##### --- m_trait_recon_cp ui ---------------------- #####
m_trait_recon_cp_ui <- function(id) {
ns <- NS(id)
tagList(
checkboxGroupButtons(
inputId = ns("m_trait_cp"),
choiceNames = "Tree plot with ancestral reconstruction for the character states with two-dimensional colorplane",
choiceValues = 1,
status = "primary",
selected = "Tree plot with ancestral reconstruction for the character states with two-dimensional colorplane"
),
conditionalPanel(
condition = paste0("input['", ns("m_trait_cp"), "'] == 1"),
wellPanel(fluidRow(
column(
width = 3,
# first char states
selectInput(
inputId = ns("focal_char"),
label = "Focal character:",
choices = c("prob_0x", "prob_x0"),
selected = "prob_0x"
),
textInput(
inputId = ns("fc_label"),
label = "Focal character name:",
placeholder = "p(0x)",
value = "p(0x)"
),
textInput(
inputId = ns("sc_label"),
label = "Second character name:",
placeholder = "p(x0)",
value = "p(x0)"
),
selectInput(
inputId = ns("tree_layout"),
label = "Tree layout:",
choices = c('rectangular', 'slanted', 'circular', 'fan', 'radial'),
selected = "slanted"
),
selectInput(
inputId = ns("tree_direction"),
label = "Tree direction:",
choices = c('right', 'left', 'up', 'down'),
selected = "right"
),
# show tip labels
checkboxInput(
inputId = ns("show_tip_labels"),
label = "Show tip labels (illegible for large trees)",
value = FALSE
),
numericInput(
inputId = ns("time_axis_ticks"),
label = "Number of ticks for the time axis:",
min = 0,
max = 20,
value = 10,
step = 1
),
numericInput(
inputId = ns("open_angle"),
label = "Space in degrees between the first and last tip (when tree layout is 'fan'):",
min = 0,
max = 360,
value = 10,
step = 5
),
actionButton(inputId = ns("plot"), label = "Plot"),
radioGroupButtons(
inputId = ns("code"),
label = "Code",
choiceNames = "Code",
choiceValues = 1
))
),
column(width = 9,
plotOutput(ns("plt"), height = 1000),
tags$hr(),
uiOutput(ns("plt_txt"), container = tags$code)
)
)))
}
##### --- n_trait_recon_cp srv ---------------------- #####
m_trait_recon_cp_srv <-
function(input,
output,
session,
h_obj) {
h_proc <- reactive({
x <- m_process_recon(h_obj ())
return(x)
})
plt <- eventReactive(input$plot, {
p <- m_trait_recon_cp(
processed_recon = h_proc(),
focal_character = input$focal_char,
focal_character_label = input$fc_label,
second_character_label = input$sc_label,
show_tip_labels = input$show_tip_labels,
tree_layout = input$tree_layout,
tree_direction = input$tree_direction,
time_axis_ticks = input$time_axis_ticks,
open_angle = input$open_angle,
colors= c("#21908CFF", "#440154FF", "#FDE725FF")
) + theme(plot.background = element_rect(color="black", size = 1))
return(p)
})
output$plt <- renderPlot({
plt()
})
plt_txt <- observeEvent(input$code == "Yes", {
code_text <- paste("<b>Code to reproduce this figure in an R session: </b><br/>",
"<br/>",
"library(hisse)",
"<br/>library(utilhisse) # will load other dependencies",
"<br/>m_proc <- m_process_recon(your_hisse_recon_object)",
"<br/>m_trait_recon_cp(",
"<br/> processed_recon = m_proc,",
"<br/> focal_character = '", input$focal_char,"',",
"<br/> focal_character_label = '", input$fc_label, "',",
"<br/> second_character_label = '", input$sc_label, "',",
"<br/> colors = c('#21908CFF', '#440154FF', '#FDE725FF'),",
"<br/> show_tip_labels = ", input$show_tip_labels, ",",
"<br/> tree_layout = '", input$tree_layout, "',",
"<br/> tree_direction = '", input$tree_direction, "',",
"<br/> time_axis_ticks = ", input$time_axis_ticks, ",",
"<br/> open_angle = ", input$open_angle,
"<br/>)",
"<br/>",
"<br/># For more information see ?utilhisse::m_trait_recon_cp", sep="")
p <-
wellPanel(
class = "code_well",
tags$style(".code_well {background-color: white ;}"),
HTML(code_text)
)
return(p)
})
output$plt_txt <- renderUI({
plt_txt()
})
}
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