如何在ggsankey中跳过具有NA值的节点？

Question

如何在ggsankey中跳过具有NA值的节点？

4

假设我有这个数据集（实际数据集有30多列和数千个ID）

    df <- data.frame(id = 1:5,
              admission = c("Severe", "Mild", "Mild", "Moderate", "Severe"),
              d1 = c(NA, "Moderate", "Mild", "Moderate", "Severe"),
              d2 = c(NA, "Moderate", NA, "Mild", "Moderate"),
              d3 = c(NA, "Severe", NA, "Mild", NA),
              d4 = c(NA, NA, NA, "Mild", NA),
              outcome = c("Dead", "Dead", "Alive", "Alive", "Dead"))

我想制作一个桑基图，以展示病人每日的严重程度变化情况。当观察值达到NA（表示已经达到某个结果）时，我希望节点直接链接到该结果。

以下是图表预期效果：

图片来自@qdread提出的问题，这里 使用能够实现吗？

这是我的当前代码：

df.sankey <- df %>%
    make_long(admission, d1, d2, d3, d4, outcome)
ggplot(df.sankey, aes(x = x,
                     next_x = next_x,
                     node = node,
                     next_node = next_node,
                     fill = factor(node),
                     label = node)) +
    geom_sankey(flow. Alpha = 0.5,
                node. Color = NA,
                show. Legend = TRUE) +
    geom_sankey_text(size = 3, color = "black", fill = NA, hjust = 0, position = position_nudge(x = 0.1))

编辑根据@Allan Cameron提供的解决方案，我成功地绕过了带有NA值的节点。然而，由于指向targets的链接没有排序，所以图表看起来相当复杂。

    do.call(rbind, apply(df, 1, function(x) {
    x <- na.omit(x[-1])
    data.frame(x = names(x), node = x, 
               next_x = dplyr::lead(names(x)), 
               next_node = dplyr::lead(x), row.names = NULL)
})) %>%
    ggplot(df.sankey, aes(x = x,
                          next_x = next_x,
                          node = node,
                          next_node = next_node,
                          fill = factor(node),
                          label = node)) +
    geom_sankey(flow.alpha = 0.5,
                node.color = NA,
                show.legend = TRUE) +
    geom_sankey_text(size = 3, color = "black", fill = NA, hjust = 0, position = position_nudge(x = 0.1))

这导致了这个图表：

是否可能对Outcome的target链接进行排序，以便所有具有Severe值的链接得到聚合？

感谢您提前的帮助。

- amedicalenthusiast

2个回答

1

将输出结果向左移动，然后绘制：

library(ggplot2)
library(dplyr)
library(ggsankey)

# fill NAs from last value
df[] <- t(apply(df, 1, zoo::na.locf, fromLast = TRUE))

head(df)
#   id admission       d1       d2     d3   d4 outcome
# 1  1    Severe     Dead     Dead   Dead Dead    Dead
# 2  2      Mild Moderate Moderate Severe Dead    Dead
# 3  3      Mild     Mild     Mild   Mild Mild   Alive
# 4  4  Moderate Moderate     Mild   Mild Mild   Alive
# 5  5    Severe   Severe Moderate Severe Dead    Dead

# then your existing code
df.sankey <- df %>%
  make_long(admission, d1, d2, d3, d4, outcome)

# ggplot...

- zx8754

谢谢您的快速回复！不填充NA并创建最后一个非空列与结果之间的直接连接是否可能？因为在真实数据集中，NA也可能意味着患者已经出院。提前致谢！ - amedicalenthusiast

@amedicalenthusiast 然后用“discharged”填充NAs。但是，肯定有办法。 - zx8754

@amedicalenthusiast 再思考一下，然后“discharged”应该在结果列中。 - zx8754

感谢反馈。是的，我认为将那些在审查时仍然存活和那些已经出院的住院患者区分开来也是值得的。在当前形式中，两者都被编码为“存活”。 - amedicalenthusiast

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原文链接

- Allan Cameron · Accepted Answer

您只需要手动重塑数据，因为 make_long 在这里无法满足您的需求。

  do.call(rbind, apply(df, 1, function(x) {
    x <- na.omit(x[-1])
    data.frame(x = names(x), node = x, 
               next_x = dplyr::lead(names(x)), 
               next_node = dplyr::lead(x), row.names = NULL)
    })) %>%
    mutate(x = factor(x, names(df)[-1]),
           next_x = factor(next_x, names(df)[-1])) %>%
    ggplot(aes(x = x,
               next_x = next_x,
               node = node,
               next_node = next_node,
               fill = node,,
               label = node)) +
    geom_sankey(flow.alpha = 0.5,
                node.color = NA,
                show.legend = TRUE) +
    geom_sankey_text(size = 3, color = "black", fill = NA, hjust = 0, 
                     position = position_nudge(x = 0.1))