has2k1 / has2k1/plotnine

quantiles drawn by geom_violin's draw_quantiles option are incorrect

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Description

The quantiles drawn by geom_violin are incorrect e.g. the 50% quantile does not correspond to the median. A simple example, where a boxplot is overlayed to show the expected position of the 25, 50 and 75% quantiles:

from plotnine import *
import pandas as pd
import numpy as np

df = pd.DataFrame({
    "y": np.random.gamma(1,2,10),
    "x": ["a"]*10
})
plt = (
    ggplot(df, aes(x="x", y="y")) +
    geom_violin(draw_quantiles=[0.25,0.5,0.75]) +
    geom_boxplot(alpha=0.5,width=0.1,fill="grey")
)
plt.show()

Plotting the mean and median for comparison:

plt = (
    ggplot(df, aes(x="x", y="y")) +
    geom_violin(draw_quantiles=0.5) +
    geom_hline(data=df.groupby(["x"])["y"].describe(), mapping=aes(yintercept="mean"), color="red",alpha=0.5) +
    geom_hline(data=df.groupby(["x"])["y"].describe(), mapping=aes(yintercept="50%"), color="blue",alpha=0.5)
)
plt.show()

Tested with plotnine-0.13.6 and Python 3.10

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Research direction

Start by reproducing the provided Python example using geom_violin(draw_quantiles=[0.25, 0.5, 0.75]) and the overlaid geom_boxplot. Trace the geom_violin draw_quantiles behavior and compare its lines with the grouped-data 25%, 50%, and 75% values. Done means the violin quantile lines align with the corresponding statistical quantiles, including the median.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-visualization
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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