ui_ref_new <- function(id) {
ns <- NS(id)
fluidRow(
.ui_notice(),
column(6,
# h4("Select Reference Directory"),
wellPanel(
tags$div(title = paste("Choose a directory for NxtIRF",
"to create its IRFinder/NxtIRF reference"),
splitLayout(cellWidths = c("30%", "70%"),
shinyDirButton(ns("dir_reference_path"),
label = "Select Reference Directory",
title = "Select Reference Directory",
buttonType = "primary"
), textOutput(ns("txt_reference_path"))
)
)
), br(),
wellPanel(
h4("Select Ensembl Reference"),
selectInput(ns('release'), 'Select Release', width = '100%',
choices = c("")),
selectInput(ns('species'), 'Select Species', width = '100%',
choices = c("")),
selectInput(ns('fasta'), 'Select Genome', width = '100%',
choices = c("")),
selectInput(ns('gtf'), 'Select Annotation', width = '100%',
choices = c(""))
),
wellPanel(
h4("or select Reference from File"),
tags$div(title = "Choose a user-supplied genome fasta file",
splitLayout(cellWidths = c("35%", "65%"),
shinyFilesButton(ns("file_genome"),
label = "Choose genome FASTA File",
title = "Choose genome FASTA File",
buttonType = "primary",
multiple = FALSE
),
textOutput(ns("txt_genome"))
)
), br(),
tags$div(title = paste("Choose a user-supplied transcript",
"reference gtf file"),
splitLayout(cellWidths = c("35%", "65%"),
shinyFilesButton(ns("file_gtf"),
label = "Choose transcriptome GTF File",
title = "Choose transcriptome GTF File",
buttonType = "primary",
multiple = FALSE
),
textOutput(ns("txt_gtf"))
)
)
)
),
column(6,
wellPanel(
tags$div(title = paste("NxtIRF will auto-populate default",
"mappability and non-polyA reference files for",
"hg38, hg19, mm10 and mm9 genomes"),
selectInput(ns('newref_genome_type'),
paste('Select Genome Type to set',
'Mappability and non-PolyA files'),
c("(custom)", "hg38", "mm10", "hg19", "mm9")
)
),
tags$div(title = paste("Select Mappability Exclusion file.",
"This is typically a 3 columns",
"of values containing seqnames,",
"start and end coordinates of low-mappability regions"),
shinyFilesButton(ns("file_mappa"),
label = "Choose Mappability Exclusion file",
title = "Choose Mappability Exclusion file",
buttonType = "primary",
multiple = FALSE
),
actionButton(ns("clear_mappa"), "Clear",
class = "btn-outline-danger"),
textOutput(ns("txt_mappa"))
), br(),
tags$div(title = paste("Select Non-PolyA reference file.",
"This is used by IRFinder",
"to calculate reads from known non-polyadenylated",
"transcripts to assess",
"quality of poly-A enrichment in sample QC"),
shinyFilesButton(ns("file_NPA"),
label = "Choose non-PolyA BED file",
title = "Choose non-PolyA BED file",
buttonType = "primary",
multiple = FALSE),
actionButton(ns("clear_NPA"), "Clear",
class = "btn-outline-danger"),
textOutput(ns("txt_NPA"))
), br(),
tags$div(title = paste("Select Blacklist file.",
"This is typically a 3 columns of values",
"containing seqnames, start and end coordinates",
"of regions to exclude from IRFinder analysis"),
shinyFilesButton(ns("file_bl"),
label = "Choose blacklist BED file",
title = "Choose blacklist BED file",
buttonType = "primary",
multiple = FALSE),
actionButton(ns("clear_bl"), "Clear",
class = "btn-outline-danger"),
textOutput(ns("txt_bl"))
)
),
wellPanel(
tags$div(
shinyWidgets::actionBttn(ns("buildRef"),
"Build Reference",
style = "gradient", color = "primary"),
shinyWidgets::actionBttn(ns("clearNewRef"),
"Clear settings",
style = "gradient", color = "warning"),
shinyWidgets::actionBttn(ns("load_ref_example"),
"Load Example FASTA / GTF",
style = "gradient", color = "danger"
)
)
),
uiOutput(ns("refStatus"))
)
)
}
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