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inst/RDMLedit/ui.R
In RDML: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files
library(shiny)
library(shinythemes)
library(shinyjs)
library(dplyr)
library(ggvis)
library(plotly)
library(shinyMolBio)
shinyUI(
tags$html(
tags$head(
useShinyjs(),
if (grepl("XP",Sys.info()['release']))
{
#this was added for compatibility with call to V8 library in WinXp
#all functions from my_shinyjs_scripts.js should be added here!
extendShinyjs(script = "www/js/my_shinyjs_scripts.js",
functions = c("pageCol",
"selectRows",
"filterTblByPositions",
"changeConfirmedStatus",
"toggleCatModal",
"changeActiveTab"))
}
else
{
#Not WinXp
extendShinyjs(script = "www/js/my_shinyjs_scripts.js")
}#,
# includeScript("www/js/single_double_click.js"),
# includeScript("www/js/scripts.js"),
# includeCSS("www/css/styles.css")
),
tags$div(
navbarPage(
# here add code for google analytics
#header = includeScript("ga.js"),
title = "rdmlEdit",
theme = shinytheme("cerulean"),
tabPanel("Files",
fluidRow(
column(3,
wellPanel(
fileInput("rdmlFiles",
HTML("Upload <b>.RDML</b>, <b>.csv</b>, <b>.lc96p</b>, <b>.xls</b> or <b>.xlsx</b> file(s):"),
multiple = TRUE),
selectizeInput("rdmlFileSlct",
"View File",
choices = "",
options= list(
create =TRUE
)),
actionButton("createSubversionRDMLBtn",
"Create Subversion"),
actionButton("removeRDMLBtn",
"Remove RDML")),
wellPanel(
selectInput("mergeRdmlsSlct",
"Merge RDMLs",
multiple = TRUE,
choices = ""),
actionButton("mergeBtn",
"Merge")
)),
column(9,
fluidRow(
column(3,
textInput("dateMadeText", "Date Made",
""),
textInput("dateUpdatedText", "Date Updated",
""))),
plotOutput("dendroRDMLplot"))
)),
navbarMenu("Metadata",
tabPanel("ID",
selectizeInput("idSlct",
"Select ID",
choices = "",
options = list(
create = TRUE
)),
textInput("idPublisherText", "Publisher",
""),
textInput("idSerialNumberText", "Serial Number",
""),
textInput("idMD5HashText", "MD5 Hash",
""),
actionButton("removeIDBtn",
"Remove ID")),
tabPanel("Experimenter",
selectizeInput("experimenterSlct",
"Select Experimenter",
choices = "",
options = list(
create = TRUE
)),
textInput("experimenterIdText", "ID",
""),
textInput("experimenterFirstNameText", "First Name",
""),
textInput("experimenterLastNameText", "Last Name",
""),
textInput("experimenterEmailText", "Email",
""),
textInput("experimenterLabNameText", "Lab Name",
""),
textInput("experimenterLabAdressText", "Lab Address",
""),
actionButton("removeExperimenterBtn",
"Remove Experimenter")),
tabPanel("Documentation",
selectizeInput("documentationSlct",
"Select Documentation",
choices = "",
options= list(
create =TRUE
)),
textInput("documentationIdText", "ID",
""),
textInput("documentationTextText", "Text",
""),
actionButton("removeDocumentationBtn",
"Remove Documentation")),
tabPanel("Dye",
selectizeInput("dyeSlct",
"Select Dye",
choices = "",
options= list(
create =TRUE
)),
# uiOutput("dyeSlct"),
# uiOutput("dyeTabWell"),
textInput("dyeIdText", "ID",
""),
textInput("dyeDescriptionText", "Text",
""),
actionButton("removeDyeBtn",
"Remove Dye")
),
tabPanel("Sample",
selectizeInput("sampleSlct",
"Select Sample",
choices = "",
options= list(
create =TRUE
)),
textInput("sampleIdText", "ID",
""),
textInput("sampleDescriptionText",
"Description",
""),
selectInput("sampleDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
wellPanel(selectizeInput("samplexRefSlct",
"Select xRef",
choices = "",
options= list(
create =TRUE
)),
textInput("samplexRefNameText",
"xRef Name",
""),
textInput("samplexRefIdText",
"xRef ID",
""),
actionButton("removeSamplexRefBtn",
"Remove xRef")),
wellPanel(selectizeInput("sampleAnnotationSlct",
"Select Annotation",
choices = "",
options= list(
create =TRUE
)),
textInput("sampleAnnotationPropertyText",
"Annotation Property",
""),
textInput("sampleAnnotationValueText",
"Annotation Value",
""),
actionButton("removeSampleAnnotationBtn",
"Remove Annotation")),
selectInput("sampleTypeSlct",
"Type",
choices = c("unkn", "ntc",
"nac",
"std", "ntp",
"nrt", "pos",
"opt")),
checkboxInput("sampleInterRunCalibratorChk",
"Inter Run Calibrator",
FALSE),
wellPanel("Quantity",
textInput("sampleQuantityValueText",
"Value",
""),
selectInput("sampleQuantityUnitSlct",
"Unit",
choices = c("other",
"cop", "fold",
"dil", "ng",
"nMol"))
),
checkboxInput("sampleCalibratorSampleChk",
"Calibartor Sample",
FALSE),
wellPanel("cDNA Synthesis Method",
textInput("sampleCsmEnzymeText",
"Enzyme",
""),
selectInput("sampleCsmPrimingMethodSlct",
"Priming Method",
choices = c("",
"oligo-dt", "random",
"target-specific",
"oligo-dt and random",
"other")),
checkboxInput("sampleCsmDnaseTreatmentChk",
"DNAase Treatment",
FALSE),
selectInput("sampleCsmTccSlct",
"Thermal Cycling Conditions",
choices = "")
),
wellPanel("Template Quantity",
textInput("sampleTemplateQuantityConcText",
"Concentration",
""),
selectInput("sampleTemplateQuantityNucleotideSlct",
"Nucleotide",
choices = c("",
"DNA",
"genomic DNA",
"cDNA",
"RNA"))
),
actionButton("removeSampleBtn",
"Remove Sample")),
tabPanel("Target",
selectizeInput("targetSlct",
"Select Target",
choices = "",
options= list(
create =TRUE
)),
textInput("targetIdText", "ID",
""),
textInput("targetDescriptionText",
"Description",
""),
selectInput("targetDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
wellPanel(selectizeInput("targetxRefSlct",
"Select xRef",
choices = "",
options= list(
create =TRUE
)),
textInput("targetxRefNameText",
"xRef Name",
""),
textInput("targetxRefIdText",
"xRef ID",
""),
actionButton("removetargetxRefBtn",
"Remove xRef")),
selectInput("targetTypeSlct",
"Type",
choices = c("toi",
"ref")),
textInput("targetAemText",
"Amplification Efficiency Method",
""),
textInput("targetAeText",
"Amplification Efficiency",
""),
textInput("targetAeSeText",
"Amplification Efficiency SE",
""),
textInput("targetDetectionLimitText",
"Detection Limit",
""),
selectInput("targetDyeIdSlct",
"Dye ID",
choices = ""),
wellPanel("Sequences",
selectInput("targetSequencesTypeSlct",
"Oligo Type",
choices = c("forwardPrimer",
"reversePrimer",
"probe1",
"probe2",
"amplicon")),
textInput("targetSequences3PrimeTagText",
"Tree Prime Tag",
""),
textInput("targetSequences5PrimeTagText",
"Five Prime Tag",
""),
textInput("targetSequencesSequenceText",
"Sequence",
"")),
wellPanel("Commercial Assay",
textInput("targetCaCompanyText",
"Company",
""),
textInput("targetCaOrderNumberText",
"Order Number",
"")),
actionButton("removeTargetBtn",
"Remove target")),
tabPanel("Thermal Cycling Conditions",
selectizeInput("tccSlct",
"Select Thermal Cycling Conditions",
choices = "",
options= list(
create =TRUE
)),
textInput("tccIdText", "ID",
""),
textInput("tccDescriptionText",
"Description",
""),
selectInput("tccDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
textInput("tccLidTemperatureText",
"Lid Temperature",
""),
selectInput("tccExperimenterSlct",
"Experimenter",
multiple = TRUE,
choices = ""),
wellPanel(selectizeInput("tccStepSlct",
"Select Step",
choices = "",
options= list(
create =TRUE
)),
textInput("tccStepNrText", "Step Number",
""),
textInput("tccStepDescriptionText",
"Description",
""),
wellPanel(
selectInput("tccStepTypeSlct",
"Step Type",
choices = c("temperature",
"gradient",
"loop",
"pause",
"lidOpen")),
conditionalPanel(
"input.tccStepTypeSlct == 'gradient'",
textInput("tccStepHighTemperatureText",
"High Temperature",
""),
textInput("tccStepLowTemperatureText",
"Low Temperature",
"")),
conditionalPanel(
"input.tccStepTypeSlct == 'temperature' || input.tccStepTypeSlct == 'pause'",
textInput("tccStepTemperatureText",
"Temperature",
"")),
conditionalPanel(
"input.tccStepTypeSlct == 'temperature' || input.tccStepTypeSlct == 'gradient'",
textInput("tccStepDurationText",
"Duration",
""),
textInput("tccStepTemperatureChangeText",
"Temperature Change",
""),
textInput("tccStepDurationChangeText",
"Duration Change",
""),
selectInput("tccStepMeasureText",
"Measure",
choices = c("real time",
"meltcurve")),
textInput("tccStepRampText",
"Ramp",
"")),
conditionalPanel(
"input.tccStepTypeSlct == 'loop'",
textInput("tccStepGotoText",
"Go To",
""),
textInput("tccStepRepeatText",
"Repeat",
"")),
conditionalPanel(
"input.tccStepTypeSlct == 'lidOpen'",
checkboxInput("tccStepLidOpenChk",
"Lid Open",
FALSE)
),
actionButton("removeTccStepBtn",
"Remove Step")
)),
actionButton("removeTccBtn",
"Remove Thermal Cycling Conditions")),
tabPanel("Experiment",
selectizeInput("experimentSlct",
"Select Experiment",
choices = "",
options= list(
create =TRUE
)),
textInput("experimentIdText", "ID",
""),
textInput("experimentDescriptionText",
"Description",
""),
selectInput("experimentDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
wellPanel(
"Run",
selectizeInput("runSlct",
"Select Run",
choices = "",
options= list(
create =TRUE
)),
textInput("runIdText", "ID",
""),
textInput("runDescriptionText",
"Description",
""),
selectInput("runDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
selectInput("runExperimenterSlct",
"Experimenter",
multiple = TRUE,
choices = ""),
textInput("runInstrumentText", "Instrument",
""),
wellPanel("Data Collection Software",
textInput("runDataCollectionSoftwareNameText",
"Name",
""),
textInput("runDataCollectionSoftwareVersionText",
"Version",
"")),
textInput("runBackgroundDeterminationMethodText",
"Background Determination Method",
""),
selectInput("runCqDetectionMethodSlct",
"Cq Detection Method",
choices = c("",
"automated threshold and baseline settings",
"manual threshold and baseline settings",
"second derivative maximum",
"other")),
selectInput("runTccSlct",
"Thermal Cycling Conditions",
choices = ""),
wellPanel(
"PCR fromat",
textInput("runRowsText", "Rows",
""),
textInput("runColumnsText", "Columns",
""),
selectInput("runRowLabelSlct",
"Row Label",
choices = c("ABC",
"123",
"A1a1")),
selectInput("runColumnLabelSlct",
"Column Label",
choices = c("123",
"ABC",
"A1a1"))
),
textInput("runDateText", "Run Date",
""),
wellPanel(
"React",
selectizeInput("reactSlct",
"Select React",
choices = "",
options= list(
create =TRUE
)),
textInput("reactIdText", "ID",
""),
selectInput("reactSampleSlct",
"Sample",
choices = ""),
wellPanel(
"Data",
selectizeInput("dataSlct",
"Select Data",
choices = "",
options= list(
create =TRUE
)),
selectInput("dataTarSlct",
"Target",
choices = ""),
textInput("dataCqText", "Cq",
""),
textInput("dataExclText", "Excluded",
""),
textInput("dataEndPtText", "End Point",
""),
textInput("dataBgFluorText",
"Background Fluorescence",
""),
textInput("dataBgFluorSlpText",
"Background Fluorescence Slope",
""),
textInput("dataQuantFluorText",
"Quantification Fluorescence",
""),
actionButton("removeDataBtn",
"Remove Data")
),
actionButton("removeReactBtn",
"Remove React")
),
actionButton("removeRunBtn",
"Remove Run")
),
actionButton("removeExperimentBtn",
"Remove Experiment")
)
),
tabPanel("qPCR",
fluidRow(
# column(2,
# numericInput("removeFirstRows",
# "Remove First N Rows",
# 0, 0, step = 1)),
column(4,
checkboxInput("preprocessqPCR",
"Preprocess")),
column(4,
selectInput("smoothqPCRmethod",
"Smoothing method",
c("None" = "none",
"LOWESS" = "lowess",
"Moving average" = "mova",
"Savitzky-Golay (recommended)" = "savgol",
"Cubic spline smooth (recommended)" = "smooth",
"Standard cubic spline smooth" = "spline",
"Friedman's SuperSmoother" = "supsmu",
"Whittaker 1" = "whit1",
"Whittaker 2" = "whit2"
# ,"All" = "all"
))),
column(4,
selectInput("normqPCRmethod",
"Normalization method",
c("None" = "none",
"Min-max" = "minm",
"Maximum normalization" = "max",
"Quantile normalization" = "luqn",
"z-score" = "zscore")))),
fluidRow(
column(6,
wellPanel(
fluidRow(
column(4,
selectInput("cqMethod",
"Cq Method",
c("None" = "none",
"Threshold" = "th",
"SDM" = "sdm"))),
conditionalPanel(
condition = "input.cqMethod == 'th'",
column(4,
checkboxInput("autoThLevel",
"Auto Threshold",
TRUE)),
conditionalPanel(
condition = "input.autoThLevel == false",
column(4,
uiOutput("thLevelsUI")))
)
)
)),
column(6,
wellPanel(
fluidRow(
column(4,
selectInput("hookMethod",
"Hook Detection Method",
c("None" = "none",
"hookreg" = "hookreg",
"hookregNL" = "hookregNL",
"both" = "Both")))
)
))
# column(2,
# actionButton("recalculateCq",
# "Recalculate Cq"))
),
wellPanel(
fluidRow(
column(2,
selectInput("colorqPCRby",
"Color by",
c("None" = "none",
"Experiment" = "exp.id",
"Run" = "run.id",
"Target" = "target",
"Dye" = "target.dyeId",
"Sample" = "sample",
"Sample Type" = "sample.type",
"Position" = "position",
"Hook" = "hook"))),
column(2,
selectInput("shapeqPCRby",
"Line Type by",
c("None" = "none",
"Experiment" = "exp.id",
"Run" = "run.id",
"Target" = "target",
"Dye" = "target.dyeId",
"Sample" = "sample",
"Sample Type" = "sample.type",
"Position" = "position",
"Hook" = "hook"))),
column(2,
selectInput("showTargetsadp",
"Show Targets",
multiple = TRUE,
choices = "")),
column(2,
selectInput("showCq",
"Show Cq",
c("None" = "none",
"Yes" = "yes",
"Mean for replicates" = "mean"))),
column(2,
checkboxInput("logScale",
"Log Scale"))),
fluidRow(
# column(6, plotlyOutput("qPCRPlot")),
column(6, uiOutput("qPCRPlotUI")),
column(6, wellPanel(
fluidRow(column(4, selectInput("showqPCRExperiment",
"Experiment", c())),
column(4, selectInput("showqPCRRun",
"Run", c()))),
htmlOutput("plateTbl"))))),
dataTableOutput("qPCRDt"),
value = "adp"),
tabPanel("Melting Curves",
fluidRow(
column(2,
checkboxInput("preprocessMelting",
"Preprocess")),
conditionalPanel(
condition = "input.preprocessMelting == true",
column(2,
checkboxInput("bgAdjMelting",
"Adjust the Background Signal",
FALSE)),
conditionalPanel(
condition = "input.bgAdjMelting == true",
column(2,
sliderInput("bgRangeMelting",
label = "Temperature Background Range (°C)", min = 0,
max = 100, value = c(50, 55), step = 1))),
column(2,
checkboxInput("minMaxMelting",
"Min-Max Normalization",
FALSE)),
column(2,
sliderInput("dfFactMelting",
label = "Factor to Smooth the Curve", min = 0.6,
max = 1.1, value = 0.95, step = 0.05))
)
),
wellPanel(
fluidRow(
column(2,
selectInput("colorMeltingBy",
"Color by",
c("None" = "none",
"Experiment" = "exp.id",
"Run" = "run.id",
"Target" = "target",
"Dye" = "target.dyeId",
"Sample" = "sample",
"Sample Type" = "sample.type",
"Position" = "position"))),
column(2,
selectInput("shapeMeltingBy",
"Line Type by",
c("None" = "none",
"Experiment" = "exp.id",
"Run" = "run.id",
"Target" = "target",
"Dye" = "target.dyeId",
"Sample" = "sample",
"Sample Type" = "sample.type",
"Position" = "position"))),
column(2,
selectInput("showTargetsmdp",
"Show Targets",
multiple = TRUE,
choices = ""))
),
fluidRow(
column(6,
wellPanel(
fluidRow(column(4, selectInput("showMeltingExperiment",
"Experiment", c())),
column(4, selectInput("showMeltingRun",
"Run", c()))),
htmlOutput("plateTblMelting")))),
plotlyOutput("meltingPlot")),
dataTableOutput("meltingDt"),
value = "mdp"),
tabPanel("Store",
wellPanel(
downloadButton("downloadRDML",
"Store RDML"),
tags$p("Note that if you made any preprocession all fluorescence points will be overwritten with the new calculated values!!!"))),
tabPanel("Help",
includeMarkdown("md/help.md")),
id = "mainNavbar"
),
wellPanel(
h4("Log:"),
actionButton("clearLogBtn",
"Clear"),
uiOutput("logText")
)
)
)
)
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library(shiny)
library(shinythemes)
library(shinyjs)
library(dplyr)
library(ggvis)
library(plotly)
library(shinyMolBio)
shinyUI(
tags$html(
tags$head(
useShinyjs(),
if (grepl("XP",Sys.info()['release']))
{
#this was added for compatibility with call to V8 library in WinXp
#all functions from my_shinyjs_scripts.js should be added here!
extendShinyjs(script = "www/js/my_shinyjs_scripts.js",
functions = c("pageCol",
"selectRows",
"filterTblByPositions",
"changeConfirmedStatus",
"toggleCatModal",
"changeActiveTab"))
}
else
{
#Not WinXp
extendShinyjs(script = "www/js/my_shinyjs_scripts.js")
}#,
# includeScript("www/js/single_double_click.js"),
# includeScript("www/js/scripts.js"),
# includeCSS("www/css/styles.css")
),
tags$div(
navbarPage(
# here add code for google analytics
#header = includeScript("ga.js"),
title = "rdmlEdit",
theme = shinytheme("cerulean"),
tabPanel("Files",
fluidRow(
column(3,
wellPanel(
fileInput("rdmlFiles",
HTML("Upload <b>.RDML</b>, <b>.csv</b>, <b>.lc96p</b>, <b>.xls</b> or <b>.xlsx</b> file(s):"),
multiple = TRUE),
selectizeInput("rdmlFileSlct",
"View File",
choices = "",
options= list(
create =TRUE
)),
actionButton("createSubversionRDMLBtn",
"Create Subversion"),
actionButton("removeRDMLBtn",
"Remove RDML")),
wellPanel(
selectInput("mergeRdmlsSlct",
"Merge RDMLs",
multiple = TRUE,
choices = ""),
actionButton("mergeBtn",
"Merge")
)),
column(9,
fluidRow(
column(3,
textInput("dateMadeText", "Date Made",
""),
textInput("dateUpdatedText", "Date Updated",
""))),
plotOutput("dendroRDMLplot"))
)),
navbarMenu("Metadata",
tabPanel("ID",
selectizeInput("idSlct",
"Select ID",
choices = "",
options = list(
create = TRUE
)),
textInput("idPublisherText", "Publisher",
""),
textInput("idSerialNumberText", "Serial Number",
""),
textInput("idMD5HashText", "MD5 Hash",
""),
actionButton("removeIDBtn",
"Remove ID")),
tabPanel("Experimenter",
selectizeInput("experimenterSlct",
"Select Experimenter",
choices = "",
options = list(
create = TRUE
)),
textInput("experimenterIdText", "ID",
""),
textInput("experimenterFirstNameText", "First Name",
""),
textInput("experimenterLastNameText", "Last Name",
""),
textInput("experimenterEmailText", "Email",
""),
textInput("experimenterLabNameText", "Lab Name",
""),
textInput("experimenterLabAdressText", "Lab Address",
""),
actionButton("removeExperimenterBtn",
"Remove Experimenter")),
tabPanel("Documentation",
selectizeInput("documentationSlct",
"Select Documentation",
choices = "",
options= list(
create =TRUE
)),
textInput("documentationIdText", "ID",
""),
textInput("documentationTextText", "Text",
""),
actionButton("removeDocumentationBtn",
"Remove Documentation")),
tabPanel("Dye",
selectizeInput("dyeSlct",
"Select Dye",
choices = "",
options= list(
create =TRUE
)),
# uiOutput("dyeSlct"),
# uiOutput("dyeTabWell"),
textInput("dyeIdText", "ID",
""),
textInput("dyeDescriptionText", "Text",
""),
actionButton("removeDyeBtn",
"Remove Dye")
),
tabPanel("Sample",
selectizeInput("sampleSlct",
"Select Sample",
choices = "",
options= list(
create =TRUE
)),
textInput("sampleIdText", "ID",
""),
textInput("sampleDescriptionText",
"Description",
""),
selectInput("sampleDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
wellPanel(selectizeInput("samplexRefSlct",
"Select xRef",
choices = "",
options= list(
create =TRUE
)),
textInput("samplexRefNameText",
"xRef Name",
""),
textInput("samplexRefIdText",
"xRef ID",
""),
actionButton("removeSamplexRefBtn",
"Remove xRef")),
wellPanel(selectizeInput("sampleAnnotationSlct",
"Select Annotation",
choices = "",
options= list(
create =TRUE
)),
textInput("sampleAnnotationPropertyText",
"Annotation Property",
""),
textInput("sampleAnnotationValueText",
"Annotation Value",
""),
actionButton("removeSampleAnnotationBtn",
"Remove Annotation")),
selectInput("sampleTypeSlct",
"Type",
choices = c("unkn", "ntc",
"nac",
"std", "ntp",
"nrt", "pos",
"opt")),
checkboxInput("sampleInterRunCalibratorChk",
"Inter Run Calibrator",
FALSE),
wellPanel("Quantity",
textInput("sampleQuantityValueText",
"Value",
""),
selectInput("sampleQuantityUnitSlct",
"Unit",
choices = c("other",
"cop", "fold",
"dil", "ng",
"nMol"))
),
checkboxInput("sampleCalibratorSampleChk",
"Calibartor Sample",
FALSE),
wellPanel("cDNA Synthesis Method",
textInput("sampleCsmEnzymeText",
"Enzyme",
""),
selectInput("sampleCsmPrimingMethodSlct",
"Priming Method",
choices = c("",
"oligo-dt", "random",
"target-specific",
"oligo-dt and random",
"other")),
checkboxInput("sampleCsmDnaseTreatmentChk",
"DNAase Treatment",
FALSE),
selectInput("sampleCsmTccSlct",
"Thermal Cycling Conditions",
choices = "")
),
wellPanel("Template Quantity",
textInput("sampleTemplateQuantityConcText",
"Concentration",
""),
selectInput("sampleTemplateQuantityNucleotideSlct",
"Nucleotide",
choices = c("",
"DNA",
"genomic DNA",
"cDNA",
"RNA"))
),
actionButton("removeSampleBtn",
"Remove Sample")),
tabPanel("Target",
selectizeInput("targetSlct",
"Select Target",
choices = "",
options= list(
create =TRUE
)),
textInput("targetIdText", "ID",
""),
textInput("targetDescriptionText",
"Description",
""),
selectInput("targetDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
wellPanel(selectizeInput("targetxRefSlct",
"Select xRef",
choices = "",
options= list(
create =TRUE
)),
textInput("targetxRefNameText",
"xRef Name",
""),
textInput("targetxRefIdText",
"xRef ID",
""),
actionButton("removetargetxRefBtn",
"Remove xRef")),
selectInput("targetTypeSlct",
"Type",
choices = c("toi",
"ref")),
textInput("targetAemText",
"Amplification Efficiency Method",
""),
textInput("targetAeText",
"Amplification Efficiency",
""),
textInput("targetAeSeText",
"Amplification Efficiency SE",
""),
textInput("targetDetectionLimitText",
"Detection Limit",
""),
selectInput("targetDyeIdSlct",
"Dye ID",
choices = ""),
wellPanel("Sequences",
selectInput("targetSequencesTypeSlct",
"Oligo Type",
choices = c("forwardPrimer",
"reversePrimer",
"probe1",
"probe2",
"amplicon")),
textInput("targetSequences3PrimeTagText",
"Tree Prime Tag",
""),
textInput("targetSequences5PrimeTagText",
"Five Prime Tag",
""),
textInput("targetSequencesSequenceText",
"Sequence",
"")),
wellPanel("Commercial Assay",
textInput("targetCaCompanyText",
"Company",
""),
textInput("targetCaOrderNumberText",
"Order Number",
"")),
actionButton("removeTargetBtn",
"Remove target")),
tabPanel("Thermal Cycling Conditions",
selectizeInput("tccSlct",
"Select Thermal Cycling Conditions",
choices = "",
options= list(
create =TRUE
)),
textInput("tccIdText", "ID",
""),
textInput("tccDescriptionText",
"Description",
""),
selectInput("tccDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
textInput("tccLidTemperatureText",
"Lid Temperature",
""),
selectInput("tccExperimenterSlct",
"Experimenter",
multiple = TRUE,
choices = ""),
wellPanel(selectizeInput("tccStepSlct",
"Select Step",
choices = "",
options= list(
create =TRUE
)),
textInput("tccStepNrText", "Step Number",
""),
textInput("tccStepDescriptionText",
"Description",
""),
wellPanel(
selectInput("tccStepTypeSlct",
"Step Type",
choices = c("temperature",
"gradient",
"loop",
"pause",
"lidOpen")),
conditionalPanel(
"input.tccStepTypeSlct == 'gradient'",
textInput("tccStepHighTemperatureText",
"High Temperature",
""),
textInput("tccStepLowTemperatureText",
"Low Temperature",
"")),
conditionalPanel(
"input.tccStepTypeSlct == 'temperature' || input.tccStepTypeSlct == 'pause'",
textInput("tccStepTemperatureText",
"Temperature",
"")),
conditionalPanel(
"input.tccStepTypeSlct == 'temperature' || input.tccStepTypeSlct == 'gradient'",
textInput("tccStepDurationText",
"Duration",
""),
textInput("tccStepTemperatureChangeText",
"Temperature Change",
""),
textInput("tccStepDurationChangeText",
"Duration Change",
""),
selectInput("tccStepMeasureText",
"Measure",
choices = c("real time",
"meltcurve")),
textInput("tccStepRampText",
"Ramp",
"")),
conditionalPanel(
"input.tccStepTypeSlct == 'loop'",
textInput("tccStepGotoText",
"Go To",
""),
textInput("tccStepRepeatText",
"Repeat",
"")),
conditionalPanel(
"input.tccStepTypeSlct == 'lidOpen'",
checkboxInput("tccStepLidOpenChk",
"Lid Open",
FALSE)
),
actionButton("removeTccStepBtn",
"Remove Step")
)),
actionButton("removeTccBtn",
"Remove Thermal Cycling Conditions")),
tabPanel("Experiment",
selectizeInput("experimentSlct",
"Select Experiment",
choices = "",
options= list(
create =TRUE
)),
textInput("experimentIdText", "ID",
""),
textInput("experimentDescriptionText",
"Description",
""),
selectInput("experimentDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
wellPanel(
"Run",
selectizeInput("runSlct",
"Select Run",
choices = "",
options= list(
create =TRUE
)),
textInput("runIdText", "ID",
""),
textInput("runDescriptionText",
"Description",
""),
selectInput("runDocumentationSlct",
"Documentation",
multiple = TRUE,
choices = ""),
selectInput("runExperimenterSlct",
"Experimenter",
multiple = TRUE,
choices = ""),
textInput("runInstrumentText", "Instrument",
""),
wellPanel("Data Collection Software",
textInput("runDataCollectionSoftwareNameText",
"Name",
""),
textInput("runDataCollectionSoftwareVersionText",
"Version",
"")),
textInput("runBackgroundDeterminationMethodText",
"Background Determination Method",
""),
selectInput("runCqDetectionMethodSlct",
"Cq Detection Method",
choices = c("",
"automated threshold and baseline settings",
"manual threshold and baseline settings",
"second derivative maximum",
"other")),
selectInput("runTccSlct",
"Thermal Cycling Conditions",
choices = ""),
wellPanel(
"PCR fromat",
textInput("runRowsText", "Rows",
""),
textInput("runColumnsText", "Columns",
""),
selectInput("runRowLabelSlct",
"Row Label",
choices = c("ABC",
"123",
"A1a1")),
selectInput("runColumnLabelSlct",
"Column Label",
choices = c("123",
"ABC",
"A1a1"))
),
textInput("runDateText", "Run Date",
""),
wellPanel(
"React",
selectizeInput("reactSlct",
"Select React",
choices = "",
options= list(
create =TRUE
)),
textInput("reactIdText", "ID",
""),
selectInput("reactSampleSlct",
"Sample",
choices = ""),
wellPanel(
"Data",
selectizeInput("dataSlct",
"Select Data",
choices = "",
options= list(
create =TRUE
)),
selectInput("dataTarSlct",
"Target",
choices = ""),
textInput("dataCqText", "Cq",
""),
textInput("dataExclText", "Excluded",
""),
textInput("dataEndPtText", "End Point",
""),
textInput("dataBgFluorText",
"Background Fluorescence",
""),
textInput("dataBgFluorSlpText",
"Background Fluorescence Slope",
""),
textInput("dataQuantFluorText",
"Quantification Fluorescence",
""),
actionButton("removeDataBtn",
"Remove Data")
),
actionButton("removeReactBtn",
"Remove React")
),
actionButton("removeRunBtn",
"Remove Run")
),
actionButton("removeExperimentBtn",
"Remove Experiment")
)
),
tabPanel("qPCR",
fluidRow(
# column(2,
# numericInput("removeFirstRows",
# "Remove First N Rows",
# 0, 0, step = 1)),
column(4,
checkboxInput("preprocessqPCR",
"Preprocess")),
column(4,
selectInput("smoothqPCRmethod",
"Smoothing method",
c("None" = "none",
"LOWESS" = "lowess",
"Moving average" = "mova",
"Savitzky-Golay (recommended)" = "savgol",
"Cubic spline smooth (recommended)" = "smooth",
"Standard cubic spline smooth" = "spline",
"Friedman's SuperSmoother" = "supsmu",
"Whittaker 1" = "whit1",
"Whittaker 2" = "whit2"
# ,"All" = "all"
))),
column(4,
selectInput("normqPCRmethod",
"Normalization method",
c("None" = "none",
"Min-max" = "minm",
"Maximum normalization" = "max",
"Quantile normalization" = "luqn",
"z-score" = "zscore")))),
fluidRow(
column(6,
wellPanel(
fluidRow(
column(4,
selectInput("cqMethod",
"Cq Method",
c("None" = "none",
"Threshold" = "th",
"SDM" = "sdm"))),
conditionalPanel(
condition = "input.cqMethod == 'th'",
column(4,
checkboxInput("autoThLevel",
"Auto Threshold",
TRUE)),
conditionalPanel(
condition = "input.autoThLevel == false",
column(4,
uiOutput("thLevelsUI")))
)
)
)),
column(6,
wellPanel(
fluidRow(
column(4,
selectInput("hookMethod",
"Hook Detection Method",
c("None" = "none",
"hookreg" = "hookreg",
"hookregNL" = "hookregNL",
"both" = "Both")))
)
))
# column(2,
# actionButton("recalculateCq",
# "Recalculate Cq"))
),
wellPanel(
fluidRow(
column(2,
selectInput("colorqPCRby",
"Color by",
c("None" = "none",
"Experiment" = "exp.id",
"Run" = "run.id",
"Target" = "target",
"Dye" = "target.dyeId",
"Sample" = "sample",
"Sample Type" = "sample.type",
"Position" = "position",
"Hook" = "hook"))),
column(2,
selectInput("shapeqPCRby",
"Line Type by",
c("None" = "none",
"Experiment" = "exp.id",
"Run" = "run.id",
"Target" = "target",
"Dye" = "target.dyeId",
"Sample" = "sample",
"Sample Type" = "sample.type",
"Position" = "position",
"Hook" = "hook"))),
column(2,
selectInput("showTargetsadp",
"Show Targets",
multiple = TRUE,
choices = "")),
column(2,
selectInput("showCq",
"Show Cq",
c("None" = "none",
"Yes" = "yes",
"Mean for replicates" = "mean"))),
column(2,
checkboxInput("logScale",
"Log Scale"))),
fluidRow(
# column(6, plotlyOutput("qPCRPlot")),
column(6, uiOutput("qPCRPlotUI")),
column(6, wellPanel(
fluidRow(column(4, selectInput("showqPCRExperiment",
"Experiment", c())),
column(4, selectInput("showqPCRRun",
"Run", c()))),
htmlOutput("plateTbl"))))),
dataTableOutput("qPCRDt"),
value = "adp"),
tabPanel("Melting Curves",
fluidRow(
column(2,
checkboxInput("preprocessMelting",
"Preprocess")),
conditionalPanel(
condition = "input.preprocessMelting == true",
column(2,
checkboxInput("bgAdjMelting",
"Adjust the Background Signal",
FALSE)),
conditionalPanel(
condition = "input.bgAdjMelting == true",
column(2,
sliderInput("bgRangeMelting",
label = "Temperature Background Range (°C)", min = 0,
max = 100, value = c(50, 55), step = 1))),
column(2,
checkboxInput("minMaxMelting",
"Min-Max Normalization",
FALSE)),
column(2,
sliderInput("dfFactMelting",
label = "Factor to Smooth the Curve", min = 0.6,
max = 1.1, value = 0.95, step = 0.05))
)
),
wellPanel(
fluidRow(
column(2,
selectInput("colorMeltingBy",
"Color by",
c("None" = "none",
"Experiment" = "exp.id",
"Run" = "run.id",
"Target" = "target",
"Dye" = "target.dyeId",
"Sample" = "sample",
"Sample Type" = "sample.type",
"Position" = "position"))),
column(2,
selectInput("shapeMeltingBy",
"Line Type by",
c("None" = "none",
"Experiment" = "exp.id",
"Run" = "run.id",
"Target" = "target",
"Dye" = "target.dyeId",
"Sample" = "sample",
"Sample Type" = "sample.type",
"Position" = "position"))),
column(2,
selectInput("showTargetsmdp",
"Show Targets",
multiple = TRUE,
choices = ""))
),
fluidRow(
column(6,
wellPanel(
fluidRow(column(4, selectInput("showMeltingExperiment",
"Experiment", c())),
column(4, selectInput("showMeltingRun",
"Run", c()))),
htmlOutput("plateTblMelting")))),
plotlyOutput("meltingPlot")),
dataTableOutput("meltingDt"),
value = "mdp"),
tabPanel("Store",
wellPanel(
downloadButton("downloadRDML",
"Store RDML"),
tags$p("Note that if you made any preprocession all fluorescence points will be overwritten with the new calculated values!!!"))),
tabPanel("Help",
includeMarkdown("md/help.md")),
id = "mainNavbar"
),
wellPanel(
h4("Log:"),
actionButton("clearLogBtn",
"Clear"),
uiOutput("logText")
)
)
)
)
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