Dear guys,

I am trying to use Sankey plot for showing correlation analysis.

As in the figure, the bridge is only grey and black.

How can I put the colors as below figure ?

My code is

parasite_data <- read.csv("18S_Clr_with first row_taxafiltered.csv")
prey_data <- read.csv("12S_Clr_with first row.csv")


parasite_data <- parasite_data %>%
  rename(Parasite_Taxon = Taxa) %>%
  pivot_longer(
    cols = starts_with("Sample"),
    names_to = "Sample",
    values_to = "Parasite_Abundance"
  )

prey_data <- prey_data %>%
  rename(Prey_Taxon = Taxa) %>%
  pivot_longer(
    cols = starts_with("Sample"),
    names_to = "Sample",
    values_to = "Prey_Abundance"
  )

merged_data <- inner_join(parasite_data, prey_data, by = "Sample")

correlations <- merged_data %>%
  group_by(Parasite_Taxon, Prey_Taxon) %>%
  summarise(
    correlation = cor(Parasite_Abundance, Prey_Abundance, method = "spearman", use = "complete.obs"),
    .groups = "drop"
  ) %>%
  filter(!is.na(correlation) & abs(correlation) > 0.3)

correlations

parasite_nodes <- unique(correlations$Parasite_Taxon)
prey_nodes <- unique(correlations$Prey_Taxon)

nodes <- data.frame(
  name = c(parasite_nodes, prey_nodes),
  group = c(rep("parasite", length(parasite_nodes)), rep("prey", length(prey_nodes)))
)

# Create a lookup table for node indices
node_lookup <- data.frame(
  name = nodes$name,
  id = 0:(nrow(nodes) - 1)
)

links <- correlations %>%
  left_join(node_lookup, by = c("Parasite_Taxon" = "name")) %>%
  rename(Source = id) %>%
  left_join(node_lookup, by = c("Prey_Taxon" = "name")) %>%
  rename(Target = id) %>%
  mutate(Value = abs(correlation)) %>%
  select(Source, Target, Value)

parasite_colors <- brewer.pal(min(length(parasite_nodes), 8), "Set1")
prey_colors <- brewer.pal(min(length(prey_nodes), 8), "Set2")

colors <- c(parasite_colors, prey_colors)

jscode <- paste0(
  "d3.scaleOrdinal()",
  ".range(['", paste(colors, collapse = "','"), "'])"
)

sankey_plot <- sankeyNetwork(
  Links = links,
  Nodes = nodes,
  Source = "Source",
  Target = "Target",
  Value = "Value",
  NodeID = "name",
  colourScale = jscode,
  sinksRight = FALSE,
  fontSize = 12,
  nodeWidth = 30
)

sankey_plot

Plz any comments for revising the code. (Even Python code is welcomed to solve the problem !! )