inst/shiny/ui.R
In kwanjeeraw/grinn: graph database and R package for omics data integration
library(shiny)
library(DT)
library(grinn)
library(shinydashboard)
dashboardPage(skin = "black",
dashboardHeader(title=img(src="logo.png", width = 200)),
dashboardSidebar(
sidebarMenu(
menuItem("fetchGrinnNetwork", tabName = "fgrinn", icon = icon("circle")),
menuItem("fetchCorrGrinnNetwork", tabName = "fcorrgrinn", icon = icon("circle")),
menuItem("fetchDiffCorrGrinnNetwork", tabName = "fdiffgrinn", icon = icon("circle")),
menuItem("fetchGrinnCorrNetwork", tabName = "fgrinncorr", icon = icon("circle")),
menuItem("fetchGrinnDiffCorrNetwork", tabName = "fgrinndiff", icon = icon("circle")),
menuItem("convertToGrinnID", tabName = "convertid", icon = icon("exchange")),
menuItem("setGrinnDb", tabName = "setdb", icon = icon("cogs"))
)
),
dashboardBody(
fluidRow(
column(width = 12,
absolutePanel(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "grinn.css")
)
)
)
),
tabItems(
tabItem(tabName = "fgrinn",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchGrinnNetwork"),
p("Query a network (grinn network) using information from the internal graph database, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchgrinn.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(4, fileInput(inputId='txtInput', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTable')))
),
hr(),
fluidRow(
column(6,radioButtons("from", label = "from",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite")),
column(6,radioButtons("to", label = "to",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "pathway"))
),
fluidRow(
column(6,checkboxGroupInput("filterSource", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
fluidRow(
column(12,radioButtons("dbXref", label ="dbXref",inline = TRUE,
choices = list("grinn"="grinn","chebi"="chebi","kegg"="kegg","pubchem"="pubchem",
"inchi"="inchi","hmdb"="hmdb","smpdb"="smpdb","reactome"="reactome",
"uniprot"="uniprot","ensembl"="ensembl","entrezgene"="entrezgene"),selected = "grinn"))
),
hr(),
actionButton("query","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeBio', 'Download Edge'),br(),
downloadButton('downloadNodeBio', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgbio")),
tabPanel("Nodes", dataTableOutput("nodeTableBio")),
tabPanel("Edges", dataTableOutput("edgeTableBio"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "fcorrgrinn",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchCorrGrinnNetwork"),
p("Compute a weighted correlation network and expand the network with information from the internal graph database, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchcorrgrinn.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(8, radioButtons('sep', 'Delimiter',c(Comma=',',Tab='\t',Semicolon=';'),',',inline=TRUE))
),
fluidRow(
column(4, fileInput(inputId='datXInput', label='datX *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datXExTable')))
),
fluidRow(
column(4, fileInput(inputId='datYInput', label='datY', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datYExTable')))
),
hr(),
fluidRow(
column(6,numericInput("corrCoef", label = "corrCoef *",value = 0.5, min = 0, max = 1, step = 0.1)),
column(6,numericInput("pval", label = "pval *",value = 0.05, min = 0, max = 0.05, step = 0.001))
),
fluidRow(
column(6,radioButtons("method", label ="method",inline = TRUE,
choices = list("spearman"="spearman","pearson"="pearson","kendall"="kendall"),selected = "spearman"))
),
fluidRow(
column(6,radioButtons("xTo", label = "xTo",inline = TRUE,
choices = list("non"="non","metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite")),
column(6,radioButtons("yTo", label = "yTo",inline = TRUE,
choices = list("non"="non","metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "non"))
),
fluidRow(
column(6,checkboxGroupInput("filterSourceCorr", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
hr(),
actionButton("computeCorr","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeCorr', 'Download Edge'),br(),
downloadButton('downloadNodeCorr', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgcorr")),
tabPanel("Nodes", dataTableOutput("nodeTableCorr")),
tabPanel("Edges", dataTableOutput("edgeTableCorr"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "fdiffgrinn",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchDiffCorrGrinnNetwork"),
p("Compute a differential correlation network and expand the network with information from the internal graph database, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchdiffcorrgrinn.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(8, radioButtons('sepDiff', 'Delimiter',c(Comma=',',Tab='\t',Semicolon=';'),',',inline=TRUE))
),
fluidRow(
column(4, fileInput(inputId='datXInputDiff', label='datX1 *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datXExTableDiff')))
),
fluidRow(
column(4, fileInput(inputId='datX2Input', label='datX2 *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datX2ExTable')))
),
hr(),
fluidRow(
column(6,numericInput("pvalDiff", label = "pDiff *",value = 0.05, min = 0, max = 0.05, step = 0.001))
),
fluidRow(
column(6,radioButtons("methodDiff", label ="method",inline = TRUE,
choices = list("spearman"="spearman","pearson"="pearson","kendall"="kendall"),selected = "spearman"))
),
fluidRow(
column(6,radioButtons("xToDiff", label = "xTo",inline = TRUE,
choices = list("non"="non","metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite"))
),
fluidRow(
column(6,checkboxGroupInput("filterSourceDiff", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
hr(),
actionButton("computeDiff","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeDiff', 'Download Edge'),br(),
downloadButton('downloadNodeDiff', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgdiff")),
tabPanel("Nodes", dataTableOutput("nodeTableDiff")),
tabPanel("Edges", dataTableOutput("edgeTableDiff"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "fgrinncorr",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchGrinnCorrNetwork"),
p("Reconstruct a grinn network using information from the internal graph database, then compute and combine with a weighted correlation network, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchgrinncorr.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
h5("Network query:"),
fluidRow(
column(4, fileInput(inputId='txtInputCorr', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTableCorr')))
),
fluidRow(
column(6,radioButtons("fromCorr", label = "from",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite")),
column(6,radioButtons("toCorr", label = "to",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "pathway"))
),
fluidRow(
column(6,checkboxGroupInput("filterSourceCorr2", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
fluidRow(
column(12,radioButtons("dbXrefCorr", label ="dbXref",inline = TRUE,
choices = list("grinn"="grinn","chebi"="chebi","kegg"="kegg","pubchem"="pubchem",
"inchi"="inchi","hmdb"="hmdb","smpdb"="smpdb","reactome"="reactome",
"uniprot"="uniprot","ensembl"="ensembl","entrezgene"="entrezgene"),selected = "grinn"))
),
hr(),
h5("Correlation analysis:"),
fluidRow(
column(8, radioButtons('sepCorr', 'Delimiter',c(Comma=',',Tab='\t',Semicolon=';'),',',inline=TRUE))
),
fluidRow(
column(4, fileInput(inputId='datXInputCorr', label='datX *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datXExTableCorr')))
),
fluidRow(
column(4, fileInput(inputId='datYInputCorr', label='datY', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datYExTableCorr')))
),
fluidRow(
column(6,numericInput("corrCoefCorr", label = "corrCoef *",value = 0.5, min = 0, max = 1, step = 0.1)),
column(6,numericInput("pvalCorr", label = "pval *",value = 0.05, min = 0, max = 0.05, step = 0.001))
),
fluidRow(
column(6,radioButtons("methodCorr", label ="method",inline = TRUE,
choices = list("spearman"="spearman","pearson"="pearson","kendall"="kendall"),selected = "spearman"))
),
hr(),
actionButton("computeCorr2","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeCorr2', 'Download Edge'),br(),
downloadButton('downloadNodeCorr2', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgcorr2")),
tabPanel("Nodes", dataTableOutput("nodeTableCorr2")),
tabPanel("Edges", dataTableOutput("edgeTableCorr2"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "fgrinndiff",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchGrinnDiffCorrNetwork"),
p("Reconstruct a grinn network queried from the internal graph database, then compute and combine with a differential correlation network, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchgrinndiffcorr.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
h5("Network query:"),
fluidRow(
column(4, fileInput(inputId='txtInputDiff', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTableDiff')))
),
fluidRow(
column(6,radioButtons("fromDiff", label = "from",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite")),
column(6,radioButtons("toDiff", label = "to",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "pathway"))
),
fluidRow(
column(6,checkboxGroupInput("filterSourceDiff2", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
fluidRow(
column(12,radioButtons("dbXrefDiff", label ="dbXref",inline = TRUE,
choices = list("grinn"="grinn","chebi"="chebi","kegg"="kegg","pubchem"="pubchem",
"inchi"="inchi","hmdb"="hmdb","smpdb"="smpdb","reactome"="reactome",
"uniprot"="uniprot","ensembl"="ensembl","entrezgene"="entrezgene"),selected = "grinn"))
),
hr(),
h5("Correlation analysis:"),
fluidRow(
column(8, radioButtons('sepDiff2', 'Delimiter',c(Comma=',',Tab='\t',Semicolon=';'),',',inline=TRUE))
),
fluidRow(
column(4, fileInput(inputId='datXInputDiff2', label='datX1 *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datXExTableDiff2')))
),
fluidRow(
column(4, fileInput(inputId='datX2InputDiff2', label='datX2 *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datX2ExTableDiff2')))
),
hr(),
fluidRow(
column(6,numericInput("pvalDiff2", label = "pDiff *",value = 0.05, min = 0, max = 0.05, step = 0.001))
),
fluidRow(
column(6,radioButtons("methodDiff2", label ="method",inline = TRUE,
choices = list("spearman"="spearman","pearson"="pearson","kendall"="kendall"),selected = "spearman"))
),
hr(),
actionButton("computeDiff2","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeDiff2', 'Download Edge'),br(),
downloadButton('downloadNodeDiff2', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgdiff2")),
tabPanel("Nodes", dataTableOutput("nodeTableDiff2")),
tabPanel("Edges", dataTableOutput("edgeTableDiff2"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "convertid",
fluidRow(column(12,
mainPanel(width=12,
h3("convertToGrinnID"),
p("Convert other database IDs to grinn IDs, see ",
a(href='http://kwanjeeraw.github.io/grinn/convert.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(4, fileInput(inputId='txtInputConv', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTableConv')))
),
hr(),
fluidRow(
column(6,radioButtons("fromConv", label = "nodetype",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite"))
),
fluidRow(
column(12,radioButtons("dbXrefConv", label ="dbXref",inline = TRUE,
choices = list("chebi"="chebi","kegg"="kegg","pubchem"="pubchem",
"inchi"="inchi","hmdb"="hmdb","smpdb"="smpdb","reactome"="reactome",
"uniprot"="uniprot","ensembl"="ensembl","entrezgene"="entrezgene"),selected = "kegg"))
),
hr(),
actionButton("convert","Submit")
),
fluidRow(column(12,
h4("Output"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadId', 'Download')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgconv")),
tabPanel("Table", dataTableOutput("idTable"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "setdb",
fluidRow(column(12,
mainPanel(width=12,
h3("setGrinnDb"),
p("Set the graph database location for the currently working environment, see ",
a(href='http://kwanjeeraw.github.io/grinn/setdb.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Current database location:"),
fluidRow(
column(12, verbatimTextOutput("currentdb"))
),
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(6, textInput(inputId='dburl', label='url *', value=""))
),
hr(),
actionButton("submit","Submit"), actionButton("resettingdb","Reset")
)
)
)# end tabItems
)# end dashboardBody
)# end dashboardPage
kwanjeeraw/grinn documentation built on May 20, 2019, 7:07 p.m.
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library(shiny)
library(DT)
library(grinn)
library(shinydashboard)
dashboardPage(skin = "black",
dashboardHeader(title=img(src="logo.png", width = 200)),
dashboardSidebar(
sidebarMenu(
menuItem("fetchGrinnNetwork", tabName = "fgrinn", icon = icon("circle")),
menuItem("fetchCorrGrinnNetwork", tabName = "fcorrgrinn", icon = icon("circle")),
menuItem("fetchDiffCorrGrinnNetwork", tabName = "fdiffgrinn", icon = icon("circle")),
menuItem("fetchGrinnCorrNetwork", tabName = "fgrinncorr", icon = icon("circle")),
menuItem("fetchGrinnDiffCorrNetwork", tabName = "fgrinndiff", icon = icon("circle")),
menuItem("convertToGrinnID", tabName = "convertid", icon = icon("exchange")),
menuItem("setGrinnDb", tabName = "setdb", icon = icon("cogs"))
)
),
dashboardBody(
fluidRow(
column(width = 12,
absolutePanel(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "grinn.css")
)
)
)
),
tabItems(
tabItem(tabName = "fgrinn",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchGrinnNetwork"),
p("Query a network (grinn network) using information from the internal graph database, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchgrinn.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(4, fileInput(inputId='txtInput', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTable')))
),
hr(),
fluidRow(
column(6,radioButtons("from", label = "from",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite")),
column(6,radioButtons("to", label = "to",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "pathway"))
),
fluidRow(
column(6,checkboxGroupInput("filterSource", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
fluidRow(
column(12,radioButtons("dbXref", label ="dbXref",inline = TRUE,
choices = list("grinn"="grinn","chebi"="chebi","kegg"="kegg","pubchem"="pubchem",
"inchi"="inchi","hmdb"="hmdb","smpdb"="smpdb","reactome"="reactome",
"uniprot"="uniprot","ensembl"="ensembl","entrezgene"="entrezgene"),selected = "grinn"))
),
hr(),
actionButton("query","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeBio', 'Download Edge'),br(),
downloadButton('downloadNodeBio', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgbio")),
tabPanel("Nodes", dataTableOutput("nodeTableBio")),
tabPanel("Edges", dataTableOutput("edgeTableBio"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "fcorrgrinn",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchCorrGrinnNetwork"),
p("Compute a weighted correlation network and expand the network with information from the internal graph database, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchcorrgrinn.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(8, radioButtons('sep', 'Delimiter',c(Comma=',',Tab='\t',Semicolon=';'),',',inline=TRUE))
),
fluidRow(
column(4, fileInput(inputId='datXInput', label='datX *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datXExTable')))
),
fluidRow(
column(4, fileInput(inputId='datYInput', label='datY', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datYExTable')))
),
hr(),
fluidRow(
column(6,numericInput("corrCoef", label = "corrCoef *",value = 0.5, min = 0, max = 1, step = 0.1)),
column(6,numericInput("pval", label = "pval *",value = 0.05, min = 0, max = 0.05, step = 0.001))
),
fluidRow(
column(6,radioButtons("method", label ="method",inline = TRUE,
choices = list("spearman"="spearman","pearson"="pearson","kendall"="kendall"),selected = "spearman"))
),
fluidRow(
column(6,radioButtons("xTo", label = "xTo",inline = TRUE,
choices = list("non"="non","metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite")),
column(6,radioButtons("yTo", label = "yTo",inline = TRUE,
choices = list("non"="non","metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "non"))
),
fluidRow(
column(6,checkboxGroupInput("filterSourceCorr", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
hr(),
actionButton("computeCorr","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeCorr', 'Download Edge'),br(),
downloadButton('downloadNodeCorr', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgcorr")),
tabPanel("Nodes", dataTableOutput("nodeTableCorr")),
tabPanel("Edges", dataTableOutput("edgeTableCorr"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "fdiffgrinn",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchDiffCorrGrinnNetwork"),
p("Compute a differential correlation network and expand the network with information from the internal graph database, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchdiffcorrgrinn.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(8, radioButtons('sepDiff', 'Delimiter',c(Comma=',',Tab='\t',Semicolon=';'),',',inline=TRUE))
),
fluidRow(
column(4, fileInput(inputId='datXInputDiff', label='datX1 *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datXExTableDiff')))
),
fluidRow(
column(4, fileInput(inputId='datX2Input', label='datX2 *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datX2ExTable')))
),
hr(),
fluidRow(
column(6,numericInput("pvalDiff", label = "pDiff *",value = 0.05, min = 0, max = 0.05, step = 0.001))
),
fluidRow(
column(6,radioButtons("methodDiff", label ="method",inline = TRUE,
choices = list("spearman"="spearman","pearson"="pearson","kendall"="kendall"),selected = "spearman"))
),
fluidRow(
column(6,radioButtons("xToDiff", label = "xTo",inline = TRUE,
choices = list("non"="non","metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite"))
),
fluidRow(
column(6,checkboxGroupInput("filterSourceDiff", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
hr(),
actionButton("computeDiff","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeDiff', 'Download Edge'),br(),
downloadButton('downloadNodeDiff', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgdiff")),
tabPanel("Nodes", dataTableOutput("nodeTableDiff")),
tabPanel("Edges", dataTableOutput("edgeTableDiff"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "fgrinncorr",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchGrinnCorrNetwork"),
p("Reconstruct a grinn network using information from the internal graph database, then compute and combine with a weighted correlation network, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchgrinncorr.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
h5("Network query:"),
fluidRow(
column(4, fileInput(inputId='txtInputCorr', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTableCorr')))
),
fluidRow(
column(6,radioButtons("fromCorr", label = "from",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite")),
column(6,radioButtons("toCorr", label = "to",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "pathway"))
),
fluidRow(
column(6,checkboxGroupInput("filterSourceCorr2", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
fluidRow(
column(12,radioButtons("dbXrefCorr", label ="dbXref",inline = TRUE,
choices = list("grinn"="grinn","chebi"="chebi","kegg"="kegg","pubchem"="pubchem",
"inchi"="inchi","hmdb"="hmdb","smpdb"="smpdb","reactome"="reactome",
"uniprot"="uniprot","ensembl"="ensembl","entrezgene"="entrezgene"),selected = "grinn"))
),
hr(),
h5("Correlation analysis:"),
fluidRow(
column(8, radioButtons('sepCorr', 'Delimiter',c(Comma=',',Tab='\t',Semicolon=';'),',',inline=TRUE))
),
fluidRow(
column(4, fileInput(inputId='datXInputCorr', label='datX *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datXExTableCorr')))
),
fluidRow(
column(4, fileInput(inputId='datYInputCorr', label='datY', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datYExTableCorr')))
),
fluidRow(
column(6,numericInput("corrCoefCorr", label = "corrCoef *",value = 0.5, min = 0, max = 1, step = 0.1)),
column(6,numericInput("pvalCorr", label = "pval *",value = 0.05, min = 0, max = 0.05, step = 0.001))
),
fluidRow(
column(6,radioButtons("methodCorr", label ="method",inline = TRUE,
choices = list("spearman"="spearman","pearson"="pearson","kendall"="kendall"),selected = "spearman"))
),
hr(),
actionButton("computeCorr2","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeCorr2', 'Download Edge'),br(),
downloadButton('downloadNodeCorr2', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgcorr2")),
tabPanel("Nodes", dataTableOutput("nodeTableCorr2")),
tabPanel("Edges", dataTableOutput("edgeTableCorr2"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "fgrinndiff",
fluidRow(column(12,
mainPanel(width=12,
h3("fetchGrinnDiffCorrNetwork"),
p("Reconstruct a grinn network queried from the internal graph database, then compute and combine with a differential correlation network, see ",
a(href='http://kwanjeeraw.github.io/grinn/fetchgrinndiffcorr.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
h5("Network query:"),
fluidRow(
column(4, fileInput(inputId='txtInputDiff', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTableDiff')))
),
fluidRow(
column(6,radioButtons("fromDiff", label = "from",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite")),
column(6,radioButtons("toDiff", label = "to",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "pathway"))
),
fluidRow(
column(6,checkboxGroupInput("filterSourceDiff2", label ="filterSource",inline = TRUE,
choices = list("SMPDB"="SMPDB","KEGG"="KEGG","REACTOME"="REACTOME"),selected = c("SMPDB","KEGG","REACTOME")))
),
fluidRow(
column(12,radioButtons("dbXrefDiff", label ="dbXref",inline = TRUE,
choices = list("grinn"="grinn","chebi"="chebi","kegg"="kegg","pubchem"="pubchem",
"inchi"="inchi","hmdb"="hmdb","smpdb"="smpdb","reactome"="reactome",
"uniprot"="uniprot","ensembl"="ensembl","entrezgene"="entrezgene"),selected = "grinn"))
),
hr(),
h5("Correlation analysis:"),
fluidRow(
column(8, radioButtons('sepDiff2', 'Delimiter',c(Comma=',',Tab='\t',Semicolon=';'),',',inline=TRUE))
),
fluidRow(
column(4, fileInput(inputId='datXInputDiff2', label='datX1 *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datXExTableDiff2')))
),
fluidRow(
column(4, fileInput(inputId='datX2InputDiff2', label='datX2 *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('datX2ExTableDiff2')))
),
hr(),
fluidRow(
column(6,numericInput("pvalDiff2", label = "pDiff *",value = 0.05, min = 0, max = 0.05, step = 0.001))
),
fluidRow(
column(6,radioButtons("methodDiff2", label ="method",inline = TRUE,
choices = list("spearman"="spearman","pearson"="pearson","kendall"="kendall"),selected = "spearman"))
),
hr(),
actionButton("computeDiff2","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdgeDiff2', 'Download Edge'),br(),
downloadButton('downloadNodeDiff2', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgdiff2")),
tabPanel("Nodes", dataTableOutput("nodeTableDiff2")),
tabPanel("Edges", dataTableOutput("edgeTableDiff2"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "convertid",
fluidRow(column(12,
mainPanel(width=12,
h3("convertToGrinnID"),
p("Convert other database IDs to grinn IDs, see ",
a(href='http://kwanjeeraw.github.io/grinn/convert.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(4, fileInput(inputId='txtInputConv', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTableConv')))
),
hr(),
fluidRow(
column(6,radioButtons("fromConv", label = "nodetype",inline = TRUE,
choices = list("metabolite"="metabolite","protein"="protein","gene"="gene","pathway"="pathway"),selected = "metabolite"))
),
fluidRow(
column(12,radioButtons("dbXrefConv", label ="dbXref",inline = TRUE,
choices = list("chebi"="chebi","kegg"="kegg","pubchem"="pubchem",
"inchi"="inchi","hmdb"="hmdb","smpdb"="smpdb","reactome"="reactome",
"uniprot"="uniprot","ensembl"="ensembl","entrezgene"="entrezgene"),selected = "kegg"))
),
hr(),
actionButton("convert","Submit")
),
fluidRow(column(12,
h4("Output"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadId', 'Download')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("consolemsgconv")),
tabPanel("Table", dataTableOutput("idTable"))
)
)
)#end sidebarLayout
))
),
tabItem(tabName = "setdb",
fluidRow(column(12,
mainPanel(width=12,
h3("setGrinnDb"),
p("Set the graph database location for the currently working environment, see ",
a(href='http://kwanjeeraw.github.io/grinn/setdb.html',target='_blank','here'),' for argument details.'
)
)#end mainPanel
)),
wellPanel(
h4("Current database location:"),
fluidRow(
column(12, verbatimTextOutput("currentdb"))
),
h4("Input arguments:"), helpText("* required field"),
fluidRow(
column(6, textInput(inputId='dburl', label='url *', value=""))
),
hr(),
actionButton("submit","Submit"), actionButton("resettingdb","Reset")
)
)
)# end tabItems
)# end dashboardBody
)# end dashboardPage
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