等高线图绘制异常求助：基于变量计算的z值绘图为空

核心问题 #

1. 数据结构不匹配等高线图要求：plotly的contour和lattice的contourplot都需要x（nodes）和y（sumJ）构成规则二维网格，每个网格点对应唯一的z（WD）值。但你的数据是长格式，sumJ取值随nodes离散变化，无法形成规则网格，导致绘图时无法生成有效等高线。
2. WD取值跨度极大：dense="not"时WD最大约0.439，dense="fully"时WD最大可达100，两种情况的数值跨度悬殊，也是空图的诱因之一。

修复步骤 #

1. 简化数据生成逻辑 #

根据公式，WD可直接由sumJ和nodes计算，无需冗余变量，简化后的数据更清晰：

library(tidyverse)
library(plotly) 
library(lattice)

# 生成两种密度类型的数据
data_not <- expand.grid(nodes = seq(2, 455, by = 1), jaccard = seq(0.1, 100, by = 0.1)) %>%
  mutate(sumJ = (nodes-1)*jaccard,
         WD = 2 * sumJ / (nodes * (nodes - 1)),
         dense = "not")

data_fully <- expand.grid(nodes = seq(2, 455, by = 1), jaccard = seq(0.1, 100, by = 0.1)) %>%
  mutate(sumJ = (nodes*(nodes-1)/2)*jaccard,
         WD = 2 * sumJ / (nodes * (nodes - 1)),
         dense = "fully")

data <- bind_rows(data_not, data_fully) %>%
  select(nodes, sumJ, WD, dense) %>%
  distinct()

2. 适配数据特性的绘图方案 #

方式一：按密度类型分组绘制

将两种dense情况分开，避免数值跨度干扰：

Plotly 实现

# 绘制非完全密度的等高线（用jaccard替代sumJ，线性关系更清晰）
plot_ly(data = data_not, x = ~nodes, y = ~jaccard, z = ~WD, type = "contour") %>%
  layout(title = "WD vs 节点数 & Jaccard（非完全密度）",
         xaxis = list(title = "节点数"),
         yaxis = list(title = "Jaccard"))

Lattice 实现

# 分面展示两种密度类型的等高线
contourplot(WD ~ nodes + jaccard | dense, data = data,
            main = "WD vs 节点数 & Jaccard（按密度类型分面）",
            xlab = "节点数", ylab = "Jaccard")

方式二：对sumJ取对数压缩范围

若必须用sumJ作为y轴，取对数可缩小数据跨度，让等高线显示：

# Plotly 对数sumJ版本
plot_ly(data = data, x = ~nodes, y = ~log10(sumJ), z = ~WD, type = "contour") %>%
  layout(title = "WD vs 节点数 & Log10(SumJ)",
         xaxis = list(title = "节点数"),
         yaxis = list(title = "Log10(SumJ)"))

# Lattice 对数sumJ版本
contourplot(WD ~ nodes + log10(sumJ), data = data,
            main = "WD vs 节点数 & Log10(SumJ)",
            xlab = "节点数", ylab = "Log10(SumJ)")

备选：用散点图展示离散分布

如果数据本身是离散的，散点图比等高线更合适：

plot_ly(data = data, x = ~nodes, y = ~sumJ, color = ~WD, type = "scatter", mode = "markers") %>%
  layout(title = "WD分布（节点数 vs SumJ）")

内容的提问来源于stack exchange，提问作者Djoustaine