求助：为NMDS排序图添加stat_ellipse分组填充椭圆

问题核心是未给stat_ellipse指定分组美学映射，且未将填充/颜色与分组变量关联，导致椭圆统一颜色且包围所有点。以下是修正方案：

关键修改点 #

• 给stat_ellipse添加aes(fill = factor(site), colour = factor(site))，让椭圆按site分组生成
• 使用geom = "polygon"参数生成填充椭圆，搭配alpha设置透明度避免遮挡散点
• 将stat_ellipse放在geom_point之前，确保散点显示在椭圆上方

完整修正代码 #

nmds.data_scores %>% 
  ggplot( aes(x=NMDS1, y=NMDS2)) + 
  # 先绘制填充椭圆（置于散点下方）
  stat_ellipse(aes(fill = factor(site), colour = factor(site)),
               geom = "polygon", alpha = 0.2, level = 0.95) +
  geom_point(aes(colour = factor(site), shape = factor(Group)), 
             size = 3, alpha=0.7) + 
  geom_text(data = nmds.species_scores, aes(x = NMDS1, y = NMDS2, label = species), alpha = 0) + 
  geom_text(aes(label = site, colour = factor(site)), vjust = 1.7, show.legend = FALSE)  +
  labs(
    title = "Ordination Plot(Years)",
    colour = "Year Communities", 
    shape = "Temp. Grouping",
    fill = "Year Communities") +
  scale_colour_manual(values = years_colors, guide = "none") +  
  scale_fill_manual(values = years_colors, guide = "none") +    # 同步填充色与散点配色
  scale_shape_manual(values = years_only$point_shape, name = "Temp. Grouping") +
  coord_equal() +
  theme_classic()+ 
  theme(
    panel.background = element_rect(fill = NA, colour = "black", size = 1, linetype = "solid"),
    legend.position = c(0.10, 0.10),
    legend.justification = c(0, 0),
    legend.text = element_text(size = 12),
    legend.title = element_text(size = 10, face = "bold"),
    legend.key = element_blank(),
    legend.box.background = element_rect(color = "black"),
) +
  theme(
    axis.text = element_text(size = 10),
    axis.title = element_text(size=12,color="grey14",face="bold")) +
  theme(plot.title = element_text(color = "#45ADA8", size=15,face="bold",hjust=0.5)) +
  geom_hline(yintercept = 0, linetype = "dashed", color = "grey") +  
  geom_vline(xintercept = 0, linetype = "dashed", color = "grey")+
  annotate("text", x = -1, y = 0.45, 
           label = paste0("stress: ", format(nmds$stress, digits = 4)), hjust = 0)

补充说明 #

• level = 0.95是默认置信水平，可根据需求调整（如改为0.90）
• 若需要显示填充/颜色图例，可删除scale_colour_manual和scale_fill_manual中的guide = "none"参数
• 调整alpha值可改变椭圆填充的透明度，数值越小越透明

内容的提问来源于stack exchange，提问作者user390865