mirror of
https://github.com/johrpan/ubigen.git
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132 lines
3.9 KiB
R
132 lines
3.9 KiB
R
#' Function for creating the main user interface.
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#' @noRd
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ui <- function() {
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navbarPage(
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theme = bslib::bs_theme(
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version = 5,
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bootswatch = "united",
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primary = "#7d19bf"
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),
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title = "Ubigen",
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header = custom_css(),
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tabPanel(
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"Explore",
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sidebarLayout(
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sidebarPanel(
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width = 3,
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h3("My genes"),
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gene_selector_ui("custom_genes"),
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h3("Scoring"),
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selectInput(
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"cross_sample_metric",
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verticalLayout(
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strong("Expression across samples"),
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paste0(
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"Proportion samples in which the gene is expressed above the ",
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"selected threshold. Select a method and a weight for the ",
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"final score."
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)
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),
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list(
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"Above 95th percentile" = "above_95",
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"Above median" = "above_median",
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"Above zero" = "above_zero"
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)
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),
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sliderInput(
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"cross_sample_weight",
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label = NULL,
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 0.5
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),
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sliderInput(
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"sd_expression",
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verticalLayout(
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strong("Standard deviation"),
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"Standard deviation of the gene's expression across all samples."
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = -0.5
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)
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),
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mainPanel(
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width = 9,
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plotly::plotlyOutput("overview_plot", height = "200px"),
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tabsetPanel(
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id = "results_panel",
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selected = "top_genes",
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header = div(class = "p-2"),
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tabPanel(
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"Your genes",
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value = "custom_genes",
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htmlOutput("custom_genes_synopsis"),
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plotly::plotlyOutput("custom_genes_boxplot")
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),
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tabPanel(
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"Top genes",
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value = "top_genes",
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div(paste0(
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"Hover over the markers to see details on each gene. Click or ",
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"drag within the figure to select genes of interest."
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)),
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plotly::plotlyOutput("scores_plot"),
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div(paste0(
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"Click on gene names to view them using the GTEx website. ",
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"There, you can see the tissue specific expression behavior ",
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"derived from the samples that this analysis is also based on."
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)),
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div(class = "p-1"),
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DT::dataTableOutput("selected_genes")
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),
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tabPanel(
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"GSEA",
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value = "gsea",
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div(
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class = "flow-layout",
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selectInput(
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"gsea_set",
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label = NULL,
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list(
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"Top genes" = "top",
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"Selected genes" = "selected",
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"Your genes" = "custom"
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)
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),
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conditionalPanel(
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"input.gsea_set == 'top'",
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sliderInput(
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"gsea_ranks",
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label = NULL,
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min = 10,
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max = 1000,
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value = 100,
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step = 10,
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ticks = FALSE
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)
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),
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actionButton(
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"gsea_run",
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"Update analysis",
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class = "btn-primary"
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)
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),
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plotly::plotlyOutput("gsea_plot"),
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div(class = "p-2"),
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DT::dataTableOutput("gsea_details")
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)
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)
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)
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)
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),
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tabPanel(
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title = "Help"
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),
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tabPanel(
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title = "Publication"
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)
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)
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}
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