scatter plot color bar does not look right

Question

I have written my code to create a scatter plot with a color bar on the right. But the color bar does not look right, in the sense that the color is too light to be mapped to the actual color used in the plot. I am not sure what is missing or wrong here. But I am hoping to get something similar to what's shown here: https://medium.com/@juliansteam/what-bert-topic-modelling-reveal-about-the-2021-unrest-in-south-africa-d0d15629a9b4 (about in the middle of the page)

df = .... # data loading
df["topic"] = topics

# Plot parameters
top_n = topn
fontsize = 15
# some data preparation
to_plot = df.copy()
to_plot[df.topic >= top_n] = -1
outliers = to_plot.loc[to_plot.topic == -1]
non_outliers = to_plot.loc[to_plot.topic != -1]

#the actual plot
fig, ax = plt.subplots(figsize=(15, 15))
scatter_outliers = ax.scatter(outliers['x'], outliers['y'], color="#E0E0E0", s=1, alpha=.3)
scatter = ax.scatter(non_outliers['x'], non_outliers['y'], c=non_outliers['topic'], s=1, alpha=.3, cmap='hsv_r')
ax.text(0.99, 0.01, f"BERTopic - Top {top_n} topics", transform=ax.transAxes, horizontalalignment="right", color="black")
plt.xticks([], [])
plt.yticks([], [])
plt.colorbar(scatter)
plt.savefig(outfile+"_1.png", format='png', dpi=300)
plt.clf()
plt.close()

As you can see, an example plot looks like this. The color bar is created, but compared to that shown in the link above, the color is very light and does not seem to map to those on the scatter plot. Any suggestions?

user_12046409 · Answer

The colorbar uses the given alpha=.3. In the scatterplot, many dots with the same color are superimposed, causing them to look brighter than a single dot.

One way to tackle this, is to create a ScalarMappable object to be used by the colorbar, taking the colormap and the norm of the scatter plot (but not its alpha). Note that simply changing the alpha of the scatter object (scatter.set_alpha(1)) would also change the plot itself.

import matplotlib.pyplot as plt
from matplotlib.cm import ScalarMappable
import numpy as np

x = np.random.normal(np.repeat(np.random.uniform(0, 20, 10), 1000))
y = np.random.normal(np.repeat(np.random.uniform(0, 10, 10), 1000))
c = np.repeat(np.arange(10), 1000)

scatter = plt.scatter(x, y, c=c, cmap='hsv_r', alpha=.3, s=3)
plt.colorbar(ScalarMappable(cmap=scatter.get_cmap(), norm=scatter.norm))
plt.tight_layout()
plt.show()

scatter plot color bar does not look right

1 Answers