#' dendrogramCreatorUI
#'
#' @param id namespace id
#'
#' @return ui to choose the algorithm for creating the dendrogram
#'
#'
dendrogramCreatorUI <- function(id) {
ns <- shiny::NS(id)
shiny::tagList(
div(class = "tooltippy", "Distance Algorithm",
span(class = "tooltippytext",
p("Method for measuring the similarity of peaks between spectra.")
)
),
shiny::selectInput(ns("distanceMethod"),
label = NULL,
choices = list("cosine" = "cosine",
"euclidean" = "euclidean",
"maximum" = "maximum",
"manhattan" = "manhattan",
"canberra" = "canberra",
"binary" = "binary",
"minkowski" = "minkowski"),
selected = "cosine",
width = "50%"),
div(class = "tooltippy", "Clustering Algorithm",
span(class = "tooltippytext",
p("Method for creating the dendrogram from a similarity/distance matrix.")
)
),
shiny::selectInput(ns("clustering"),
label = NULL,
choices = list("ward.D" = "ward.D",
"ward.D2" = "ward.D2",
"single" = "single",
"complete" = "complete",
"average (UPGMA)" = "average",
"mcquitty (WPGMA)" = "mcquitty",
"median (WPGMC)" = "median",
"centroid (UPGMC)" = "centroid"),
selected = "average",
width = "50%"),
fluidRow(
div(style = "text-align: left;",
shiny::radioButtons(ns("booled"),
label = p("Include peak intensities, or use presence/absence?"),
choices = list("Presence/Absence" = TRUE,
"Intensities" = FALSE),
selected = FALSE)
)
),
# shiny::numericInput(ns("ppm"),
# label = shiny::h5(shiny::strong("Select ppm tolerance for peak binning")),
# min = 50,
# max = 10000,
# value = 300),
fluidRow(
shiny::numericInput(ns("bootstraps"),
label = "Bootstraps",
value = "",
min = 1,
max = 1000)
)
)
}
#' Title
#'
#' @param input sd
#' @param output sd
#' @param session sd
#' @param proteinMatrix sd
#'
#' @return sd
#'
dendrogramCreator <- function(input,
output,
session,
proteinMatrix){
pMatrixReactive <- reactive({
#require more than two samples
req(ncol(proteinMatrix() > 2))
idbac_dendrogram_creator(bootstraps = 0L,
distanceMethod = input$distanceMethod,
clusteringMethod = input$clustering,
proteinMatrix = proteinMatrix())
})
}
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