shinyPanelvam <- fluidPage(
tags$script("Shiny.addCustomMessageHandler('close_dropDownPathway', function(x){
$('html').click();
});"),
tags$div(
class = "container",
h1("Pathway Analysis"),
h5(tags$a(href = paste0(docs.artPath, "pathwayAnalysis.html"),
"(help)", target = "_blank")),
sidebarLayout(
sidebarPanel(
selectizeInput(
inputId = "vamAssay",
label = "Select input matrix:",
choices = NULL,
selected = NULL,
multiple = FALSE,
options = NULL),
#uiOutput("vamAssay"),
selectInput(
inputId = "pathway",
label = "Select Method: ",
choices = c(
"VAM" = "VAM",
"GSVA" = "GSVA"
)
),
#uiOutput("selectPathwayGeneLists"),
selectizeInput("PathwayGeneLists", "Select Geneset Collection:",
choices = "Import geneset before using", multiple = FALSE),
actionLink("pathwayImportGS", "Import Gene Sets", icon = icon("upload")),
br(),
conditionalPanel(
condition = "input.pathway == 'VAM'",
checkboxInput("vamCenterParameter", "Select center value",
value = TRUE),
checkboxInput("vamGammaParameter", "Select gamma value",
value = TRUE),
),
actionButton("pathwayRun", "Run"),
tags$hr(),
#h3("Save results:"),
#downloadButton("downloadPathway", "Download Results")
),
mainPanel(
dropdown(
fluidRow(
column(
12,
fluidRow(actionBttn(inputId = "closeDropDownPathway",
label = NULL, style = "simple",
color = "danger", icon = icon("times"),
size = "xs"),
align = "right"),
selectizeInput("pathwayRedDimNames",
"Select score matrix which you want to plot:",
choices = NULL,
multiple = FALSE),
selectizeInput("pathwayPlotGS", "Select Geneset:",
choices = "", multiple = FALSE),
selectInput(inputId = 'pathwayPlotVar',
label = 'Select condition of interest to group data: ',
choices = clusterChoice,
multiple = FALSE),
checkboxInput("pathwayPlotBoxplot", "Add box plot",
value = FALSE),
checkboxInput("pathwayPlotViolinplot", "Add violin plot",
value = TRUE),
checkboxInput("pathwayPlotDots", "Add dots",
value = TRUE),
pickerInput(
inputId = "pathwayPlotSummary",
label = "Select Summary parameter: ",
choices = c("mean", "median"),
selected = "median"),
actionBttn(
inputId = "pathwayPlot",
label = "Update Plot",
style = "bordered",
color = "primary",
size = "sm"
),
)
),
#tags$style(".btn-custom {background-color: #e5e5e5; ;}"),
#label = "Plot Options",
inputId = "dropDownPathway",
icon = icon("cog"),
status = "primary",
circle = FALSE,
inline = TRUE
),
shinyjqui::jqui_resizable(plotOutput("pathwayPlot"))
)
)
)
)
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