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ui.R
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ui.R
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#HudsonAlpha Cancer Variant Annotation Tool
#Brittany N. Lasseigne, 160119
#v1.0
###Utilizes v1.0 cancer variant cache (Kandoth curated mutation data only)
library(shiny)
shinyUI(fluidPage(
#title panel
titlePanel(
h1("HudsonAlpha Cancer Variant Annotation Tool", align="center")
),
fluidRow(
column(10,
offset=1,
h4("Fast Annotation of Known Cancer-Associated Variants",align="center"))
),
fluidRow(
column(12,
br(),
tags$hr()
)
),
#Upload data
fluidRow(
column(3,
wellPanel(
h4("Upload Data", align="center"),
p("HudsonAlpha's Cancer Variant Annotation tool requires an input VCF file containing variants of interest:"),
a("Click for more information about VCF files", href="http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it"),
br(),
br(),
fileInput('datafile', 'Choose VCF Text File'),
p("Alternatively, download example input VCF from the 'Download Center'"),
tags$hr(),
selectInput("uniqueAll",
"Would you like to annotate all variants or only unique variants in the file?",
choices = c("All Variants", "Unique Variants Only"),
selected="Unique Variants Only"),
tags$hr(),
#message handler for popup
#tags$head(tags$script(src = "message-handler.js")),
actionButton("submitButton", "Execute Analysis")
),
p("Developed and Maintained by:"),
a("Rick Myers' and", href="http://research.hudsonalpha.org/Myers/"),
a("Sara Cooper's Labs", href="http://research.hudsonalpha.org/CooperS/"),
br(),
p("Contact: Brittany Lasseigne (blasseigne@hudsonalpha.org) or Ryne Ramaker (rramaker@hudsonalpha.org)"),
a("HudsonAlpha Institute for Biotechnology", href="http://hudsonalpha.org", align="center"),
img(src = "hudson-logo.png", height=50, width=200, align="center")
),
#file stats
column(6,
h4("Input File Information", align="center"),
br(),
textOutput("numVarFile"), #show number of variants in file
conditionalPanel(
condition = "infile!==NULL",
textOutput("infile$datapath")),
textOutput("options"), #show whether annotating all/unique variants
conditionalPanel(
condition = "options!==NULL",
textOutput("variantInput")),
br(),
p("The first five lines of a successfully loaded file display here:"),
tableOutput("view"),
br(),
p("The first five annotated variants display here:"),
tableOutput("viewAnno"),
textOutput("annotatedVariants"), #number of annotated variants
textOutput("unannotatedVariants"), #number of variants not in cache (unannotated)
br()
),
#download files
column(3,
#info about CADD
h5("CADD v1.3 C Scores", align="center"),
p("See the following links for more information about CADD and c scores, or to annotate variants not in the cancer mutation cache:"),
a("Combined Annotation Dependent Depletion (CADD)", href="http://cadd.gs.washington.edu"),
a("Kircher & Witten, et al. 2014", href="http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html"),
br(),
br(),
#download center
wellPanel(
h4("Download Center", align="center"),
p("This is where you download annotated and nonannotated variants"),
selectInput("dataOut", "Select file to download:",
choices = c("Example_Input_Data", "Annotated_Variants", "Unannotated_Variants")),
downloadButton('downloadData', 'Download')
), #end of wellPanel
#info about mutation cache
h5("Cancer Mutation Cache v1.0", align="center"),
p("The current cancer mutation cache includes all curated variants previously reported by the TCGA PanCancer Project in"),
a("Kandoth, et al. 2013", href="http://www.nature.com/nature/journal/v502/n7471/full/nature12634.html"),
br(),
br(),
p("Additional variants and annotations will be added soon.")
)
)
))