How to skip nodes with NA value in ggsankey?

Question

Suppose I have this dataset (the actual dataset has 30+ columns and thousands of ids)

    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"))

I want to make a Sankey diagram that illustrates the daily severity of the patients over time. However, when the observation reaches NA (means that an outcome has been reached), I want the node to directly link to the outcome.

This is how the diagram should look like:

Image fetched from the question asked by @qdread here

Is this possible with ggsankey?

This is my current code:

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))

EDIT Based on the solution provided by @Allan Cameron, I managed to bypass the nodes with NA values. However, the diagram looks quite complex because the links to the targets are not sorted.

    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))

which results in this diagram:

Is it possible to sort the links to the Outcome target so that all links with Severe value gets aggregated?

Thanks in advance for the help.

score 3 · Accepted Answer · answered Oct 20 '22 at 14:45

3

You just need to reshape your data "manually", since make_long doesn't do what you need here.

  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))

answered Oct 20 '22 at 14:45

Allan Cameron

147,086
7
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Thanks! This is what I've been looking for! Do you perhaps have any insights on how to sort the direct links in the `Outcome` vertical bar? Since the real dataset has tens of columns, the branches looks too complex as they are not sorted – amedicalenthusiast Oct 20 '22 at 15:08
Update: sorry for the additional request, I have updated the dataset and the line of codes to illustrate the issue. Is it possible to sort the nodes? – amedicalenthusiast Oct 21 '22 at 14:29
@amedicalenthusiast I don't think this is possible within the ggsankey interface, since most of the position choices are hard-coded within `StatSankeyFlow`, which is what actually calculates the polygons. What you are suggesting sounds like it would need to be hand-coded, since the choices would need to be made based on a global understanding of the flows and how they should be arranged. I can see a way to do this manually, but it would be very complex and would probably be done purely within ggplot using polygons. – Allan Cameron Oct 21 '22 at 15:27
You may possibly want to use the riverplot package. https://stackoverflow.com/questions/9968433/sankey-diagrams-in-r – Takuro Ikeda Apr 17 '23 at 17:19

score 1 · Answer 2 · answered Oct 20 '22 at 14:32

1

Move the outcome to the left, then plot:

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...

answered Oct 20 '22 at 14:32

zx8754

52,746
12
114
209

Hi thanks for the quick answer! Is it possible to not fill the NAs with `Dead` and create a direct connection between the last non-blank column to the outcome? Because in the real dataset NA may also mean that the patient is discharged. Thanks in advance! – amedicalenthusiast Oct 20 '22 at 14:38
@amedicalenthusiast then fill in the NAs with "discharged". But yes, there must be a way. – zx8754 Oct 20 '22 at 14:42
@amedicalenthusiast thinking a bit more, then "discharged" should be in the outcome column. – zx8754 Oct 20 '22 at 14:44
Thanks for the feedback. Yes, I think it's also worthwhile to distinct those inpatients that are Alive at censoring and those that are already discharged at censoring. In the current form, both are coded as Alive – amedicalenthusiast Oct 20 '22 at 15:00

How to skip nodes with NA value in ggsankey?

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