
fig, ax = plt.subplots(1, 1, subplot_kw={'projection': ccrs.PlateCarree()})
ax2 = fig.add_axes([0.8, 0, 0.2, 0.2], transform=ax.transAxes, projection=ccrs.PlateCarree())
And inset_axes() doesn't accept the projection arg, so I can't add ax2 as a cartopy geo-axes.
from mpl_toolkits.axes_grid.inset_locator import inset_axes
import matplotlib.pyplot as plt
import cartopy.crs as ccrs
fig, ax = plt.subplots(1, 1, subplot_kw={'projection': ccrs.PlateCarree()})
# The following line doesn't work
ax2 = inset_axes(ax, width='20%', height='20%', axes_kwargs={'projection': ccrs.PlateCarree()})
# Doesn't work neither:
ax2 = inset_axes(ax, width='20%', height='20%', projection=ccrs.PlateCarree())
I've asked the question at matplotlib issue. It seems the following code works well as long as it's not a cartopy axes.
import matplotlib as mpl
fig, ax = plt.subplots(1, 1)
box = mpl.transforms.Bbox.from_bounds(0.8, 0.8, 0.2, 0.2)
ax2 = fig.add_axes(fig.transFigure.inverted().transform_bbox(ax.transAxes.transform_bbox(box)))
Question:
How to easily add a sub_axes with proper position and size in matplotlib and cartopy?
As I understand, after ax.set_extend(), the size of axes will change. So maybe is there a way that some point of sub_axes (eg: top right corner of ax2) can be anchored at one fixed position of the parent_axes (eg: top right corner of ax1)?
As inset_axes() doesn't accept projection arg, the roundabout way is to use InsetPosition(). This way you can create an axes in the usual way (using projection), and then "link" both axes using InsetPosition(). The main advantage over using subplots or similar is that the inset position is fixed, you can resize the figure or change the main plot area and the inset will always be in the same place relative to the main axes. This was based on this answer: specific location for inset axes, just adding the cartopy way of doing things.
import numpy as np
import matplotlib.pyplot as plt
import cartopy.crs as ccrs
import cartopy.feature as cfeature
from mpl_toolkits.axes_grid1.inset_locator import InsetPosition
from shapely.geometry.polygon import LinearRing
extent = [-60, -30, -40, -10]
lonmin, lonmax, latmin, latmax = extent
fig = plt.figure(figsize=(10, 8))
ax = fig.add_subplot(1, 1, 1, projection=ccrs.PlateCarree())
ax.set_extent(extent, crs=ccrs.PlateCarree())
ax.add_feature(cfeature.LAND)
ax.add_feature(cfeature.OCEAN)
ax.add_feature(cfeature.COASTLINE)
# inset location relative to main plot (ax) in normalized units
inset_x = 1
inset_y = 1
inset_size = 0.2
ax2 = plt.axes([0, 0, 1, 1], projection=ccrs.Orthographic(
central_latitude=(latmin + latmax) / 2,
central_longitude=(lonmin + lonmax) / 2))
ax2.set_global()
ax2.add_feature(cfeature.LAND)
ax2.add_feature(cfeature.OCEAN)
ax2.add_feature(cfeature.COASTLINE)
ip = InsetPosition(ax, [inset_x - inset_size / 2,
inset_y - inset_size / 2,
inset_size,
inset_size])
ax2.set_axes_locator(ip)
nvert = 100
lons = np.r_[np.linspace(lonmin, lonmin, nvert),
np.linspace(lonmin, lonmax, nvert),
np.linspace(lonmax, lonmax, nvert)].tolist()
lats = np.r_[np.linspace(latmin, latmax, nvert),
np.linspace(latmax, latmax, nvert),
np.linspace(latmax, latmin, nvert)].tolist()
ring = LinearRing(list(zip(lons, lats)))
ax2.add_geometries([ring], ccrs.PlateCarree(),
facecolor='none', edgecolor='red', linewidth=0.75)
I may have figured something out.
According to the answer this question. I can get the position of both axes, then reposition the 2nd axes. The code was like:
import matplotlib.pyplot as plt
from cartopy import crs as ccrs
fig, ax = plt.subplots(1, 1, subplot_kw={'projection': ccrs.PlateCarree()})
ax2 = fig.add_axes([0.8, 0.8, 0.2, 0.2], projection=ccrs.PlateCarree())
ax.set_extent([100, 120, 20, 40])
ax.coastlines()
ax2.set_global()
ax2.coastlines()
ax2.stock_img()
def reposition():
plt.draw()
p1 = ax.get_position()
p2 = ax2.get_position()
ax2.set_position([p1.x1-p2.width, p1.y1-p2.height, p2.width, p2.height])
reposition()
plt.show()
The result is just what I want.