Nothing
inst/shiny/microhaplot/ui.R
In microhaplot: Microhaplotype Constructor and Visualizer
library(shiny)
library(shinyBS)
library(shinyWidgets)
# Define UI for application that draws a histogram
shinyUI(
fluidPage(
style = "padding-top: 200px;z-index: -1;", #180
# Application title
# titlePanel("Haplotype Viewer"),
absolutePanel(
style = "z-index:10",
top = 0,
left = 0,
right = 0,
fixed = TRUE,
div(style = "padding: 10px 4px 0px 4px; border-bottom: 0px solid #CCC; margin-bottom: 0px; background: #F3FCFF",
fluidRow(
column(12,
tabsetPanel(
tabPanel("> field selection",
column(
12,
column(
6,
column(2,
"Group:", style = "margin-top:21px;font-weight:bold; padding-left:0px",
offset = 0),
column(
8,
selectInput("selectGroup", label = "", "", selected = ""),
style = "margin-top:-10px;margin-bottom:-10px;"
),
style = "padding-left:0px"
),
column(
6,
column(2, "Indiv:", style = "margin-top:21px;font-weight:bold; padding-left:0px"),
column(
8,
selectInput("selectIndiv", label = "", "", selected = ""),
style = "margin-top:-10px;margin-bottom:-10px;"
),
column(1,
actionButton(
"indivBack", label = "<", width = "80%"
),
style = "margin-top:10px; padding: 0 0% 0 0%"),
column(1, actionButton(
"indivFor", label = ">", width = "80%"
),
style = "margin-top:10px;padding:0 0% 0 0%; margin-left: 0px;"),
style = "padding-left:0px"
),
column(10,
column(2, "Locus:", style = "margin-top:22px;font-weight:bold; padding-left:0px"),
column(
6,
selectInput("selectLocus", label = "", "", selected = "", width = "100%"),
style = "margin-top:-10px;margin-bottom:-10px; margin-left: -5%;padding-left:0px"
),
column(2,
column(
5,
actionButton("locusBack", label = "<", width = "80%"),
style = "margin-top:10px; padding: 0 0% 0 0%",
offset = 0
),
column(5, actionButton(
"locusFor", label = ">", width = "80%"
),
style = "margin-top:10px;padding:0 0% 0 0%; margin-left: 0px;"),
style = "padding-left:0px"
),
style = "padding-left:0px"
),
style="background:#F7F7F7; padding-top:8px;padding-bottom:10px"
),
style="padding-bottom:20px"
),
tabPanel("+ read criteria",
column(
12,
column(
7,
column(4,
chooseSliderSkin("Modern", color = "#3A75DC"),
shinyWidgets::sliderTextInput("n.alleles",
label = "Top n Alleles:",
choices = c(0:20,Inf),
selected = 2,
grid = FALSE,
width = 150),
style = "margin-top:10px;text-align:center; margin-bottom:0px; padding-bottom:0px"),
column(4,
shinyWidgets::sliderTextInput("coverageMin",
label = "Min Total Read Depth",
choices = c(0:30,50,100,1000,Inf),
selected = 2,
grid = FALSE,
width = 150),
style = "margin-top:10px;text-align:center; margin-bottom:0px; margin-right:0px; padding-bottom:0px;padding-right:0px"),
column(4,
shinyWidgets::sliderTextInput("minAlleleRatio",
label = "Min Allelic Ratio:",
choices = seq(0,1,0.01),
selected = 0,
grid = FALSE,
width = 150),
style = "margin-top:10px;text-align:center; margin-bottom:0px; padding-bottom:0px"),
style = "padding: 0 0 0 0; margin: -1% 0 0 0;"
),
column(
2,
column(10, verticalLayout(actionButton("updateFilter", label = "apply",
width="100%",
style="text-align:center"),
actionButton(
"filterSave",
"save",
#icon("hdd-o"),
width="100%",
style = "margin-top:10px; text-align:center"
)), style =
"margin-top:0px; padding-right: 0px;")
),
column(
3,
checkboxGroupInput("filterOpts", label = "", choices=list()),
style = "margin-top:-15px; margin-left:0px; padding: 0 0 0 0"
),
style="background:#F7F7F7; padding-top:10px")
),
tabPanel("+ locus annotation",
column(12,
column(
5,
column(3, "Locus:", style ="margin-top:21px;font-weight:bold; padding-left:0px"),
column(9, textOutput("locusSelect1"), style =
"margin-left: 0px; color:grey; margin-top:21px;padding-left: 0px")
),
column(5,
column(2, "status:",style = "margin-top:23px;font-weight:normal; padding-left:0px"),
column(4,
selectInput("locusAccept",
"",
choices=c("Accept","Reject","NA"),
selected="NA"),
style = "margin-top:-8px; margin-bottom:0px"
)
),
column(2,
actionButton(
"annotateSave",
"save",
icon("hdd-o"),
style = "margin-top:10px; padding-right: 0px; text-align:center",
width = "90%"
),
offset=0
),
column(12,
column(1, "Note:", style ="margin-top:5px; padding-left:0px"),
column(11,
textInput("locusComment", label = "", value = "", width="100%"),
style = "margin-top:-20px;padding-top:0px;padding-right: 0px;padding-left:0px")),
style="background:#F7F7F7; padding-top:2px;padding-left:0px; margin-left:0px"
)
)
))
))
),
bsAlert("alert"),
navbarPage(
"",
tabPanel("Data Set",
fluidRow(column(
12,
column(
10,
selectInput(
"selectDB",
label = "Select Data Set:",
"",
selected = NULL,
width = "80%"
),
style = "padding-left:0px;margin-top:10%;margin-bottom:-10px;",
offset = 1
)
))),
# group label panel
navbarMenu("Summary",
tabPanel(h5("By Group"),
fluidRow(
column(5, plotOutput("fIndivByGroupPlot", height =
"auto")),
column(5, plotOutput("fLociByGroupPlot", height =
"auto"))
),
fluidRow(
div(style = "padding: 40px; border-bottom: 20px solid white; background: white")
)
),
tabPanel(
h5("By Individual"),
fluidRow(
column(4, column(
12,
column(7, h6("Display (indiv/pg) : ")),
column(
5,
selectInput(
"indivPerDisplay",
label = NULL,
choices = list(
"15" = 15,
"30" =
30,
"60" =
60,
"ALL" =
100
),
selected =
15
)
)
)),
column(4, column(
12,
column(1, h6("Page:")),
column(
5,
numericInput(
"indivPage",
label = NULL,
value = 1,
min = 1,
step = 1
),
offset = 1
),
column(1, h6("of ")),
column(1, h6(textOutput("maxIndivPage")))
)),
column(4,column(4,h6("Height:")),
column(8,
selectInput(
"indivHeight",
label = NULL,
choices = list("50%" = 0.5, "100%" = 1, "150%" = 1.5,
"200%" = 2,"500%" = 5),
selected = 1)
)),
style = "border-bottom: 1px double #d9d9d9; margin-bottom: 20px; padding-top:15px"
),
fluidRow(
column(
5,
plotOutput(
"AlleleRatioByIndiv",
height = "auto",
dblclick = dblclickOpts(id = "plot_dblclick"),
brush = brushOpts(
id = "plot_brush",
direction = "y",
resetOnNew = TRUE
)
)
),
column(2, plotOutput("numUniqHapByIndiv", height =
"auto")),
column(2, plotOutput("fracHaploPlot", height = "auto")),
column(3, plotOutput("readDepthByIndiv", height =
"auto"))
),
column(12, h1("")),
br(),
fluidRow(
div(style = "padding: 10px; border-bottom: 8px solid white; background: white")
)
),
tabPanel(
h5("By Locus"),
fluidRow(
column(4, column(
12,
column(7, h6("Display (loci/pg) : ")),
column(
5,
selectInput(
"locusPerDisplay",
label = NULL,
choices = list(
"15" = 15,
"30" =
30,
"60" =
60,
"ALL" =
100
),
selected =
15
)
)
)),
column(4, column(
12,
column(1, h6("Page:")),
column(
5,
numericInput(
"locusPage",
label = NULL,
value = 1,
min = 1,
step = 1
),
offset = 1
),
column(1, h6(" of ")),
column(1, h6(textOutput("maxlocusPage")))
)),
column(4,column(4,h6("Height:")),
column(8,
selectInput(
"lociHeight",
label = NULL,
choices = list(
"50%" = 0.5,
"100%" =
1,
"150%" =
1.5,
"200%" =
2,
"500%" =
5
),
selected =
1
)
)),
style = "border-bottom: 1px double #d9d9d9; margin-bottom: 20px; padding-top:15px"
),
fluidRow(
column(
5,
plotOutput(
"haplDensityPlot",
height = "auto",
dblclick = dblclickOpts(id = "plotH_dblclick"),
brush = brushOpts(
id = "plotH_brush",
direction = "y",
resetOnNew = TRUE
)
)
),
column(2, plotOutput("numHapPlot", height = "auto")),
column(2, plotOutput("fracIndivPlot", height = "auto")),
column(3, plotOutput("readDepthPerLocus", height =
"auto"))
),
fluidRow(
div(style = "padding: 40px; border-bottom: 20px solid white; background: white")
)
)
),
navbarMenu("Criteria Cutoff",
# table panel
tabPanel(
h5("Global Scope"),
fluidRow(
column(5, plotOutput("allReadDepth", height = "auto",
# hover = hoverOpts(
# id = "RDplot_hover",
# delay = 500,
# delayType = "debounce"
# ),
dblclick = dblclickOpts(id = "RDplot_dblclick")),
offset=2),
column(5, plotOutput("allAllelicRatio", height = "auto",
dblclick = dblclickOpts(id = "ARplot_dblclick")
))
),
fluidRow(
column(12, h4(textOutput("DP1"))),
column(2, plotOutput("haplabel", height = "auto"),
style="padding-left:0px; padding-right:0px"
),
column(5, plotOutput("hapReadDepth", height = "auto",
click = "hapRDClick")),
column(5, plotOutput("hapAllelicRatio", height = "auto",
click = "hapARClick"))
),
fluidRow(
div(style = "padding: 10px; border-bottom: 2px solid white; background: white")
),
fluidRow(
column(12, plotOutput("RDnARplot", height = "auto"))
),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
),
tabPanel(
h5("Quality Profiling"),
column(12, HTML("The following content disregards the <b>min total read depth</b>. Instead, it will relied on the following filter:")),
column(6,
shinyWidgets::sliderTextInput("rdMin",
label = "Min read depth (per haplotype)",
choices = c(0:30,50,100,1000,Inf),
selected = 2,
grid = FALSE),
style = "margin-top:10px;text-align:center; margin-bottom:0px; margin-right:0px; padding-bottom:0px;padding-right:0px", offset=3),
column(2, verticalLayout(actionButton("updateRdMin", label = "update",
width="100%",
style="text-align:center")),
style = "margin-top:25px;text-align:center; margin-bottom:0px; margin-right:0px; padding-bottom:0px;padding-right:0px;padding-left:0px",
offset=0),
column(6, h4("Individual list:")),
column(6, h4("Loci list:")),
# mod to add interactive table, ranks of ranks (based on rank of rd, calleable hap)
column(6, plotOutput("ambigIndivPlot", height = "auto",
dblclick = dblclickOpts(id = "aip_dblclick"),
brush = brushOpts(
id = "aip_Brush",
direction = "x",
resetOnNew = TRUE
))),
column(6, plotOutput("ambigLociPlot", height = "auto",
dblclick = dblclickOpts(id = "alp_dblclick"),
brush = brushOpts(
id = "alp_Brush",
direction = "x",
resetOnNew = TRUE
))),
column(6, h5("Of loci and individuals that have more than 'Top n' qualified alleles:")),
column(12, DT::dataTableOutput('indivProfileTbl')),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
)
),
navbarMenu("Genotype Call",
# table panel
tabPanel(
h5("AR Refinement"),
fluidRow(
bsAlert("ARalert")
),
fluidRow(
column(12,
column(5, checkboxInput("keepSel", label = "keeps pt selection between loci"),
style="margin-top:4px;"),
column(3, h6("Scale: max read depth displayed"),offset = 0,
style="padding-top:0px; margin-top:8px"),
column(4, shinyWidgets::sliderTextInput("max_read_depth",
label = "",
choices = 10 * 2^(0:13),
selected = 1280,
grid = FALSE),
style="padding-top:-20px; margin-top:-20px"),
style = "border-bottom: 1px double #d9d9d9; margin-bottom: 20px; padding-top:-10px; margin-top:-10px"
),
column(4,
column(12, plotOutput("pieCallChart",height="auto"),style="padding:0 0 0 0; margin:0 0 0 0"),
column(6, actionButton(
"preL",
"prev locus",
width="100%",
style = "margin-top:10px; text-align:center; margin-bottom:15px"
)),
column(6, actionButton(
"nextL",
"next locus",
width="100%",
style = "margin-top:10px; text-align:center; margin-bottom:15px"
)),
column(12, htmlOutput("savedARstat"), style="margin-bottom:4px"),
column(12, sliderInput("max.ar.hm",
label = "Max AR for Homoz (blue)",
min = 0,
max = 1,
value = 0.3,
ticks= FALSE,
step = 0.01)),
column(12, sliderInput("min.ar.hz",
label = "Min AR for Het (yellow)",
min = 0,
max = 1,
value = 0.4,
ticks=F,
step = 0.01))
),
column(8,
ggiraph::ggiraphOutput("biplot", height = "450px"),
height="auto",
style= "width:'100%'"),
column(12,
DT::dataTableOutput("biPlotTbl")),
column(12, h4(textOutput("DP2")), textOutput("DP3")),
column(12, ""),
column(1, plotOutput("uchaplabel", height = "auto"),
style="padding-left:0px; padding-right:0px"
),
column(6, plotOutput("uchapReadDepth", height = "auto")),
column(5, plotOutput("uchapAllelicRatio", height = "auto"))
),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
),
#locus assessement panel
tabPanel(
h5("Summaries"),
fluidRow(
bsAlert("hapAlert")
),
fluidRow(
column(12,
column(6, htmlOutput("hapFreqClicked")),
column(6, htmlOutput("hwClicked"))),
column(6, plotOutput("hapFreq",
height ="auto",
click = "hapFreqPlotClick",
hover=hoverOpts(id="hapFreqPlotHover",
delay=300,
delayType = "throttle")),
style="padding-right:0px"),
column(6, plotOutput("PairWiseHap", height =
"auto",
click = "HWplotClick",
hover=hoverOpts(id="HWPlotHover",
delay=300,
delayType = "throttle")),
style="padding-left:0px"),
column(12, htmlOutput("hapByGroupPlotClicked")),
column(12, plotOutput("hapByGroupPlot",
height ="auto",
click = "hapByGroupPlotClick",
hover=hoverOpts(id="hapByGroupPlotHover",
delay=300,
delayType = "throttle"))),
column(12, plotOutput("hapSeq", height = "auto"))
),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
)
),
# tabPanel(
# "Inferential Analysis",
# "SrMicroHap is sensitive only to the changes in \"Locus\" selector tab\n",
# wellPanel(fluidRow(
# column(
# 12,
# column(
# 2,
# numericInput(
# "gibbIter",
# "Num of Iter:",
# min = 1,
# value = 1000,
# step=1)
# ),
# column(
# 2,
# numericInput(
# "fracBurn",
# "% for Burn-in",
# min = 0,
# max = 99,
# value = 0
# )
# ),
# column(
# 2,
# numericInput(
# "randomSeed",
# label = "Random Seed",
# value = 34532,
# min = 1,
# step = 1
# ),
# offset=1
# ),
# column(
# 2,
# selectInput(
# "selectPrior",
# label = "Prior Model",
# c("uniform", "empirical"),
# selected = "empirical"
# )
# ),
# column(
# 2,
# actionButton(
# "submitSrMicroHap",
# "Submit",
# icon("random"),
# style = "margin-top:20px; padding-right: 0px;",
# width = "100%"
# ),
# offset=1
# )
# ),
# column(12, "Parameters define the characteristic of true haplotypes:"),
# column(12,
# column(3, numericInput(
# "minRDsr",
# label = "min read depth (total indiv)",
# value = 10,
# min = 1,
# step = 1
# )),
# column(3, numericInput(
# "minARsr",
# "min allelic ratio",
# min = 0,
# max = 1,
# value = 0.2,
# step=0.01
# ))
# ))),
# fluidRow(column(
# 12, plotOutput("indivHapPosPlot", height = "auto")
# ),
# #column(12, plotOutput("allHapFreqPlot", height = "auto")),
# column(
# 12, plotOutput("HapFreqByGroupPlot", height = "auto")
# )),
# fluidRow(
# div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
# )
# ),
# table panel
tabPanel(
"Table",
fixedPanel(
#top="200px",
style = "z-index:9;background-color:white; margin-top: -40px; padding-top: 15px; height:90px",
width="100%",
fluidRow(
column(
6,
column(4, h5("Select Table:"), offset =
0),
column(
8,
selectInput(
"selectTbl",
label = "",
c("observed variants (unfiltered)","observed variants (filtered)",
"reported indiv haplotype (diploid)", "reported haplotype (flat)", "SNP report", "locus annotation"),
selected = "observed variants (unfiltered)"
),
style = "background-color:white; padding-right: 0px; margin-top:-20px;margin-bottom:-30px;padding-left:0%; padding-right: 0px;"
)
),
column(6, column(
12,
column(4, downloadButton('downloadData', 'Download'))
)),
style = "border-bottom: 1px double #d9d9d9; margin-bottom: 40px; padding-top:15px; padding-bottom:20px")
),
column(12, DT::dataTableOutput('haploTbl'),
style = "padding-bottom: 40px; border-bottom: 8px solid white; background: white; margin-top: 100px;"),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
),
tabPanel(
"About",
column(12,
column(8,
htmlOutput("about"),
offset=2
))
),
position = "fixed-bottom"
),
titlePanel("", windowTitle = "HapPLOType: a view to your haplotypes")
)
)
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microhaplot documentation built on Oct. 3, 2019, 9:03 a.m.
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library(shiny)
library(shinyBS)
library(shinyWidgets)
# Define UI for application that draws a histogram
shinyUI(
fluidPage(
style = "padding-top: 200px;z-index: -1;", #180
# Application title
# titlePanel("Haplotype Viewer"),
absolutePanel(
style = "z-index:10",
top = 0,
left = 0,
right = 0,
fixed = TRUE,
div(style = "padding: 10px 4px 0px 4px; border-bottom: 0px solid #CCC; margin-bottom: 0px; background: #F3FCFF",
fluidRow(
column(12,
tabsetPanel(
tabPanel("> field selection",
column(
12,
column(
6,
column(2,
"Group:", style = "margin-top:21px;font-weight:bold; padding-left:0px",
offset = 0),
column(
8,
selectInput("selectGroup", label = "", "", selected = ""),
style = "margin-top:-10px;margin-bottom:-10px;"
),
style = "padding-left:0px"
),
column(
6,
column(2, "Indiv:", style = "margin-top:21px;font-weight:bold; padding-left:0px"),
column(
8,
selectInput("selectIndiv", label = "", "", selected = ""),
style = "margin-top:-10px;margin-bottom:-10px;"
),
column(1,
actionButton(
"indivBack", label = "<", width = "80%"
),
style = "margin-top:10px; padding: 0 0% 0 0%"),
column(1, actionButton(
"indivFor", label = ">", width = "80%"
),
style = "margin-top:10px;padding:0 0% 0 0%; margin-left: 0px;"),
style = "padding-left:0px"
),
column(10,
column(2, "Locus:", style = "margin-top:22px;font-weight:bold; padding-left:0px"),
column(
6,
selectInput("selectLocus", label = "", "", selected = "", width = "100%"),
style = "margin-top:-10px;margin-bottom:-10px; margin-left: -5%;padding-left:0px"
),
column(2,
column(
5,
actionButton("locusBack", label = "<", width = "80%"),
style = "margin-top:10px; padding: 0 0% 0 0%",
offset = 0
),
column(5, actionButton(
"locusFor", label = ">", width = "80%"
),
style = "margin-top:10px;padding:0 0% 0 0%; margin-left: 0px;"),
style = "padding-left:0px"
),
style = "padding-left:0px"
),
style="background:#F7F7F7; padding-top:8px;padding-bottom:10px"
),
style="padding-bottom:20px"
),
tabPanel("+ read criteria",
column(
12,
column(
7,
column(4,
chooseSliderSkin("Modern", color = "#3A75DC"),
shinyWidgets::sliderTextInput("n.alleles",
label = "Top n Alleles:",
choices = c(0:20,Inf),
selected = 2,
grid = FALSE,
width = 150),
style = "margin-top:10px;text-align:center; margin-bottom:0px; padding-bottom:0px"),
column(4,
shinyWidgets::sliderTextInput("coverageMin",
label = "Min Total Read Depth",
choices = c(0:30,50,100,1000,Inf),
selected = 2,
grid = FALSE,
width = 150),
style = "margin-top:10px;text-align:center; margin-bottom:0px; margin-right:0px; padding-bottom:0px;padding-right:0px"),
column(4,
shinyWidgets::sliderTextInput("minAlleleRatio",
label = "Min Allelic Ratio:",
choices = seq(0,1,0.01),
selected = 0,
grid = FALSE,
width = 150),
style = "margin-top:10px;text-align:center; margin-bottom:0px; padding-bottom:0px"),
style = "padding: 0 0 0 0; margin: -1% 0 0 0;"
),
column(
2,
column(10, verticalLayout(actionButton("updateFilter", label = "apply",
width="100%",
style="text-align:center"),
actionButton(
"filterSave",
"save",
#icon("hdd-o"),
width="100%",
style = "margin-top:10px; text-align:center"
)), style =
"margin-top:0px; padding-right: 0px;")
),
column(
3,
checkboxGroupInput("filterOpts", label = "", choices=list()),
style = "margin-top:-15px; margin-left:0px; padding: 0 0 0 0"
),
style="background:#F7F7F7; padding-top:10px")
),
tabPanel("+ locus annotation",
column(12,
column(
5,
column(3, "Locus:", style ="margin-top:21px;font-weight:bold; padding-left:0px"),
column(9, textOutput("locusSelect1"), style =
"margin-left: 0px; color:grey; margin-top:21px;padding-left: 0px")
),
column(5,
column(2, "status:",style = "margin-top:23px;font-weight:normal; padding-left:0px"),
column(4,
selectInput("locusAccept",
"",
choices=c("Accept","Reject","NA"),
selected="NA"),
style = "margin-top:-8px; margin-bottom:0px"
)
),
column(2,
actionButton(
"annotateSave",
"save",
icon("hdd-o"),
style = "margin-top:10px; padding-right: 0px; text-align:center",
width = "90%"
),
offset=0
),
column(12,
column(1, "Note:", style ="margin-top:5px; padding-left:0px"),
column(11,
textInput("locusComment", label = "", value = "", width="100%"),
style = "margin-top:-20px;padding-top:0px;padding-right: 0px;padding-left:0px")),
style="background:#F7F7F7; padding-top:2px;padding-left:0px; margin-left:0px"
)
)
))
))
),
bsAlert("alert"),
navbarPage(
"",
tabPanel("Data Set",
fluidRow(column(
12,
column(
10,
selectInput(
"selectDB",
label = "Select Data Set:",
"",
selected = NULL,
width = "80%"
),
style = "padding-left:0px;margin-top:10%;margin-bottom:-10px;",
offset = 1
)
))),
# group label panel
navbarMenu("Summary",
tabPanel(h5("By Group"),
fluidRow(
column(5, plotOutput("fIndivByGroupPlot", height =
"auto")),
column(5, plotOutput("fLociByGroupPlot", height =
"auto"))
),
fluidRow(
div(style = "padding: 40px; border-bottom: 20px solid white; background: white")
)
),
tabPanel(
h5("By Individual"),
fluidRow(
column(4, column(
12,
column(7, h6("Display (indiv/pg) : ")),
column(
5,
selectInput(
"indivPerDisplay",
label = NULL,
choices = list(
"15" = 15,
"30" =
30,
"60" =
60,
"ALL" =
100
),
selected =
15
)
)
)),
column(4, column(
12,
column(1, h6("Page:")),
column(
5,
numericInput(
"indivPage",
label = NULL,
value = 1,
min = 1,
step = 1
),
offset = 1
),
column(1, h6("of ")),
column(1, h6(textOutput("maxIndivPage")))
)),
column(4,column(4,h6("Height:")),
column(8,
selectInput(
"indivHeight",
label = NULL,
choices = list("50%" = 0.5, "100%" = 1, "150%" = 1.5,
"200%" = 2,"500%" = 5),
selected = 1)
)),
style = "border-bottom: 1px double #d9d9d9; margin-bottom: 20px; padding-top:15px"
),
fluidRow(
column(
5,
plotOutput(
"AlleleRatioByIndiv",
height = "auto",
dblclick = dblclickOpts(id = "plot_dblclick"),
brush = brushOpts(
id = "plot_brush",
direction = "y",
resetOnNew = TRUE
)
)
),
column(2, plotOutput("numUniqHapByIndiv", height =
"auto")),
column(2, plotOutput("fracHaploPlot", height = "auto")),
column(3, plotOutput("readDepthByIndiv", height =
"auto"))
),
column(12, h1("")),
br(),
fluidRow(
div(style = "padding: 10px; border-bottom: 8px solid white; background: white")
)
),
tabPanel(
h5("By Locus"),
fluidRow(
column(4, column(
12,
column(7, h6("Display (loci/pg) : ")),
column(
5,
selectInput(
"locusPerDisplay",
label = NULL,
choices = list(
"15" = 15,
"30" =
30,
"60" =
60,
"ALL" =
100
),
selected =
15
)
)
)),
column(4, column(
12,
column(1, h6("Page:")),
column(
5,
numericInput(
"locusPage",
label = NULL,
value = 1,
min = 1,
step = 1
),
offset = 1
),
column(1, h6(" of ")),
column(1, h6(textOutput("maxlocusPage")))
)),
column(4,column(4,h6("Height:")),
column(8,
selectInput(
"lociHeight",
label = NULL,
choices = list(
"50%" = 0.5,
"100%" =
1,
"150%" =
1.5,
"200%" =
2,
"500%" =
5
),
selected =
1
)
)),
style = "border-bottom: 1px double #d9d9d9; margin-bottom: 20px; padding-top:15px"
),
fluidRow(
column(
5,
plotOutput(
"haplDensityPlot",
height = "auto",
dblclick = dblclickOpts(id = "plotH_dblclick"),
brush = brushOpts(
id = "plotH_brush",
direction = "y",
resetOnNew = TRUE
)
)
),
column(2, plotOutput("numHapPlot", height = "auto")),
column(2, plotOutput("fracIndivPlot", height = "auto")),
column(3, plotOutput("readDepthPerLocus", height =
"auto"))
),
fluidRow(
div(style = "padding: 40px; border-bottom: 20px solid white; background: white")
)
)
),
navbarMenu("Criteria Cutoff",
# table panel
tabPanel(
h5("Global Scope"),
fluidRow(
column(5, plotOutput("allReadDepth", height = "auto",
# hover = hoverOpts(
# id = "RDplot_hover",
# delay = 500,
# delayType = "debounce"
# ),
dblclick = dblclickOpts(id = "RDplot_dblclick")),
offset=2),
column(5, plotOutput("allAllelicRatio", height = "auto",
dblclick = dblclickOpts(id = "ARplot_dblclick")
))
),
fluidRow(
column(12, h4(textOutput("DP1"))),
column(2, plotOutput("haplabel", height = "auto"),
style="padding-left:0px; padding-right:0px"
),
column(5, plotOutput("hapReadDepth", height = "auto",
click = "hapRDClick")),
column(5, plotOutput("hapAllelicRatio", height = "auto",
click = "hapARClick"))
),
fluidRow(
div(style = "padding: 10px; border-bottom: 2px solid white; background: white")
),
fluidRow(
column(12, plotOutput("RDnARplot", height = "auto"))
),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
),
tabPanel(
h5("Quality Profiling"),
column(12, HTML("The following content disregards the <b>min total read depth</b>. Instead, it will relied on the following filter:")),
column(6,
shinyWidgets::sliderTextInput("rdMin",
label = "Min read depth (per haplotype)",
choices = c(0:30,50,100,1000,Inf),
selected = 2,
grid = FALSE),
style = "margin-top:10px;text-align:center; margin-bottom:0px; margin-right:0px; padding-bottom:0px;padding-right:0px", offset=3),
column(2, verticalLayout(actionButton("updateRdMin", label = "update",
width="100%",
style="text-align:center")),
style = "margin-top:25px;text-align:center; margin-bottom:0px; margin-right:0px; padding-bottom:0px;padding-right:0px;padding-left:0px",
offset=0),
column(6, h4("Individual list:")),
column(6, h4("Loci list:")),
# mod to add interactive table, ranks of ranks (based on rank of rd, calleable hap)
column(6, plotOutput("ambigIndivPlot", height = "auto",
dblclick = dblclickOpts(id = "aip_dblclick"),
brush = brushOpts(
id = "aip_Brush",
direction = "x",
resetOnNew = TRUE
))),
column(6, plotOutput("ambigLociPlot", height = "auto",
dblclick = dblclickOpts(id = "alp_dblclick"),
brush = brushOpts(
id = "alp_Brush",
direction = "x",
resetOnNew = TRUE
))),
column(6, h5("Of loci and individuals that have more than 'Top n' qualified alleles:")),
column(12, DT::dataTableOutput('indivProfileTbl')),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
)
),
navbarMenu("Genotype Call",
# table panel
tabPanel(
h5("AR Refinement"),
fluidRow(
bsAlert("ARalert")
),
fluidRow(
column(12,
column(5, checkboxInput("keepSel", label = "keeps pt selection between loci"),
style="margin-top:4px;"),
column(3, h6("Scale: max read depth displayed"),offset = 0,
style="padding-top:0px; margin-top:8px"),
column(4, shinyWidgets::sliderTextInput("max_read_depth",
label = "",
choices = 10 * 2^(0:13),
selected = 1280,
grid = FALSE),
style="padding-top:-20px; margin-top:-20px"),
style = "border-bottom: 1px double #d9d9d9; margin-bottom: 20px; padding-top:-10px; margin-top:-10px"
),
column(4,
column(12, plotOutput("pieCallChart",height="auto"),style="padding:0 0 0 0; margin:0 0 0 0"),
column(6, actionButton(
"preL",
"prev locus",
width="100%",
style = "margin-top:10px; text-align:center; margin-bottom:15px"
)),
column(6, actionButton(
"nextL",
"next locus",
width="100%",
style = "margin-top:10px; text-align:center; margin-bottom:15px"
)),
column(12, htmlOutput("savedARstat"), style="margin-bottom:4px"),
column(12, sliderInput("max.ar.hm",
label = "Max AR for Homoz (blue)",
min = 0,
max = 1,
value = 0.3,
ticks= FALSE,
step = 0.01)),
column(12, sliderInput("min.ar.hz",
label = "Min AR for Het (yellow)",
min = 0,
max = 1,
value = 0.4,
ticks=F,
step = 0.01))
),
column(8,
ggiraph::ggiraphOutput("biplot", height = "450px"),
height="auto",
style= "width:'100%'"),
column(12,
DT::dataTableOutput("biPlotTbl")),
column(12, h4(textOutput("DP2")), textOutput("DP3")),
column(12, ""),
column(1, plotOutput("uchaplabel", height = "auto"),
style="padding-left:0px; padding-right:0px"
),
column(6, plotOutput("uchapReadDepth", height = "auto")),
column(5, plotOutput("uchapAllelicRatio", height = "auto"))
),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
),
#locus assessement panel
tabPanel(
h5("Summaries"),
fluidRow(
bsAlert("hapAlert")
),
fluidRow(
column(12,
column(6, htmlOutput("hapFreqClicked")),
column(6, htmlOutput("hwClicked"))),
column(6, plotOutput("hapFreq",
height ="auto",
click = "hapFreqPlotClick",
hover=hoverOpts(id="hapFreqPlotHover",
delay=300,
delayType = "throttle")),
style="padding-right:0px"),
column(6, plotOutput("PairWiseHap", height =
"auto",
click = "HWplotClick",
hover=hoverOpts(id="HWPlotHover",
delay=300,
delayType = "throttle")),
style="padding-left:0px"),
column(12, htmlOutput("hapByGroupPlotClicked")),
column(12, plotOutput("hapByGroupPlot",
height ="auto",
click = "hapByGroupPlotClick",
hover=hoverOpts(id="hapByGroupPlotHover",
delay=300,
delayType = "throttle"))),
column(12, plotOutput("hapSeq", height = "auto"))
),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
)
),
# tabPanel(
# "Inferential Analysis",
# "SrMicroHap is sensitive only to the changes in \"Locus\" selector tab\n",
# wellPanel(fluidRow(
# column(
# 12,
# column(
# 2,
# numericInput(
# "gibbIter",
# "Num of Iter:",
# min = 1,
# value = 1000,
# step=1)
# ),
# column(
# 2,
# numericInput(
# "fracBurn",
# "% for Burn-in",
# min = 0,
# max = 99,
# value = 0
# )
# ),
# column(
# 2,
# numericInput(
# "randomSeed",
# label = "Random Seed",
# value = 34532,
# min = 1,
# step = 1
# ),
# offset=1
# ),
# column(
# 2,
# selectInput(
# "selectPrior",
# label = "Prior Model",
# c("uniform", "empirical"),
# selected = "empirical"
# )
# ),
# column(
# 2,
# actionButton(
# "submitSrMicroHap",
# "Submit",
# icon("random"),
# style = "margin-top:20px; padding-right: 0px;",
# width = "100%"
# ),
# offset=1
# )
# ),
# column(12, "Parameters define the characteristic of true haplotypes:"),
# column(12,
# column(3, numericInput(
# "minRDsr",
# label = "min read depth (total indiv)",
# value = 10,
# min = 1,
# step = 1
# )),
# column(3, numericInput(
# "minARsr",
# "min allelic ratio",
# min = 0,
# max = 1,
# value = 0.2,
# step=0.01
# ))
# ))),
# fluidRow(column(
# 12, plotOutput("indivHapPosPlot", height = "auto")
# ),
# #column(12, plotOutput("allHapFreqPlot", height = "auto")),
# column(
# 12, plotOutput("HapFreqByGroupPlot", height = "auto")
# )),
# fluidRow(
# div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
# )
# ),
# table panel
tabPanel(
"Table",
fixedPanel(
#top="200px",
style = "z-index:9;background-color:white; margin-top: -40px; padding-top: 15px; height:90px",
width="100%",
fluidRow(
column(
6,
column(4, h5("Select Table:"), offset =
0),
column(
8,
selectInput(
"selectTbl",
label = "",
c("observed variants (unfiltered)","observed variants (filtered)",
"reported indiv haplotype (diploid)", "reported haplotype (flat)", "SNP report", "locus annotation"),
selected = "observed variants (unfiltered)"
),
style = "background-color:white; padding-right: 0px; margin-top:-20px;margin-bottom:-30px;padding-left:0%; padding-right: 0px;"
)
),
column(6, column(
12,
column(4, downloadButton('downloadData', 'Download'))
)),
style = "border-bottom: 1px double #d9d9d9; margin-bottom: 40px; padding-top:15px; padding-bottom:20px")
),
column(12, DT::dataTableOutput('haploTbl'),
style = "padding-bottom: 40px; border-bottom: 8px solid white; background: white; margin-top: 100px;"),
fluidRow(
div(style = "padding: 20px; border-bottom: 8px solid white; background: white")
)
),
tabPanel(
"About",
column(12,
column(8,
htmlOutput("about"),
offset=2
))
),
position = "fixed-bottom"
),
titlePanel("", windowTitle = "HapPLOType: a view to your haplotypes")
)
)
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