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ui_Amy.R
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ui_Amy.R
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## Load R packages
library(shiny)
library(shinythemes)
library(markdown)
## set working directory
#setwd("~/Desktop/NEW_ChROseq_HIO/miRNA_effect_2021/shiny")
## Load required data
# gene name list include genes with mean of RNA nc > 50 and mean of ChRO TPM > 10 in each of the comparison
gc <- scan('./data/geneNameChoices_HIO.csv', as.character(), sep = '\n')
## miR list include miRs with mean RPMMM > 50 across all stages
mc <- scan('./data/miRNameChoices_HIO.csv', as.character(), sep = '\n')
## Define UI -------------------------------------------------------
UI <- fixedPage(
theme = shinytheme("simplex"),
navbarPage(
"Post-transcriptional Regulation of Human Intestinal Development (ProHumID)",
tabPanel("Introduction",
fluidRow(
column(7, offset = 0,
includeMarkdown("md/intro_Amy.md"),
hr()),
column(3,
br(),
br(),
br(),
br(),
img(src='graphical_abstract.png',width="430",height="500"))
)
), # tabPanel
tabPanel("Data exploration",
sidebarPanel(width = 3,
style="min-width:300px; max-width:300px",
selectInput('moi',
HTML('<b>miRNA of interest:<b>'),
mc,
multiple = F,
selected = 'miR-182-5p'),
selectInput('goi',
HTML('<b>Gene of interest:<b>'),
gc,
multiple = F,
selected = 'SOX2'),
h5(HTML('<b>Is the gene a target of the miRNA?<b>')),
h4(textOutput('mirtarget')),
submitButton("Update View")
), # sidebarPanel
mainPanel(width = 12,
h5(HTML('<b>Plots and statisitcal significance are summarized below:<b>')),
br(),
#HTML('<center><img src="directed_differentiation.png" style="width: 300px"><center>'),
tabsetPanel(
id = 'dataset',
tabPanel(
'Definitive endoderm formation',
fixedRow(
div(style = "padding: 10px 0px",
column(3,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_miRNA1', width = "250px", height = "250px"),
h5("Level of miRNA is:"),
verbatimTextOutput("miR_summary1")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_ChRO1', width = "250px", height = "250px"),
h5("Transcription activity of gene is:"),
verbatimTextOutput("ChRO_summary1")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_RNA1', width = "250px", height = "250px"),
h5("Steady state level of gene is:"),
verbatimTextOutput("RNA_summary1")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('scatter_1', width = "250px", height = "250px"),
h5("Post-transcriptional status of gene is:"),
verbatimTextOutput("tf_summary1")
)
)
) # divstyle
), # fixedRow
fixedRow(
column(12,
div(style = "padding: 10px 0px",
h5("Is the miR:target relationship likely present in this stage transition? (based on smRNA-seq and two-factor analysis)"),
verbatimTextOutput("axis1"),
br()
) # div style
) # column
) # fixedRow
), # tabPanel
tabPanel(
'Intestinal lineage specification',
fixedRow(
div(style = "padding: 10px 0px",
column(3,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_miRNA2', width = "250px", height = "250px"),
h5("Level of miRNA is:"),
verbatimTextOutput("miR_summary2")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_ChRO2', width = "250px", height = "250px"),
h5("Transcription activity of gene is:"),
verbatimTextOutput("ChRO_summary2")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_RNA2', width = "250px", height = "250px"),
h5("Steady state level of gene is:"),
verbatimTextOutput("RNA_summary2")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('scatter_2', width = "250px", height = "250px"),
h5("Post-transcriptional status of gene is:"),
verbatimTextOutput("tf_summary2")
)
)
) # div style
), # fixeddRow
fixedRow(
column(12,
div(style = "padding: 10px 0px",
h5("Is the miR:target relationship likely present in this stage transition? (based on smRNA-seq and two-factor analysis)"),
verbatimTextOutput("axis2"),
br()
) # div style
) # column
) # fixedRow
), # tabPanel
tabPanel(
'Intestinal regional specification',
fixedRow(
div(style = "padding: 10px 0px",
column(3,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_miRNA3', width = "250px", height = "250px"),
h5("Level of miRNA is:"),
verbatimTextOutput("miR_summary3")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_ChRO3', width = "250px", height = "250px"),
h5("Transcription activity of gene is:"),
verbatimTextOutput("ChRO_summary3")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('expression_RNA3', width = "250px", height = "250px"),
h5("Steady state level of gene is:"),
verbatimTextOutput("RNA_summary3")
)
),
column(3, offset = 0,
div(style = "height:320px; width:250px; background-color: white",
plotOutput('scatter_3', width = "250px", height = "250px"),
h5("Post-transcriptional status of gene is:"),
verbatimTextOutput("tf_summary3")
)
)
) # div style
), # fluidRow
fixedRow(
column(12,
div(style = "padding: 10px 0px",
h5("Is the miR:target relationship likely present in this stage transition? (based on smRNA-seq and two-factor analysis)"),
verbatimTextOutput("axis3"),
br()
) # div style
) # column
) # fixedRow
) # tabPanel
) # tabsetPanel
) # mainPanel
))) # fluidPage