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Bachi Shashikadze
Asked: 2024-03-27 18:11:29 +0800 CST

R 和plotly 中的桑基图：意外的连接

  • 772

我正在尝试使用plotly包（plotly_4.10.2）在R中构建三层桑基图。尽管从“链接”数据来看，从源到目标的连接似乎是合理的，但绘图本身显示的连接不正确。

例如，“example.data”-> Gene3-Treatment- Catogory2显示为 Gene3-Treatment- Category1，Gene8 的连接也是错误的。在绘图之前我应该​​重新排列标签吗？

剧情截图

在此输入图像描述

library(plotly)

# this is an example data

example.data <- data.frame(
  genes = c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5", "Gene6", "Gene7", "Gene8", "Gene9"),
  conditions = c("Control", "Control", "Treatment", "Treatment", "Treatment", "Treatment", "Treatment", "Treatment", "Treatment"),
  category = c("Category1", "Category1", "Category2", "Category2", "Category2", "Category2", "Category2", "Category1", "Category2")
)

nodes <- data.frame(name = unique(c(as.character(example.data$genes),
                                    as.character(example.data$conditions),
                                    as.character(example.data$category))))

links <- data.frame(source = match(example.data$genes, nodes$name) - 1,
                    target = match(example.data$conditions, nodes$name) - 1,
                    stringsAsFactors = FALSE)

links <- rbind(links,
               data.frame(source = match(example.data$conditions, nodes$name) - 1,
                          target = match(example.data$category, nodes$name) - 1,
                          stringsAsFactors = FALSE))


plotly::plot_ly(
  type = "sankey",
  domain = list(x =  c(0,1),
                y =  c(0,1)),
  orientation = "h",
  customdata = nodes$name,
  node = list(
    label = nodes$name,
    pad = 15,
    thickness = 15,
    line = list(color = "black",
                width = 0.5)),
  link = list(source = links$source,
              target = links$target,
              value =   rep(1, nrow(links))
  ))

2 个回答

  1. Best Answer

    也许尝试按以下顺序绘制condition -> genes -> category：：

    nodes <- unique(unlist(example.data))

links <- list(
  source = c(match(example.data$conditions, nodes) - 1, 
             match(example.data$genes, nodes) - 1),
  target = c(match(example.data$genes, nodes) - 1,
             match(example.data$category, nodes) - 1),
  value = rep(1, nrow(example.data) * 2))

plot_ly(type = "sankey",
        node = list(label = nodes),
        link = links)

    在此输入图像描述

    • 1

  2. 连接实际上是正确的，桑基图显示了状态 1（源节点）genes和状态 2（目标节点）之间的流，然后分别显示了状态 2和状态 3conditions之间的流。conditionscategory

    如果将鼠标悬停在流上，则更有意义，例如，您会看到一个值 from Treatmentgone to Category1。然而，仅仅因为流程似乎与以下内容相关Gene3并不一定意味着它是：

    在此输入图像描述

    • 0

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