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ui.R
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586 lines (510 loc) · 32.3 KB
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suppressPackageStartupMessages(library(shiny))
fluidPage(
# Application title:
titlePanel("Genomic PR-2 Simulations"),
# Sidebar with a number of filtering input:
sidebarLayout(
sidebarPanel(
h4("Mutation Rate Constants"),
selectInput(inputId = "muttype",
label = "Select the model",
choices = c("Non Symmetric", "Strand-Symmetric", "Hypercube", "Hypercube ZNE")),
#-----------------------------------------------------------------------------------------------------
conditionalPanel(condition = 'input.muttype=="Strand-Symmetric" | input.muttype=="Non Symmetric"',
tags$head(tags$style(
type="text/css",
"#logo img {max-width: 70%; width: auto; max-height: 100%;
padding-bottom: 10px}"
)),
imageOutput("logo", height="240px")),
conditionalPanel(condition = 'input.muttype=="Hypercube" | input.muttype=="Hypercube ZNE"',
tags$head(tags$style(
type="text/css",
"#logo6 img {max-width: 70%; width: auto; max-height: 100%;
padding-bottom: 10px}"
)),
imageOutput("logo6", height="220px")),
#-----------------------------------------------------------------------------------------------------
#-----------------------------------------------------------------------------------------------------
conditionalPanel(condition = 'input.muttype=="Strand-Symmetric" | input.muttype=="Hypercube ZNE"',
tags$head(tags$style(
type="text/css",
"#logo2 img {max-width: 100%; width: auto; max-height: 100%;
padding-top: 10px;}"
)),
imageOutput("logo2", height="240px"),
#-- sliders for Strand-Symmetric and Hypercube ZNE
sliderInput('k.ag.tc', 'k_AG&TC',
min=0, max=1.5,
value=0.545,
step=0.001, round=FALSE),
sliderInput('k.ct.ga', 'k_CT&GA',
min=0, max=1.5,
value=1.055,
step=0.001, round=FALSE),
sliderInput('k.ac.tg', 'k_AC&TG',
min=0, max=1.5,
value=0.175,
step=0.001, round=FALSE),
sliderInput('k.ca.gt', 'k_CA>',
min=0, max=1.5,
value=0.285,
step=0.001, round=FALSE),
sliderInput('k.at.ta', 'k_AT&TA',
min=0, max=1.5,
value=0.205,
step=0.001, round=FALSE),
sliderInput('k.cg.gc', 'k_CG&GC',
min=0, max=1.5,
value=0.235,
step=0.001, round=FALSE)
#-- end of sliders for Strand-Symmetric and Hypercube ZNE
),
#-----------------------------------------------------------------------------------------------------
#-----------------------------------------------------------------------------------------------------
conditionalPanel(condition = 'input.muttype=="Non Symmetric"',
tags$head(tags$style(
type="text/css",
"#logo3 img {max-width: 100%; width: auto; max-height: 100%;
padding-top: 10px;}"
)),
imageOutput("logo3", height="220px"),
#-- sliders for Non Symmetric
sliderInput('k.ag', 'k_AG',
min=0, max=1.5,
value=0.545,
step=0.001, round=FALSE),
sliderInput('k.tc', 'k_TC',
min=0, max=1.5,
value=0.545,
step=0.001, round=FALSE),
sliderInput('k.ct', 'k_CT',
min=0, max=1.5,
value=1.055,
step=0.001, round=FALSE),
sliderInput('k.ga', 'k_GA',
min=0, max=1.5,
value=1.055,
step=0.001, round=FALSE),
sliderInput('k.ac', 'k_AC',
min=0, max=1.5,
value=0.175,
step=0.001, round=FALSE),
sliderInput('k.tg', 'k_TG',
min=0, max=1.5,
value=0.175,
step=0.001, round=FALSE),
sliderInput('k.ca', 'k_CA',
min=0, max=1.5,
value=0.285,
step=0.001, round=FALSE),
sliderInput('k.gt', 'k_GT',
min=0, max=1.5,
value=0.285,
step=0.001, round=FALSE),
sliderInput('k.at', 'k_AT',
min=0, max=1.5,
value=0.205,
step=0.001, round=FALSE),
sliderInput('k.ta', 'k_TA',
min=0, max=1.5,
value=0.205,
step=0.001, round=FALSE),
sliderInput('k.cg', 'k_CG',
min=0, max=1.5,
value=0.235,
step=0.001, round=FALSE),
sliderInput('k.gc', 'k_GC',
min=0, max=1.5,
value=0.235,
step=0.001, round=FALSE)
#-- end of sliders for Non Symmetric
),
#-----------------------------------------------------------------------------------------------------
#-----------------------------------------------------------------------------------------------------
conditionalPanel(condition = 'input.muttype=="Hypercube"',
#-- sliders for Hypercube
sliderInput('kAA2AC', 'kAA2AC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAA2AG', 'kAA2AG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAA2AT', 'kAA2AT',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAA2CA', 'kAA2CA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAA2GA', 'kAA2GA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAA2TA', 'kAA2TA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAC2AA', 'kAC2AA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAC2AG', 'kAC2AG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAC2AT', 'kAC2AT',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAC2CC', 'kAC2CC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAC2GC', 'kAC2GC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAC2TC', 'kAC2TC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAG2AA', 'kAG2AA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAG2AC', 'kAG2AC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAG2AT', 'kAG2AT',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAG2CG', 'kAG2CG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAG2GG', 'kAG2GG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAG2TG', 'kAG2TG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAT2AA', 'kAT2AA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAT2AC', 'kAT2AC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kAT2AG', 'kAT2AG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCA2AA', 'kCA2AA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCA2CC', 'kCA2CC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCA2CG', 'kCA2CG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCA2CT', 'kCA2CT',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCA2GA', 'kCA2GA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCA2TA', 'kCA2TA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCC2AC', 'kCC2AC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCC2CA', 'kCC2CA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCC2CG', 'kCC2CG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCC2CT', 'kCC2CT',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCC2GC', 'kCC2GC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCC2TC', 'kCC2TC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCG2AG', 'kCG2AG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCG2CA', 'kCG2CA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kCG2CC', 'kCG2CC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGA2AA', 'kGA2AA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGA2CA', 'kGA2CA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGA2GC', 'kGA2GC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGA2GG', 'kGA2GG',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGA2GT', 'kGA2GT',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGA2TA', 'kGA2TA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGC2AC', 'kGC2AC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGC2CC', 'kGC2CC',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kGC2GA', 'kGC2GA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kTA2AA', 'kTA2AA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kTA2CA', 'kTA2CA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE),
sliderInput('kTA2GA', 'kTA2GA',
min=0, max=1.5,
value=runif(1, min=0, max=1.5),
step=0.001, round=FALSE)
#-- end of sliders for Hypercube
)
),
# Show a plot of the generated distribution
#-- mainPanel
mainPanel(
#-- tabsetPanel
tabsetPanel(type = "tabs",
#-- tabPanel
tabPanel("Explore",
##---------------------------------------------------
conditionalPanel(condition = 'input.muttype=="Strand-Symmetric"',
tags$head(tags$style(
type="text/css",
"#logo4 img {max-width: 100%; width: auto; max-height: 100%;
padding-bottom: 10px;}"
)),
imageOutput("logo4", height="200px")),
conditionalPanel(condition = 'input.muttype=="Non Symmetric"',
tags$head(tags$style(
type="text/css",
"#logo5 img {max-width: 100%; width: auto; max-height: 100%;
padding-bottom: 10px;}"
)),
imageOutput("logo5", height="200px")),
conditionalPanel(condition = 'input.muttype=="Hypercube"',
tags$head(tags$style(
type="text/css",
"#logo7 img {max-width: 100%; width: auto; max-height: 100%;
padding-bottom: 10px;}"
)),
imageOutput("logo7", height="220px")),
conditionalPanel(condition = 'input.muttype=="Hypercube ZNE"',
tags$head(tags$style(
type="text/css",
"#logo8 img {max-width: 100%; width: auto; max-height: 100%;
padding-bottom: 10px;}"
)),
imageOutput("logo8", height="200px")),
##---------------------------------------------------
##**************************
conditionalPanel(condition = 'input.muttype=="Strand-Symmetric" | input.muttype=="Non Symmetric"',
##---------------------------------------------------
h4("Initial (t=0) Genome Composition"),
fluidRow(
column(width=3,
sliderInput('Gcont', 'G content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('Ccont', 'C content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('Acont', 'A content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('Tcont', 'T content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
)
)
##---------------------------------------------------
),
##**************************
conditionalPanel(condition = 'input.muttype=="Hypercube" | input.muttype=="Hypercube ZNE"',
##---------------------------------------------------
h4("Initial (t=0) Genome Composition"),
fluidRow(
column(width=3,
sliderInput('GAcont', 'GA content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('CAcont', 'CA content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('AAcont', 'AA content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('TAcont', 'TA content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
)
),
fluidRow(
column(width=3,
sliderInput('GTcont', 'GT content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('CTcont', 'CT content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('ATcont', 'AT content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('TTcont', 'TT content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
)
),
fluidRow(
column(width=3,
sliderInput('GGcont', 'GG content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('CGcont', 'CG content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('AGcont', 'AG content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('TGcont', 'TG content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
)
),
fluidRow(
column(width=3,
sliderInput('GCcont', 'GC content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('CCcont', 'CC content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('ACcont', 'AC content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
),
column(width=3,
sliderInput('TCcont', 'TC content, wt',
min=0, max=10,
value=5,
step=0.1, round=TRUE)
)
)
##---------------------------------------------------
),
##**************************
plotOutput("EvoPlot")
)
#-- tabPanel
)
#-- tabsetPanel
)
#-- mainPanel
)
)