#' ui_proteinClustering
#'
#' @return NA
#' @export
#'
ui_proteinClustering <- function() {
# in hier -> delineatwe settings menu vs optional
fluidPage(
# sidebarLayout(
sidebarPanel(style = "background-color:#7777770d",
width = 4,
wellPanel(
div(p("Analysis Settings",
style = "text-decoration: underline; font-weight: bold; font-size: 1.2em;"),
align = "center"),
tempRepo::bsCollapse(id = "proteinPeakSettingsDropDown",
open = "Panel 1",
tempRepo::bsCollapsePanel(title = div(p("Choose how Peaks are Retained for Analyses", align = "center"),
p("(Effects all protein analysis)",
style = "font-size: 0.75em",
align = "center")),
value = "proteinPeakSettingsDropDown2",
div(align = "center",
tempRepo::peakRetentionSettings_UI("protMirror")
)
),
tempRepo::bsCollapsePanel(p("Select Samples",
align = "center"),
value = "selectProteinSamplesDropDown",
p("Move samples between boxes by clicking the samples's name
and then an arrow. Samples in the right box will be used for analysis."),
tempRepo::sampleChooser_UI("proteinSampleChooser")
),
tempRepo::bsCollapsePanel(p("Choose Clustering Settings",
align = "center"),
value = "proteinClustSettingsDropDown",
div(align = "center",
tempRepo::dendrogramCreatorUI("proteinHierOptions")
)
) )
),
wellPanel(
div(p("Optional Settings", style = "text-decoration: underline; font-weight: bold; font-size: 1.2em;"), align = "center" ),
tempRepo::bsCollapse(id = "optionalProteinPeakSettingsDropDown",
tempRepo::bsCollapsePanel(p("Adjust the Dendrogram",
align = "center"),
value = "adjustProteinDendDropDown",
numericInput("hclustHeight",
label = h5(strong("Expand dendrogram")),
value = 750,
step = 50,
min = 100),
numericInput("dendparmar",
label = h5(strong("Adjust right margin of dendrogram")),
value = 20),
radioButtons("dendOrPhylo",
label = p("Label Positions:"),
choices = list("Plot all labels at x = 0" = "Dendrogram",
"Hang labels" = "Phylogram"),
selected = "Dendrogram"),
fluidRow(tempRepo::colordendLabelsUI("proth")),
fluidRow(tempRepo::colordendLinesUI("proth")),
fluidRow(tempRepo::addDotsActionUI("proth"))
),
tempRepo::bsCollapsePanel(p("Insert Samples from Another Experiment",
align = "center"),
value = "proteinInjectDropDown",
tempRepo::selectInjections_UI("proteinInject")
),
tempRepo::bsCollapsePanel(p("PCA, PCoA, t-SNE",
align = "center"),
value = "proteinMuliDimDropDown",
p("Principal Component Analysis (PCA)"),
tempRepo::popupPlot_UI("proteinPCA", "PCA"),
p("Principal Coordinates Analysis (PCoA)"),
tempRepo::popupPlot_UI("proteinPCOA", "PCoA"),
p("t-Distributed Stochastic Neighbor Embedding (t-SNE)"),
tempRepo::popupPlotTsne_UI("tsnePanel")
),
tempRepo::bsCollapsePanel(p("Save Dendrogram",
align = "center"),
value = "proteinDendSaveDropDown",
tempRepo::downloadHier("proth"),
tempRepo::downloadSvg("proth")
) )
),
br(),
uiOutput("proteinReport")
),
mainPanel(
tabsetPanel(type = "tabs",
tabPanel(value = "proteinMirror","Mirror Plots",
h3("Mirror Plot", align = "center"),
br(),
p("Choose two samples to compare in the mirror plot below.
Matching peaks will be colored blue and non-matching peaks
will be colored red."),
p("Note: Binning algorithm for mirror plot and dendrogram is different.", style = "font-size: 0.75em"),
br(),
fluidRow(
tempRepo::mirrorPlotsSettings_UI("protMirror")
),
fluidRow(
tempRepo::mirrorPlots_UI("protMirror")
),
fluidRow(
tempRepo::mirrorPlotDownload_UI("protMirror")
)
),
tabPanel(value = "proteinDendrogram","Dendrogram",
tempRepo::displayMissingProteinUI("proth"),
tempRepo::plotHier("proth"),
tempRepo::dendDotsUI("proth")
)
)
)
)
}
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