Is it possible to do scatter plot in python, having points have minimal size of 1 pixel at given scale? I.e. points should not scale as I scale the plot and have size of 1 pixel always.
In pyplot
plt.scatter(d3_transformed[:,0], d3_transformed[:,1], s=1)
I still get fat point like this
You can change the marker to a point by setting marker='.', and then further reduce its size by removing the outline using linewidths=0. Note that markeredgewidth does not work with scatter.
Consider this example. As you can see, the last line of points plotted (marker='.', s=1, linewidths=0) gives the smallest markers:
import matplotlib.pyplot as plt
import numpy as np
fig, ax = plt.subplots(1)
x = np.linspace(0, 10, 100)
ax.scatter(x, np.ones_like(x)+0, marker='o', s=1, color='k')
ax.scatter(x, np.ones_like(x)+1, marker='o', s=1, color='k', linewidths=0)
ax.scatter(x, np.ones_like(x)+2, marker='.', s=1, color='k')
ax.scatter(x, np.ones_like(x)+3, marker='.', s=1, color='k', linewidths=0)
plt.show()
In scatterplot, the points have marker which is a symbol, like circle, and this symbol has also a border. I think the border is on by default. Try to turn off the bored, like set its width to 0.
http://matplotlib.org/api/lines_api.html#matplotlib.lines.Line2D.set_markeredgewidth
Related
I have a function that inputs a string (the name of the dataframe we're visualizing) and returns two histograms that visualize that data. The first plot (on the left) is the raw data, the one on the right is it after being normalized (same, just plotted using the matplotlib parameter density=True). But as you can see, this leads to transparency issues when the plots overlap. This is my code for this particular plot:
plt.rcParams["figure.figsize"] = [12, 8]
plt.rcParams["figure.autolayout"] = True
ax0_1 = plt.subplot(121)
_,bins,_ = ax0_1.hist(filtered_0,alpha=1,color='b',bins=15,label='All apples')
ax0_1.hist(filtered_1,alpha=0.9,color='gold',bins=bins,label='Less than two apples')
ax0_1.set_title('Condition 0 vs Condition 1: '+'{}'.format(apple_data),fontsize=14)
ax0_1.set_xlabel('{}'.format(apple_data),fontsize=13)
ax0_1.set_ylabel('Frequency',fontsize=13)
ax0_1.grid(axis='y',linewidth=0.4)
ax0_1.tick_params(axis='x',labelsize=13)
ax0_1.tick_params(axis='y',labelsize=13)
ax0_1_norm = plt.subplot(122)
_,bins,_ = ax0_1_norm.hist(filtered_0,alpha=1,color='b',bins=15,label='All apples',density=True)
ax0_1_norm.hist(filtered_1,alpha=0.9,color='gold',bins=bins,label='Less than two apples',density=True)
ax0_1_norm.set_title('Condition 0 vs Condition 1: '+'{} - Normalized'.format(apple_data),fontsize=14)
ax0_1_norm.set_xlabel('{}'.format(apple_data),fontsize=13)
ax0_1_norm.set_ylabel('Frequency',fontsize=13)
ax0_1_norm.legend(bbox_to_anchor=(2, 0.95))
ax0_1_norm.grid(axis='y',linewidth=0.4)
ax0_1_norm.tick_params(axis='x',labelsize=13)
ax0_1_norm.tick_params(axis='y',labelsize=13)
plt.tight_layout(pad=0.5)
plt.show()
What my current plot looks like
Any ideas on how to make the colors blend a bit better would be helpful. Alternatively, if there are any other combinations you know of that would work instead, feel free to share. I'm not picky about the color choice. Thanks!
I think it is better to emphasize such a histogram by distinguishing it by the shape of the histogram or by the difference in transparency rather than visualizing it by color. I have coded an example from the official reference with additional overlap.
import matplotlib.pyplot as plt
import numpy as np
np.random.seed(20211021)
N_points = 100000
n_bins = 20
x = np.random.randn(N_points)
y = .4 * x + np.random.randn(100000) + 2
fig, axs = plt.subplots(2, 2, sharey=True, tight_layout=True)
# We can set the number of bins with the `bins` kwarg
axs[0,0].hist(x, color='b', alpha=0.9, bins=n_bins, ec='b', fc='None')
axs[0,0].hist(y, color='gold', alpha=0.6, bins=21)
axs[0,0].set_title('edgecolor and facecolor None')
axs[0,1].hist(x, color='b', alpha=0.9, bins=n_bins)
axs[0,1].hist(y, color='gold', alpha=0.6, bins=21, ec='b')
axs[0,1].set_title('edgecolor and facecolor')
axs[1,0].hist(x, alpha=0.9, bins=n_bins, histtype='step', facecolor='b')
axs[1,0].hist(y, color='gold', alpha=0.6, bins=21)
axs[1,0].set_title('step')
axs[1,1].hist(x, color='b', alpha=0.9, bins=n_bins, histtype='bar', rwidth=0.8)
axs[1,1].hist(y, color='gold', alpha=0.6, bins=21, ec='b')
axs[1,1].set_title('bar')
plt.show()
I would like to make a scatter plot with unfilled squares. markerfacecolor is not an option recognized by scatter. I made a MarkerStyle but the fill style seems to be ignored by the scatter plot. Is there a way to make unfilled markers in the scatterplot?
import matplotlib.markers as markers
import matplotlib.pyplot as plt
import numpy as np
def main():
size = [595, 842] # in pixels
dpi = 72. # dots per inch
figsize = [i / dpi for i in size]
fig = plt.figure(figsize=figsize)
ax = fig.add_axes([0,0,1,1])
x_max = 52
y_max = 90
ax.set_xlim([0, x_max+1])
ax.set_ylim([0, y_max + 1])
x = np.arange(1, x_max+1)
y = [np.arange(1, y_max+1) for i in range(x_max)]
marker = markers.MarkerStyle(marker='s', fillstyle='none')
for temp in zip(*y):
plt.scatter(x, temp, color='green', marker=marker)
plt.show()
main()
It would appear that if you want to use plt.scatter() then you have to use facecolors = 'none' instead of setting fillstyle = 'none' in construction of the MarkerStyle, e.g.
marker = markers.MarkerStyle(marker='s')
for temp in zip(*y):
plt.scatter(x, temp, color='green', marker=marker, facecolors='none')
plt.show()
or, use plt.plot() with fillstyle = 'none' and linestyle = 'none' but since the marker keyword in plt.plot does not support MarkerStyle objects you have to specify the style inline, i.e.
for temp in zip(*y):
plt.plot(x, temp, color='green', marker='s', fillstyle='none')
plt.show()
either of which will give you something that looks like this
Refer to: How to do a scatter plot with empty circles in Python?
Try adding facecolors='none' to your plt.scatter
plt.scatter(x, temp, color='green', marker=marker, facecolors='none')
In pyplot, you can change the order of different graphs using the zorder option or by changing the order of the plot() commands. However, when you add an alternative axis via ax2 = twinx(), the new axis will always overlay the old axis (as described in the documentation).
Is it possible to change the order of the axis to move the alternative (twinned) y-axis to background?
In the example below, I would like to display the blue line on top of the histogram:
import numpy as np
import matplotlib.pyplot as plt
import random
# Data
x = np.arange(-3.0, 3.01, 0.1)
y = np.power(x,2)
y2 = 1/np.sqrt(2*np.pi) * np.exp(-y/2)
data = [random.gauss(0.0, 1.0) for i in range(1000)]
# Plot figure
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax2 = ax1.twinx()
ax2.hist(data, bins=40, normed=True, color='g',zorder=0)
ax2.plot(x, y2, color='r', linewidth=2, zorder=2)
ax1.plot(x, y, color='b', linewidth=2, zorder=5)
ax1.set_ylabel("Parabola")
ax2.set_ylabel("Normal distribution")
ax1.yaxis.label.set_color('b')
ax2.yaxis.label.set_color('r')
plt.show()
Edit: For some reason, I am unable to upload the image generated by this code. I will try again later.
You can set the zorder of an axes, ax.set_zorder(). One would then need to remove the background of that axes, such that the axes below is still visible.
ax2 = ax1.twinx()
ax1.set_zorder(10)
ax1.patch.set_visible(False)
In pyplot, you can change the order of different graphs using the zorder option or by changing the order of the plot() commands. However, when you add an alternative axis via ax2 = twinx(), the new axis will always overlay the old axis (as described in the documentation).
Is it possible to change the order of the axis to move the alternative (twinned) y-axis to background?
In the example below, I would like to display the blue line on top of the histogram:
import numpy as np
import matplotlib.pyplot as plt
import random
# Data
x = np.arange(-3.0, 3.01, 0.1)
y = np.power(x,2)
y2 = 1/np.sqrt(2*np.pi) * np.exp(-y/2)
data = [random.gauss(0.0, 1.0) for i in range(1000)]
# Plot figure
fig = plt.figure()
ax1 = fig.add_subplot(111)
ax2 = ax1.twinx()
ax2.hist(data, bins=40, normed=True, color='g',zorder=0)
ax2.plot(x, y2, color='r', linewidth=2, zorder=2)
ax1.plot(x, y, color='b', linewidth=2, zorder=5)
ax1.set_ylabel("Parabola")
ax2.set_ylabel("Normal distribution")
ax1.yaxis.label.set_color('b')
ax2.yaxis.label.set_color('r')
plt.show()
Edit: For some reason, I am unable to upload the image generated by this code. I will try again later.
You can set the zorder of an axes, ax.set_zorder(). One would then need to remove the background of that axes, such that the axes below is still visible.
ax2 = ax1.twinx()
ax1.set_zorder(10)
ax1.patch.set_visible(False)
How to change axis weight in matplotlib (make the axis much bolder)?
from pylab import *
x = [5,7,5,9,11,14]
y = [4,5,3,11,15,14]
scatter(x, y, s=50, color='green',marker='h')
show()
You can set the width of whats called a spine (a side of the axes) in Matplotlib:
fig, ax = plt.subplots()
ax.plot(np.random.randn(100).cumsum())
# The spines
plt.setp(ax.spines.values(), linewidth=3)
# The ticks
ax.xaxis.set_tick_params(width=3)
ax.yaxis.set_tick_params(width=3)
Use axhline, axvline:
axhline(linewidth=5, color='black')
axvline(linewidth=5, color='black')
axhline(linewidth=5, y=max(y)*1.1, color='black')
axvline(linewidth=5, x=max(x)*1.1, color='black')