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ui.R
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# Shiny App GUI code
# Define UI for application
# sidebar
sidebar <- dashboardSidebar(
sidebarMenu(
id="sidebar_id",
menuItem("Start Pipeline", tabName = "pipeline"),
menuItem("Short Variants", tabName="short_vars"),
menuItem("Structural Variants", tabName="sv_tab"),
# Filters side panel
#---------------------------------------------------------------------------
conditionalPanel(
'input.sidebar_id == "short_vars"',
uiOutput("filters")
),
conditionalPanel(
'input.sidebar_id == "sv_tab"',
uiOutput("sv_filters_ui")
)
)
)
# dashboard body
body <- dashboardBody(
tabItems(
# Starting pipeline
#-------------------------------------------------------------------------------
tabItem(
tabName="pipeline",
fluidRow(
box(title="Short Variants",
status="primary",
width=9,
height = "100%",
tags$head(
tags$style(
HTML(".form-control.shiny-bound-input{
width: 75px;
}
#sh_email{
width: 75%
}
#sv_email{
width: 75%
}
"))),
column(6,
tags$h4(
"General Settings"
),
fluidRow(
column(12,
htmlOutput("sh_vcf_label")
)
),
fluidRow(
column(3,
shinyFilesButton("sh_vcf",
"Browse...",
title="Upload input short variants VCF file (compressed)",
filetype=c("vcf.gz"), multiple=F),
),
column(9,
textOutput("sh_vcf_name"),
)),
fluidRow(
column(12,
br(),
htmlOutput("sh_outdir_label")),
),
fluidRow(
column(3,
shinyDirButton("sh_outdir", "Browse...",
title="Output folder", multiple=F)),
column(9,
textOutput("sh_outdir_txt")
)
),
br(),
numericInput("sh_threads", "Number of threads (CPU)", value=4,
min=1, max=99),
textInput("sh_email","Email address"),
br(),
tags$h4(
"PLINK Dataset Generation"
),
numericInput("min_af", "Min. Allele Frequency threshold for variants in PLINK dataset", value=0.05, max=1,
min=0.01, step=0.01),
tags$h4("Max missing genotype rates (for PLINK dataset)"),
numericInput("mind", "Max per SAMPLE e.g. 0.1 excludes samples with missing call rates > 10%", value=0.05, max=1,
min=0.1, step=0.01),
numericInput("geno", "Max per VARIANT missing call rates e.g. 0.1 excludes variants with missing call rates > 10%", value=0.01, max=1,
min=0.1, step=0.01)
),
column(6,
tags$h4(
"QC Filtering"
),
numericInput("GQ", "Minimum genotype quality (GQ) per sample threshold", value=20,
min=1, max=99),
numericInput("DP", "Minimum read depth (DP) per sample threshold", value=10, min=1,
max=100),
br(),
tags$h4(
"IBD Segment Detection"
),
numericInput("ibis_mt1",
"Minimum number of (SNP) markers to call a region IBD1",
value=50, min=10, max=1000),
numericInput("ibis_mt2",
"Minimum number of (SNP) markers to call region IBD2",
value=10, min=1, max=400),
br(),
tags$h4("Protein-impacting Variant Selection"),
numericInput("max_af", "Max Allele Frequency in any of the following populations: gnomAD, 1000 genomes or ESP", value=0.05, max=1,
min=0.01, step=0.01),
HTML("<b>(OPTIONAL) Upload a genes of interest list (.xlsx/.txt)</b>"),
fluidRow(
column(3,
shinyFilesButton("sh_start_genes",
"Browse...",
title="Upload a list of genes of interest",
multiple=FALSE,
filetype=c(".xlsx", ".txt"))),
column(9,
textOutput("sh_start_genes_name"))
),
br(),
actionButton("sh_start", "Start")
)
),
box(
title="Structural Variants",
status = "primary",
height="100%",
width=3,
column(12,
fluidRow(
column(12,
HTML("<b>Upload a compressed input SV VCF file (.vcf.gz)</b>")
)
),
fluidRow(
column(3,
shinyFilesButton("sv_vcf", "Browse...",
title="Upload input structural variants VCF file (compressed)",
filetype=c(".vcf.gz"), multiple=F)
),
column(9,
textOutput("sv_vcf_name")
)
),
br(),
HTML("<b>Select an output folder</b>"),
fluidRow(
column(3,
shinyDirButton("sv_outdir", "Browse...",
title="Output folder", multiple=F)
),
column(9,
textOutput("sv_outdir_txt")
)
),
br(),
HTML("<b>Upload an IBIS IBD segment file (.seg)</b>"),
fluidRow(
column(3,
shinyFilesButton("sv_start_ibis_seg", "Browse...",
title="Upload an IBIS IBD segment file (.seg)",
filetype=c(".seg"), multiple=F)
),
column(9,
textOutput("sv_ibis_seg")
)
),
br(),
numericInput("sv_threads", "Number of threads", value=4,
min=1, max=99),
textInput("sv_email","Email address"),
HTML("<b>(OPTIONAL) Upload a genes of interest list (.xlsx/.txt)</b>"),
fluidRow(
column(3,
shinyFilesButton("sv_start_genes",
"Browse...",
title="Upload a list of genes of interest",
multiple=FALSE,
filetype=c(".xlsx", ".txt"))),
column(9,
textOutput("sv_start_genes_name"))
),
br(),
actionButton("sv_start", "Start")
)
)
)
),
#---------------------------------------------------------------------------
# Short variants tab
#---------------------------------------------------------------------------
tabItem(
tabName="short_vars",
fluidRow(
box(
title = "IBD regions Ideogram",
status="primary",
width = 9,
height="610px",
box(
width = 12,
height="540px",
ideogramOutput("ideogram_plot")
)
),
column(
width=3,
box(
title="Files",
width=12,
fluidRow(column(12,
htmlOutput("sh_tsv_label")
)),
fluidRow(
column(3,
br(),
shinyFilesButton(
"short_tsv", "Browse...",
title="Upload pipeline output file (.tsv/.txt)",
filetype=c(".tsv", ".txt"), multiple = FALSE)),
column(9,
br(),
textOutput("short_tsv_name"))
),
fluidRow(
column(12,
br(),
htmlOutput("sh_seg_label")
)
),
fluidRow(
column(3,
br(),
shinyFilesButton(
"ibd_seg", "Browse...",
title="Upload (IBIS) IBD segment file (.seg)",
filetype=c(".tsv", ".txt"),
multiple = FALSE)
),
column(9,
br(),
textOutput("ibd_seg_name"))
),
fluidRow(
column(12,
br(),
htmlOutput("sh_gene_label")
)),
fluidRow(
column(3,
br(),
shinyFilesButton("sh_gene_list", "Browse...",
title="(Optional) Upload a list of genes of interest (.xlsx, .txt)",
filetype=c(".xlsx", ".txt"),
multiple=FALSE)
),
column(9,
br(),
textOutput("sh_gene_name"))
),
status = "primary"
),
box(
title="Summary",
width=12,
height="250px",
status="primary",
column(12,
fluidRow(
textOutput("sh_vars_total"),
br()
),
fluidRow(
textOutput("clinvar_vars"),
br()
),
fluidRow(
textOutput("impact_vars"),
br()
),
fluidRow(
textOutput("missense_vars"),
br()
),
fluidRow(
textOutput("ibd_seg_total")
)
))
)
),
fluidRow(
box(
width=12,
height="100%",
column(12,
fluidRow(
downloadButton("download", "Download")
),
br(),
fluidRow(
DTOutput("short_tab")
)
)
,
status = "primary"
)
)
),
#---------------------------------------------------------------------------
# SV tab
#---------------------------------------------------------------------------
tabItem(
tabName="sv_tab",
fluidRow(
box(
title = "Summary",
status="primary",
width = 8,
height="100%",
fluidRow(
column(4,
textOutput("total_sv"),
br(),
textOutput("ins_sum"),
br(),
textOutput("del_sum"),
br(),
textOutput("dup_sum")
),
column(4,
textOutput("bnd_sum"),
br(),
textOutput("imprecise_sum"),
br(),
textOutput("max_sv_len"),
br(),
textOutput("ave_ins_len")
),
column(4,
textOutput("ave_del_len"),
br(),
textOutput("ave_dup_len"),
br(),
textOutput("sv_genes_sum"),
br(),
textOutput("genes_list_sum")
)
)
)
,
box(
title="Files",
width=4,
fluidRow(
column(12,
htmlOutput("sv_tsv_label"),
br()
)
),
fluidRow(
column(3,
shinyFilesButton("sv_tsv", "Browse...",title="Upload SV pipeline output file (.tsv/.txt)",
filetype=c(".tsv", ".txt"), multiple=F)
),
column(9,
textOutput("sv_tsv_name")
)
),
fluidRow(
column(12,
htmlOutput("sv_gene_list_label"),
br()
)
),
fluidRow(
column(3,
shinyFilesButton("sv_gene_list", "Browse...",
title="Upload a list of genes of interest (.xlsx/.txt)",
filetype=c(".xlsx", ".txt"), multiple=F)
),
column(9,
textOutput("sv_gene_list_name")
)
),
status = "primary",
textOutput("text")
)),
fluidRow(
box(
title = "Stuctural Variants",
status="primary",
height="100%",
width = "100%",
downloadButton("sv_download", "Download"),
tags$br(),
DTOutput("sv_table")
)
)
)
)
)
# define user interface
ui <- dashboardPage(
dashboardHeader(title="IBD Variants"),
sidebar,
body
)