桑基图可视化

Question

我正在尝试通过桑基图可视化我的数据。

我有以下数据框：

sankey1 <- structure(list(pat_id = c(10037, 10264, 10302, 10302, 10302, 
10344, 10482, 10482, 10482, 10613, 10613, 10613, 10628, 10851, 
11052, 11203, 11214, 11214, 11566, 11684, 11821, 11945, 11945, 
11952, 11952, 12122, 12183, 12774, 13391, 13573, 13643, 14298, 
14556, 14556, 14648, 14862, 14935, 14935, 14999, 15514, 15811, 
16045, 16045, 16190, 16190, 16190, 16220, 16220, 16220, 16220
), contactnummer = c(1, 1, 1, 2, 3, 1, 1, 2, 3, 1, 2, 3, 1, 1, 
1, 1, 1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 
1, 1, 2, 1, 1, 1, 1, 2, 1, 2, 3, 1, 2, 3, 99), Combo2 = c(1, 
1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 
2, 4, 4, 1, 5, 1, 1, 1, 1, 3, 3, 1, 5, 1, 1, 3, 1, 1, 1, 1, 1, 
3, 6, 3, 1, 1, 1, 1), treatment = c(99, 0, 0, 1, 1, 0, 99, 99, 
99, 99, 99, 1, 1, 0, 1, 99, 99, 99, 0, 99, 99, 0, 0, 0, 1, 99, 
99, 0, 0, 0, 0, 0, 1, 1, 1, 99, 99, 1, 0, 0, 1, 0, 0, 0, 1, 1, 
99, 99, 99, 99)), row.names = c(NA, 50L), class = c("data.table", 
"data.frame"))

一个ID号（“pat_id”）可以有多行，每行是一个联系人（“contactnummer”） 我的目标是可视化哪些组合（“combo2”）导致哪些治疗（“治疗”）以及接触方式。

我希望通过桑基图将其可视化（https://r-graph-gallery.com/321-introduction-to-interactive-sankey-diagram-2.html）。

理想情况下，所需的输出看起来类似于这样： 其中左侧的箭头应该可视化组合，这可以导致 3 种不同的治疗。然后向右显示其中哪一个有第二次接触，箭头再次显示导致 3 种治疗的组合。

我尝试使用以下脚本，但没有成功。

library(networkD3)
library(d3Network)

 # Create a data frame for the Sankey diagram
      sankey_data <- sankey %>%
        group_by(pat_id, Combo2, treatment, contactnummer) %>%
        summarise(Count = n()) %>%
        mutate(Target = lead(treatment), Value = Count) %>%
        filter(!is.na(Target))
      
      # Create a list of unique nodes with color attributes
      combo2_nodes <- unique(sankey_data$Combo2)
      treatment_nodes <- unique(sankey_data$treatment)
      nodes <- data.frame(
        name = c(combo2_nodes, treatment_nodes),
        color = c(rep("Combo2", length(combo2_nodes)), rep("Treatment", length(treatment_nodes)))
      )
      
      # Create a list of links
      links <- data.frame(
        source = match(sankey_data$Combo2, nodes$name) - 1,
        target = match(sankey_data$Target, nodes$name) - 1,
        value = sankey_data$Value
      )
      
      # Create the Sankey diagram with color attributes
      sankey_plot <- sankeyNetwork(
        Links = links,
        Nodes = nodes,
        Source = "source",
        Target = "target",
        Value = "value",
        NodeID = "name",
        units = "Count",
        NodeGroup = "color"  # Specify the color attribute
      )
      
      # Display the plot
      sankey_plot

但这并没有创造出我想要的效果。我对桑基图非常缺乏经验。有什么建议吗？

Answer 1

抱歉，但对我来说，不太清楚如何管理组等，但我们可以从这样的事情开始：

# load necessary libraries
library(networkD3)
library(d3Network)
library(dplyr)

# define source and target
links <- data.frame(source = paste0('combo_',sankey1$Combo2),
                    target   =paste0('treatment_',sankey1$treatment))

# getting unique nodes
nodes <- data.frame(name = as.character(unique(c(links$source, links$target))))

# now convert as character
links$source <- as.character(links$source)
links$target<- as.character(links$target)

# matching links and node, then indexing to 0
links$source <- match(links$source, nodes$name) - 1
links$target <- match(links$target, nodes$name) - 1

# group by (we are grouping by number of rows)
links <- links %>% group_by(source, target) %>% tally()

# plot it!
sankeyNetwork(Links = links
              , Nodes = nodes
              , Source = 'source'
              , Target = 'target'
              , Value = 'n'
              , NodeID = 'name'
              ,fontSize = 15)

你可以这样得到一个情节：

希望有帮助！