library(shiny)
library(treesiftr)
library(ggtree)
library(ggplot2)
library(alignfigR)
library(Biostrings)
library(phangorn)
library(shinyBS)
data(bears)
# Define UI for app that draws a histogram ----
ui <- fluidPage(
# App title ----
titlePanel("treesiftr"),
# Sidebar layout with input and output definitions ----
sidebarLayout(
# Sidebar panel for inputs ----
sidebarPanel("Below, indicate at which characters you would like to begin
visualization, and how many characters to visualize.
Mouse over options and tree for further information.",
popify(el = numericInput(inputId = "min_val",
label = "First character to visualize:",
min = 1,
max = 61,
value = 1),
title = "Characters",
content = "Character at which to begin visualizing data. For \\
example, to begin visualizing from the fifth character \\
in the matrix, enter `5`",
trigger = "hover"
),
popify(el = numericInput(inputId = "step_val",
label = "Number of characters to visualize (max 5):",
min = 1,
max = 5,
value = 3),
title = "Number of Characters",
content = "Number of Characters from the matrix to visualize. For \\
example, to visualize 3 characters, choose `3`",
trigger = "hover"
),
popify(el = checkboxInput(inputId = "pscore",
label = "Print the parsimony score?",
value = FALSE,
width = NULL),
title = "Parsimony or likelihood score",
content = "The parsimony score or the likelihood score under the \\
Mk model of morphological evolution, for the visualized \\
characters along the visualized tree, as calculated in \\
Phangorn",
trigger = "hover"
),
checkboxInput(inputId = "lscore",
label = "Print the likelihood score under the Mk
model?",
value = FALSE,
width = NULL),
popify(el = checkboxInput(inputId = "random_tree",
label = "View random set of trees rather than an
estimated tree",
value = FALSE,
width = NULL),
title = "Random tree",
content = "Rather than estimating a tree for the selected characters, \\
map the characters to a randomly-generated topology",
trigger = "hover"
)
),
# Main panel for displaying outputs ----
mainPanel(
popify(el = plotOutput(outputId = "treeAlign"),
title = "Dataset",
content = "The dataset is from Abella et al. 2012 \\
https://doi.org/10.1371/journal.pone.0048985",
trigger = "hover"
)
)
)
)
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