sankey diagram visualisation

Question

I am trying to visualize my data via a sankey diagram.

I have the following dataframe:

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"))

An ID number ("pat_id") can have multiple rows, each row is a contact ("contactnummer") My aim is to visualize which combinations ("combo2") lead to which treatments ("treatment) and at what contact.

I hope to visualise this via a sankey diagram (https://r-graph-gallery.com/321-introduction-to-interactive-sankey-diagram-2.html).

Ideally the desired output would look similar like this:

Ideally i would like to have the combinations ("Combo2") as arrows, showed in different colours per unique combination. These arrows should then lead to a treatment. But then i would like them continue, so after contact 1 - if an ID number has a second contact, the arrow shows again what combinations after that treatment occurs and to what treatment it leads in the second contact.

I've tried using the following script, but without succes.

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

But this does not create it the I would like. I am very unexperienced with the sankey diagram. Any tips?

Answer 1

sorry but to me it is not too much clear how would you manage groups etc., but we can start with something like this:

EDIT AFTER COMMENT

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


# messing up with data: the goal is to create data.frame
# with source and targets to feed the sankey
df <-
sankey1 %>%  
  # wide format to gives an order
  pivot_wider(id_cols = pat_id
               , names_from = contactnummer
               , values_from = c(Combo2,treatment)
               ,names_glue = "{contactnummer}_{.value}"
               ,names_sort=TRUE) %>% 
  # put in a long format
  pivot_longer(!pat_id, names_to = 'variable', values_to = 'value') %>%
  # remove nas
  filter(!is.na(value)) %>%
  # grouping and creating the source field by pat_id
  group_by(pat_id) %>% 
  mutate(source = paste(substr(variable,1,15),value, sep = '_')) %>% 
  # useful columns
  select(pat_id, source) %>% 
  # arrange 
  arrange(pat_id, source) %>% 
  # adding by group the target column
  mutate(target = c(source[2:length(source)],NA)) 

# define source and target
links <- data.frame(source =df$source,
                    target   =df$target) %>% 
  filter(!is.na(target))

# 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)

Hope it helps!