ggdump example

ggdump_example.R

library(ggplot2)
library(dplyr)
library(ggbump)

tmp.subset = lr_df_merged %>% filter(ligand %in% c('WNT9A','ARTN', 'ANGPTL2') )
tmp.subset = tmp.subset |> arrange(ligand,desc(copula_coeff))

to_nodes = distinct(tmp.subset, receptor) |> mutate(to_y = row_number())
num_senders = (distinct(tmp.subset, ligand) %>% dim)[[1]]
from_nodes = distinct(tmp.subset, ligand) |> mutate(from_y = round(dim(to_nodes)[[1]])/(num_senders+1) + row_number()-1+0.5)

fig.size(8,10)

df = tmp.subset |> arrange(desc(copula_coeff)) |>
    ## generate mapping type/case variables
    group_by(ligand) |>
    mutate(n_dest = n()) |>
    ungroup() |>
    group_by(receptor) |>
    mutate(n_origin = n(),
           min_weight = min(copula_coeff)) |>
    ungroup() |>
    mutate(value_case = case_when(copula_coeff <= 0 ~ "negative",
                                  copula_coeff > 0 ~ "positive")) |>
    left_join(tribble(~value_case, ~line_type, ~font_type,
                      "positive", "solid", "bold",
                      "negative", "dashed", "italic"),
              by = "value_case") |>
    left_join(from_nodes, by = "ligand") |>
    left_join(to_nodes, by = "receptor") |>
    ## add x-coordinates
    mutate(from_x = 0,
           to_x = 10) |>
    ## give each from-out instruction a unique id
    mutate(idx = row_number())

df |>
    ggplot(aes(x = from_x , xend = to_x, y = from_y, yend = to_y, group = idx)) +
    ## edges as sigmoid curves with line type
    geom_sigmoid(aes(linetype = I(line_type))) +
    # to/from nodes
    scale_y_reverse() +
    geom_label(
        data = df %>% distinct(ligand, .keep_all = TRUE),
        aes(
        x = from_x-0.1, 
        label=ligand),size=5,hjust = 1) +
    #geom_label(aes(x = from_x - 0.5, y = to_y, label=receptor),hjust = 1) +
    geom_label(aes(x = to_x , y = to_y, label=receptor, fill = value_case),hjust = 0) +
    # edge labels
    geom_label(data = df,
               aes(x = (((from_x + to_x) / 2) + to_x) / 2,
                   y = to_y,
                   label = round(copula_coeff,2),
                   alpha = copula_coeff),
               fill = "gray") +
    scale_fill_manual(values = wesanderson::wes_palette(n = 4, name = "GrandBudapest2")) +
    scale_color_manual(values = wesanderson::wes_palette(n = 4, name = "GrandBudapest2")) +
    cowplot::theme_minimal_grid(font_size = 14, line_size = 0) +
    theme(legend.position = "none",
          panel.grid.major = element_blank(),
          axis.text.y = element_blank(),
          axis.text.x = element_blank()
        ) +
    scale_x_continuous(limits = c(-1, 11)) +
    labs(x = "Copula Coefficients", y = 'Ligand', fill = "Target", fontface="Source")