利用平行坐标图探索不同种类狐猴的最大年龄

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd

from matplotlib.lines import Line2D

lemurs = pd.read_csv(
    "https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2021/2021-08-24/lemur_data.csv",
    engine = "python",
    encoding = "ISO-8859-1"
)

taxonomy = pd.read_csv(
    "https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2021/2021-08-24/taxonomy.csv"
)

data = (
    lemurs
    # 删除重复
    .drop_duplicates(["dlc_id", "taxon", "sex", "age_max_live_or_dead_y"])
    # 清洗性别
    .query("sex != 'ND'")
    # 按taxon、sex汇总
    .groupby(["taxon", "sex"])
    .agg(
        age_max=pd.NamedAgg("age_max_live_or_dead_y", max), # 计算最大值
        count=pd.NamedAgg("age_max_live_or_dead_y", "size") # 统计数量
    )
    .reset_index()
)

data.head()

# 按照sex对age_max和count进行数据透视
data = pd.pivot_table(
    data, index="taxon", columns="sex", values=["age_max", "count"]
).reset_index()

# 对透视后的列名处理，按_连接
data.columns = data.columns.map("_".join).str.strip("_")

# 修改CMED为CMEAD
data["taxon"] = np.where(data["taxon"] == "CMED", "CMEAD", data["taxon"])

# 匹配taxonomy获取物种信息
data = pd.merge(data, taxonomy, how="left", on="taxon")

data.head()

# 颜色变量
GREY96 = "0.96"
GREY30 = "0.3"
GREY15 = "0.15"

BLUE = "#3A8AD8"
ORANGE = "#F2A039"

# 物种名称、性别
names = data["latin_name"].values
age_max_F = data["age_max_F"].values
age_max_M = data["age_max_M"].values
# 自定义颜色判断：age_max_F>age_max_M
color =  np.where(data["age_max_F"] > data["age_max_M"], BLUE, ORANGE)

# 自定义缩放函数：用于缩放lemurs数量
def scale(x, x_min=None, x_max=None, lower=0, upper=1):
    if x_min is None:
        x_min = np.min(x)
    if x_max is None:
        x_max = np.max(x)
    return (x - x_min) / (x_max - x_min) * (upper - lower) + lower

# 计算lemurs的大小：用于点的size
n_lemurs_min = min(np.min(data["count_F"]), np.min(data["count_M"]))
n_lemurs_max = max(np.max(data["count_F"]), np.max(data["count_M"]))

lower = 10
upper = 100

size_F = scale(data["count_F"].values, n_lemurs_min, n_lemurs_max, lower, upper)
size_M = scale(data["count_M"].values, n_lemurs_min, n_lemurs_max, lower, upper)

# 各物种的垂直位置调整（手动）：adjustText效果不好
vertical_adjustments = {
    "Varecia rubra": 0,
    "Daubentonia madagascariensis": 0.6,
    "Eulemur macaco": 0.6,
    "Eulemur rubriventer": 0.4,
    "Eulemur sanfordi": 0.5,
    "Eulemur collaris": -0.1,
    "Perodicticus potto": -0.6,
    "Lemur catta": 0,
    "Eulemur flavifrons": 0,
    "Nycticebus coucang": 0,
    "Otolemur garnettii garnettii": 0,
    "Mircocebus murinus": 0,
    "Galago moholi": 0,
    "Varecia variegata variegata": 0,
    "Eulemur mongoz": 0,
    "Eulemur fulvus": 0,
    "Eulemur rufus": 0,
    "Propithecus coquereli": 0.3,
    "Cheirogaleus medius": 0.3,
    "Eulemur Eulemur": -0.1,
    "Eulemur coronatus": -0.35,
    "Eulemur albifrons": -0.25,
    "Hapalemur griseus griseus": 0,
    "Loris tardigradus": 0,
    "Mirza coquereli": 0,
    "Varecia Varecia": 0,
    "Nycticebus pygmaeus": 0
}

# 初始化布局
fig, ax = plt.subplots(figsize = (9, 11))

# 调整布局边距
fig.subplots_adjust(left=0.05, right=0.90, top=0.9, bottom=0.075)

# 背景颜色
fig.set_facecolor(GREY96)
ax.set_facecolor(GREY96)

# 迭代绘制线图和散点图
for y0, y1, c, s0, s1 in zip(age_max_F, age_max_M, color, size_F, size_M):
    ax.plot([1, 2], [y0, y1], c=c, lw=1)
    ax.scatter(1, y0, c = c, s=s0, zorder=10)
    ax.scatter(2, y1, c = c, s=s1, zorder=10)

# 点和标签的空间距离
TEXT_HPADDING = 0.08
# 线和点之间的空间距离
LINE_HPADDING1 = 0.02
# 线条和标签之间的空间距离
LINE_HPADDING2 = 0.07

for i, name in enumerate(names):
    # 对物种名称进行垂直调整
    VA = vertical_adjustments[name]
    
    # 奇数将物种名称绘制在左侧
    if i % 2 != 0:
        # 添加标签
        x = 1 - TEXT_HPADDING
        y = age_max_F[i] + VA
        ax.text(
            x, y, name, size=11, name="Faune", 
            color=GREY15, ha="right", va="center" 
        )
        
        # 添加标签与点之间的连接线
        x = [1 - LINE_HPADDING2, 1 - LINE_HPADDING1]
        y = [age_max_F[i] + VA, age_max_F[i]]
        ax.plot(x, y, color=GREY15, lw=0.5)
        
    # 偶数将物种名称绘制在左侧
    else:
        # 添加标签
        x = 2 + TEXT_HPADDING
        y = age_max_M[i] + VA
        ax.text(
            x, y, name, size=11, name="Faune", 
            color=GREY15, va="center" 
        )
        # 添加标签与点之间的连接线
        x = [2 + LINE_HPADDING1, 2 + LINE_HPADDING2]
        y = [age_max_M[i], age_max_M[i] + VA]
        ax.plot(x, y, color=GREY15, lw=0.5)
fig

# 删除边框
ax.set_frame_on(False)

# 删除x、y轴刻度
ax.set_xticks([])
ax.set_yticks([])

# 自定义x轴范围
ax.set_xlim(0.5, 2.5)

# 背景中添加水平线
ax.hlines(np.arange(10, 41), 1.1, 1.9, alpha=0.2, lw=0.5, color=GREY15, zorder=0)

# 添加文本注释（10～40；Female；Male）
for y in np.arange(10, 45, 5):
    ax.scatter(1.5, y, s=1200, color=GREY96)
    ax.text(
        1.5, y, str(y), 
        size=22, name="Faune", color="darkgreen", weight="bold",
        alpha=0.2, va="center", ha="center"
    )


ax.text(
    0.9, 11.25, "Female", 
    name="Faune", size=27, color="darkgreen", 
    weight="bold", alpha=0.3, ha="right"
)

ax.text(
    2.1, 11.25, "Male", name="Faune", size=27, color="darkgreen", 
    weight="bold", alpha=0.3,ha="left"
)    
    
fig

# 图例的值
labels = np.array([20, 40, 60, 80, 100])

# 将值的size进行缩放
sizes = scale(labels, n_lemurs_min, n_lemurs_max, lower, upper)

# 创建handles：首个是文本注释
handles = [Line2D([], [], label="Total number of lemurs hosted at DLC by species and sex", lw=0)]

# 其余的handles是点
handles += [
    Line2D(
        [], 
        [], 
        label=str(label), 
        lw=0, 
        color="None",
        marker="o",
        markersize=np.sqrt(size),
        markerfacecolor="black"
    )
    for label, size in zip(labels, sizes)
]

# 添加图例
legend = fig.legend(
    handles=handles,
    bbox_to_anchor=[0.5, 0.05],
    handletextpad=0.5,
    handlelength=1, 
    columnspacing=1,
    loc="center", 
    ncol=6,
    frameon=False
)

# 自定义图例样式
for i, text in enumerate(legend.get_texts()):
    text.set_fontfamily("Faune")
    text.set_color("darkgreen")
    if i == 0:
        text.set_fontsize(11)
    else:
        text.set_fontsize(9)

fig

# 标题
fig.text(
    0.5, 0.94, "Longest lived lemurs at the Duke Lemur Center",
    size=28,
    name="Faune",
    weight="bold",
    ha="center",
    color="darkgreen",
)

# 副标题
fig.text(
    0.5, 0.905, "Maximum age recorded in years (living or dead), by species and sex",
    size=18,
    name="Faune",
    color=GREY30,
    ha="center",
)

# 著作信息
fig.text(
    0.5, 0.025, "Source: Duke Lemur Center · Graphic: Georgios Karamanis",
    size=10, 
    color=GREY30, 
    family="Faune", 
    ha="center"
)


fig