Making Plots With plotnine (aka ggplot)

Instructor notes

Estimated teaching time: 40 min

Estimated challenge time: 50 min

Key questions:

” How can I visualize data in Python ?”
” What is ‘grammar of graphics’ ?”

Learning objectives:

“Familiarise yourself with The Grammar of Graphics through plotinine library”
“Create a ggplot object.”
“Explore different geom objects”
“Explore other layers of ggplot, including themes and labels”

Key points:

“plotnine is python implementation of The Gramma of Graphics”
“ggplot is a set of gramma rules to make publication quality plots”
“ggplot has idea of layer, building a plot is just adding different layers together”

Introduction

Python has a number of powerful plotting libraries to choose from. One of the oldest and most popular is matplotlib - it forms the foundation for many other Python plotting libraries. For this exercise we are going to use plotnine which is a Python implementation of the The Grammar of Graphics, inspired by the interface of the ggplot2 package from R. plotnine (and it’s R cousin ggplot2) is a very nice way to create publication quality plots.

The Grammar of Graphics

Statistical graphics is a mapping from data to aesthetic attributes (colour, shape, size) of geometric objects (points, lines, bars)

Faceting can be used to generate the same plot for different subsets of the dataset

These are basic building blocks according to the grammar of graphics:

data The data + a set of aesthetic mappings that describing variables mapping
geom Geometric objects, represent what you actually see on the plot: points, lines, polygons, etc.
stats Statistical transformations, summarise data in many useful ways.
scale The scales map values in the data space to values in an aesthetic space
coord A coordinate system, describes how data coordinates are mapped to the plane of the graphic.
facet A faceting specification describes how to break up the data into subsets for plotting individual set

Let’s explore these in detail.

First, install the pandas and plotnine packages to ensure they are available.

!pip install pandas plotnine

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[notice] A new release of pip is available: 24.1 -> 24.1.1
[notice] To update, run: pip install --upgrade pip

# We run this to suppress various deprecation warnings from plotnine - keeps our notebook cleaner
import warnings
warnings.filterwarnings('ignore')

Plotting in ggplot style

Let’s set up our working environment with necessary libraries and also load our csv file into data frame called survs_df,

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

%matplotlib inline
survs_df = pd.read_csv('surveys.csv').dropna()

To produce a plot with the ggplot class from plotnine, we must provide three things:

A data frame containing our data.
How the columns of the data frame can be translated into positions, colors, sizes, and shapes of graphical elements (“aesthetics”).
The actual graphical elements to display (“geometric objects”).

Introduction to plotting

ggplot(survs_df, aes(x='weight', y='hindfoot_length')) + geom_point()

Let’s see if we can also include information about species and year.

ggplot(survs_df, aes(x='weight', y='hindfoot_length',
    size = 'year')) + geom_point()

Notice that we’ve dropped the x= and y= ? These are implied for the first and second argument of aes().

ggplot(survs_df, aes(x='weight', y='hindfoot_length', 
    size = 'year', color = 'species_id')) + geom_point()

We can do simple counting plot, to see how many observation (data points) we have for each year for example

ggplot(survs_df, aes(x='year')) + \
    geom_bar(stat = 'count')

Let’s now also color by species to see how many observation we have per species in a given year

ggplot(survs_df, aes(x='year', fill = 'species_id')) + \
    geom_bar(stat = 'count')

Challenges

Produce a plot comparing the number of observations for each species at each site. The plot should have site_id on the x axis, ideally as categorical data. (HINT: You can convert a column in a DataFrame df to the ‘category’ type using: df['some_col_name'] = df['some_col_name'].astype('category'))
Create a boxplot of hindfoot_length across different species (species_id column) (HINT: There’s a list of geoms available for plotnine in the docs - instead of geom_bar, which one should you use ?)

Solutions

# Part 1

# We convert site_id into a categorical column.
# This isn't strictly nessecary, but with categories we get all the x-axis labels 
# (with continuous we don't by default) - try both and see
survs_df['site_id'] = survs_df['site_id'].astype('category')

ggplot(survs_df, aes(x='site_id', fill = 'species_id')) \
    + geom_bar(stat='count')

# Part 2
ggplot(survs_df, aes(x='species_id', y='hindfoot_length')) + \
    geom_boxplot() + \
    theme(axis_text_x = element_text(angle=90, hjust=1))

More geom types

ggplot(survs_df, aes(x='year', y='weight')) + \
    geom_boxplot()

Why are we not seeing mulitple boxplots, one for each year? This is because year variable is continuous in our data frame, but for this purpose we want it to be categorical.

survs_df['year_fact'] = survs_df['year'].astype("category")

ggplot(survs_df, aes(x='year_fact', y='weight')) + \
    geom_boxplot()

You’ll notice the x-axis labels are overlapped. To flip them 90-degrees we can apply a theme so they look less cluttered. We will revisit themes later.

ggplot(survs_df, aes(x='year_fact', y='weight')) + \
    geom_boxplot() + \
    theme(axis_text_x = element_text(angle=90, hjust=1))

To save some typing, let’s define this x-axis label rotating theme as a short variable name that we can reuse:

flip_xlabels = theme(axis_text_x = element_text(angle=90, hjust=1))

ggplot(survs_df, aes(x='year_fact', y='weight')) + \
    geom_violin() + \
    flip_xlabels

To save an image for later:

plt1 = ggplot(survs_df, aes(x='year_fact', y='weight')) + \
           geom_boxplot() + \
           xlab("Years") + \
           ylab("Weight log2(kg)") + \
           ggtitle("Boxplots, summary of species weight in each year")

plt1.save(filename="plot1.png",
          format='png',
          dpi=300,
          height=25,
          width=25)

Challenges

Can you log2 transform weight and plot a “normalised” boxplot ? Hint: use np.log2() function and name new column weight_log.
Does a log2 transform make this data visualisation better ?

Solution

survs_df['weight_log'] = np.log2(survs_df['weight'])
    
ggplot(survs_df, aes(x='year_fact', y='weight_log')) + \
    geom_boxplot() + \
    xlab("Years") + \
    ylab("Weight log2(kg)") + \
    ggtitle("Boxplots, summary of species wieght in each year") + \
    theme(axis_text_x = element_text(angle=90, hjust=1))

Faceting

ggplot has a special technique called faceting that allows to split one plot into multiple plots based on a factor included in the dataset. We will use it to make one plot for a time series for each species.

ggplot(survs_df, aes(x='year_fact', y='weight')) + \
    geom_boxplot() + \
    facet_wrap(['sex']) + \
    flip_xlabels + \
    theme(axis_text_x = element_text(size=6))

ggplot(survs_df, aes(x='year_fact', y='weight')) + \
    geom_boxplot() + \
    theme(axis_text_x = element_text(size=4)) + \
    facet_wrap(['species_id']) + \
    flip_xlabels

The two faceted plots above are probably easier to interpret using the weight_log column we created - give it a try !

The “Layered Grammar of Graphics”

ggplot(data = <DATA>) + 
  <GEOM_FUNCTION>(
     mapping = aes(<MAPPINGS>),
     stat = <STAT>, 
     position = <POSITION>
  ) +
  <COORDINATE_FUNCTION> +
  <FACET_FUNCTION>

Theming

plotnine allows pre-defined ‘themes’ to be applied as aesthetics to the plot.

A list available theme you may want to experiment with is here: https://plotnine.readthedocs.io/en/stable/api.html#themes

ggplot(survs_df, aes(x='year_fact', y='weight')) + \
    geom_boxplot() + \
    theme_bw() + \
    flip_xlabels

ggplot(survs_df, aes(x='year_fact', y='weight_log')) + \
    geom_boxplot() + \
    facet_wrap(['species_id']) + \
    theme_xkcd() + \
    theme(axis_text_x = element_text(size=4, angle=90, hjust=1))

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findfont: Font family 'Comic Sans MS' not found.
findfont: Font family 'xkcd' not found.
findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
findfont: Font family 'xkcd' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
findfont: Font family 'xkcd' not found.
findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
findfont: Font family 'xkcd' not found.
findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
findfont: Font family 'xkcd' not found.
findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
findfont: Font family 'xkcd' not found.
findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
findfont: Font family 'xkcd' not found.
findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Humor Sans' not found.
findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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findfont: Font family 'Comic Sans MS' not found.
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Extra bits 1

Let’s try to bin years into decades, which could be crude but might gives simple images to look at.

bins = [(survs_df['year'] < 1980),
        (survs_df['year'] < 1990),
        (survs_df['year'] < 2000),
        (survs_df['year'] >= 2000)]

labels = ['70s', '80s', '90s', 'Z']

survs_df['year_bins'] = np.select(bins, labels, default='unknown')

plt2 = ggplot(survs_df, aes(x='year_bins', y='weight_log')) + \
           geom_boxplot()
plt2

plt2 = ggplot(survs_df, aes(x='year_bins', y='weight_log')) + \
           geom_boxplot() + \
           flip_xlabels + \
           facet_wrap(['species_id'])
plt2

Extra bits 2

This is a different way to look at your data

ggplot(survs_df, aes("year_fact", "weight")) + \
    stat_summary(fun_y = np.mean, fun_ymin=np.min, fun_ymax=np.max) + \
    theme(axis_text_x = element_text(angle=90, hjust=1))
    
ggplot(survs_df, aes("year_fact", "weight")) + \
    stat_summary(fun_y = np.median, fun_ymin=np.min, fun_ymax=np.max) + \
    theme(axis_text_x = element_text(angle=90, hjust=1))
    
ggplot(survs_df, aes("year_fact", "weight_log")) + \
    stat_summary(fun_y = np.mean, fun_ymin=np.min, fun_ymax=np.max) + \
    theme(axis_text_x = element_text(angle=90, hjust=1))