ggtree conflict between viewClade,scale_y_reverse, rotate

[yoelii]

trafficstars

Hi,

I have a ggtree tree object and I want to explore them in a RShiny app. My ggtree is not compatible with plotly plot (I losted highlight, clade, ..). To conturn incompability with plotly, I use ggtree in a simple plot. With help of Shiny, I made a kind a interactivity with some selectInput Menu and a kind of zoom with viewClade() function.

But with viewClade, I losted the order of my branches. I need to rotate it. But with rotatation, the highlight become incorrect.

Please find following my code with a more simple tree but reproducible example of my problem.

Thanks for your help

# Load libraries
library(shiny)
library(ggtree)
library(ggplot2)
library(ape)
library(TDbook)
#install.packages("gridExtra")
library(gridExtra)

# Define colors for tree
trophic_colors <- c("carnivore" = "red", "herbivore" = "green", "omnivore" = "blue")
trophic_shapes <- c("carnivore" = 15, "herbivore" = 16, "omnivore" = 17)

# Prepare data for selectInput
p <- ggtree(tree_boots) %<+% df_tip_data
node_data <- p$data
internal_nodes <- node_data[node_data$isTip == FALSE, c("label","node")]
nodes_for_select <- internal_nodes$node
names(nodes_for_select) <- internal_nodes$label

nodes_for_select <- as.list(nodes_for_select)
label_nodes_h <- internal_nodes$label
names(label_nodes_h) <- internal_nodes$node

nodes_for_select_zoom <- node_data[node_data$isTip == TRUE, c("label","node")]
list_nodes_for_select_zoom <- nodes_for_select_zoom$node
names(list_nodes_for_select_zoom ) <- nodes_for_select_zoom$label
list_nodes_for_select_zoom <- as.list(list_nodes_for_select_zoom)

# define ui
ui <- fluidPage(
  titlePanel("Tree with ggtree"),
  sidebarLayout(
    sidebarPanel(
      selectInput("nodeSelect", "Select a node of interest to highlight :",
                  choices = list_nodes_for_select_zoom,
                  selected = list_nodes_for_select_zoom$Rangifer_tarandus),

                  # selected = nodes_for_select$Cervidae),
      checkboxGroupInput("trophicHabitSelect", " Choose trophic habits to display :",
                         choices = unique(df_tip_data$trophic_habit),
                         selected = unique(df_tip_data$trophic_habit)),
      selectInput("zoomNode", "Select a node to zoom:",
                  choices = nodes_for_select,
                  selected = nodes_for_select$Mammalia)
    ),
    mainPanel(
      plotOutput("treePlot"), 
      plotOutput("zoomPlot")
    )
  )
)

# Defin server part
server <- function(input, output) {
  output$treePlot <- renderPlot({
    # Filter data according to user's selection
    selected_habits <- input$trophicHabitSelect
    df_filtered <- df_tip_data[df_tip_data$trophic_habit %in% selected_habits, ]
    
    selected_colors <- trophic_colors[selected_habits]
    selected_shapes <- trophic_shapes[selected_habits]
    
    df_filtered$trophic_habit <- factor(df_filtered$trophic_habit, levels = selected_habits)
    
    # Made the complete Tree with ggtree 
    p_full <- ggtree(tree_boots) %<+% df_filtered + xlim(-0.1, 4)
    p_full <- p_full + geom_tiplab(offset = 0.6, hjust = 0.5) +
      geom_point(aes(shape = trophic_habit, color = trophic_habit,
                     size = mass_in_kg), show.legend = TRUE, na.rm = TRUE) +
      theme(legend.position = "right") +
      scale_size_continuous(range = c(3, 10)) +
      scale_shape_manual(values = selected_shapes) +
      scale_color_manual(values = selected_colors)+ scale_y_reverse()
    
    # Add highlight
    selected_node <- input$nodeSelect
    p_full <- p_full + geom_highlight(node = as.numeric(selected_node),
                                      fill = "NA", alpha = 0.01, extend = 1,
                                      color = "deepskyblue", linetype = 3)
 
    p_full
    
  })
  
  output$zoomPlot <- renderPlot({

    # Made the complete Tree with ggtree 
    p_full <- ggtree(tree_boots) %<+% df_tip_data
    p_full <- p_full + geom_tiplab(offset = 0.6, hjust = 0.5) +
      geom_point(aes(shape = trophic_habit, color = trophic_habit,
                     size = mass_in_kg), na.rm = TRUE) +
      scale_shape_manual(values = trophic_shapes) +
      scale_color_manual(values = trophic_colors)+ scale_y_reverse()
    
    # Add highlight
    selected_node <- input$nodeSelect
    p_full <- p_full + geom_highlight(node = as.numeric(selected_node),
                                      fill = "NA", alpha = 0.01, extend = 1.5,
                                      color = "deepskyblue", linetype = 3)

    # Create the "zoom" tree
    zoom_node <- input$zoomNode
  
    p_clade <- viewClade(p_full, node = as.numeric(zoom_node)) 
    p_clade <- ggtree::rotate(p_clade,as.numeric(zoom_node)) 

    p_clade

  })
}

# Load Shiny App
shinyApp(ui = ui, server = server)