mainPanel(width=12,
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='txtInput', label='txtInput *', accept=c('text/csv','text/comma-separated-values,text/plain','.csv'))),
column(8, mainPanel(tableOutput('txtExTable')))
),
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(),
h5("Correlation analysis:"),
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')))
),
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"))
),
hr(),
actionButton("submit","Submit")
),
fluidRow(column(12,
h4("Output network"),
sidebarLayout(
sidebarPanel(width=3,
downloadButton('downloadEdge', 'Download Edge'),br(),
downloadButton('downloadNode', 'Download Node')
),
mainPanel(width=9,
tabsetPanel(type = "tabs",
tabPanel("Summary", verbatimTextOutput("summaryCode")),
tabPanel("Nodes", tableOutput("nodeTable")),
tabPanel("Edges", tableOutput("edgeTable"))
)
)
)#end sidebarLayout
))
)
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