Entanglement

Assessing recombination history through comparison of subgenomic region phylogenies

Read Gene Trees

Segment specific phylogenies. Note that the_rev subfix indicates that the original Nexus files were revised to swap tip labels for names in the description block (see, preprocessing)

Show code

# phylogeny list from directory
tree_files <- list.files(here("local/paktrees/original"), pattern="_rev\\.nex$")

# read ML trees & convert
IRES_Lpro.tree <- read.nexus(here("local/paktrees/original", tree_files[8]))
IRES_Lpro.den <- get_dendro(
  extract_subtree(IRES_Lpro.tree))

seg_2C.tree <- read.nexus(here("local/paktrees/original", tree_files[1]))
seg_2C.den <- get_dendro(
  extract_subtree(seg_2C.tree))

seg_3A.tree <- read.nexus(here("local/paktrees/original", tree_files[2]))
seg_3A.den <- get_dendro(
  extract_subtree(seg_3A.tree))

seg_3C.tree <- read.nexus(here("local/paktrees/original", tree_files[3]))
seg_3C.den <- get_dendro(
  extract_subtree(seg_3C.tree))

seg_3D.tree <- read.nexus(here("local/paktrees/original", tree_files[4]))
seg_3D.den <- get_dendro(
  extract_subtree(seg_3D.tree))

Entanglement

Entanglement scores range from 0.00 - 1.00 with a values of 0.00 indicating the trees are exactly the same and a score of 1.00 indicating they are opposites. Essentially, the score can be interpreted as a proportion or percent change.

Table to summarize comparisons

Show code

entangle_tab <- as.data.frame(matrix(nrow = 10, ncol = 2))
names(entangle_tab) <- c("Compared", "Score")

Select tabs to view comparisons

IRES_Lpro vs. 2C

Show code

dends <- dendlist(IRES_Lpro.den, seg_2C.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[1] <- "IRES_Lpro vs. 2C"
entangle_tab$Score[1] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "IRES_Lpro",
                      cex_main_left = 4,
                      main_right = "2C",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

IRES_Lpro vs. 3A

Show code

dends <- dendlist(IRES_Lpro.den, seg_3A.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[2] <- "IRES_Lpro vs. 3A"
entangle_tab$Score[2] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "IRES_Lpro",
                      cex_main_left = 4,
                      main_right = "3A",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

IRES_Lpro vs. 3C

Show code

dends <- dendlist(IRES_Lpro.den, seg_3C.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[3] <- "IRES_Lpro vs. 3C"
entangle_tab$Score[3] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "IRES_Lpro",
                      cex_main_left = 4,
                      main_right = "3C",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

IRES_Lpro vs. 3D

Show code

dends <- dendlist(IRES_Lpro.den, seg_3D.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[4] <- "IRES_Lpro vs. 3D"
entangle_tab$Score[4] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "IRES_Lpro",
                      cex_main_left = 4,
                      main_right = "3D",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

2C vs. 3A

Show code

dends <- dendlist(seg_2C.den, seg_3A.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[5] <- "2C vs. 3A"
entangle_tab$Score[5] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "2C",
                      cex_main_left = 4,
                      main_right = "3A",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

2C vs. 3C

Show code

dends <- dendlist(seg_2C.den, seg_3C.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[6] <- "2C vs. 3C"
entangle_tab$Score[6] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "2C",
                      cex_main_left = 4,
                      main_right = "3C",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

2C vs. 3D

Show code

dends <- dendlist(seg_2C.den, seg_3D.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[7] <- "2C vs. 3D"
entangle_tab$Score[7] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "2C",
                      cex_main_left = 4,
                      main_right = "3D",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

3A vs. 3C

Show code

dends <- dendlist(seg_3A.den, seg_3C.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[8] <- "3A vs. 3C"
entangle_tab$Score[8] <- entang_score


x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "3A",
                      cex_main_left = 4,
                      main_right = "3C",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

3A vs. 3D

Show code

dends <- dendlist(seg_3A.den, seg_3D.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[9] <- "3A vs. 3D"
entangle_tab$Score[9] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "3A",
                      cex_main_left = 4,
                      main_right = "3D",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

3C vs. 3D

Show code

dends <- dendlist(seg_3C.den, seg_3D.den)
entang_score <- round(entanglement(dends), 2)

entangle_tab$Compared[10] <- "3C vs. 3D"
entangle_tab$Score[10] <- entang_score

x <- dends %>% dendextend::untangle(method = "step2side") 

x %>% set("rank_branches") %>%
      set("branches_lwd", 1.5) %>%
      set("branches_col", value = c("gray40")) %>%
           tanglegram(main_left = "3C",
                      cex_main_left = 4,
                      main_right = "3D",
                      cex_main_right = 4,
                      columns_width = c(5,0.5,5),
                      lwd = 1.8,
                      lab.cex = 0.8,
                      dLeaf_left = -0.15,
                      dLeaf_right = 0.15,
                      margin_outer = 4,
                      margin_inner = 10,
                      color_lines = tol(12), 
                      axes=FALSE,
                      sub = paste("Entanglement:", entang_score),
                      common_subtrees_color_branches = FALSE)

Entanglement Scores

Show code

entangle_tab %>%
  gt() %>%
  tab_header(
    title = md("Score Summary")) %>%
  cols_width(everything() ~ px(150)) %>%
   tab_options(table.font.size = "small",
              row_group.font.size = "small",
              stub.font.size = "small",
              column_labels.font.size = "medium",
              heading.title.font.size = "large",
              data_row.padding = px(2),
              heading.title.font.weight = "bold",
              column_labels.font.weight = "bold") %>%
  opt_stylize(style = 6, color = 'gray')

Score Summary
Compared	Score
IRES_Lpro vs. 2C	0.53
IRES_Lpro vs. 3A	0.32
IRES_Lpro vs. 3C	0.74
IRES_Lpro vs. 3D	0.42
2C vs. 3A	0.58
2C vs. 3C	0.55
2C vs. 3D	0.54
3A vs. 3C	0.80
3A vs. 3D	0.16
3C vs. 3D	0.78

Matrix View

Show code

mat_view <- entangle_tab %>%
  separate(Compared, into = c("Var1", "Var2"), sep = " vs. ", remove = FALSE)

mat_view <- mat_view %>%
  select(Var1, Var2, Score)

unique_vars <- unique(c(mat_view$Var1, mat_view$Var2))
self_comparisons <- data.frame(
  Var1 = unique_vars,
  Var2 = unique_vars,
  Score = 0  # self-comparisons
)

mat_view <- bind_rows(mat_view, self_comparisons)

mat_view <- bind_rows(
  mat_view,
  mat_view %>% rename(Var1 = Var2, Var2 = Var1)
)

mat_view <- mat_view %>%
  distinct()

mat_view$Var1 <- gsub("_", " ", mat_view$Var1)
mat_view$Var2 <- gsub("_", " ", mat_view$Var2)

ggplot(mat_view, aes(Var1, Var2, fill = Score)) +
  geom_tile() +
   scale_fill_gradientn(
    colors = (pals::ocean.ice(100)[20:100]) 
  ) +
  theme_classic() +
  theme(
    plot.margin = unit(c(2, 2, 2, 2), "mm"),
    axis.title.x = element_text(size = 24, face = "bold"),
    axis.title.y = element_text(size = 24, face = "bold"),
    axis.text.x = element_text(size = 23, face = "bold"),
    axis.text.y = element_text(size = 23, face = "bold"),
    legend.direction = "vertical",
    legend.position = "right",
    strip.text = element_blank(), 
    strip.background = element_blank(),
    legend.key.size = unit(2, "line"),
    legend.key.width = unit(1, "line"),
    legend.text = element_text(size = 20, face = "bold"),
    legend.title = element_text(size = 25, face = "bold"),
    plot.title = element_text(size = 28, face = "bold") 
    ) +
  labs(title = "Entanglement Scores",
       x = " ", y = " ", fill = "Entanglement")

Figure 1: Compare entanglement scores.