# Tab 4
#
#
tabItem4<- shinydashboard::tabItem(
tabName = "geneCataComp",
shinydashboard::tabBox(width = 12,id = "tabset4",height = "100%",
shiny::tabPanel(
title = strong("Input metabolite or gene one by one"),
"",
#box for important note
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = TRUE,
status = "primary",
title = strong("IMPORTANT NOTE/INSTRUCTIONS"),
shiny::mainPanel(
width = 12,
h5("When inputting source IDs, it is important to add a prefix to denote the id type. This is important because it is possible for two different metabolites to have the same IDs, although each ID may be from a different database source."),
h5("Metabolites can be searched with the following ID types: CAS, chebi, chemspider, hmdb, kegg, LIPIDMAPS, and pubchem. To search for a metabolite, the ID type must be added as a prefix. For example, the compound 'HMDB0000562' must be searched by 'hmdb:HMDB0000562', the compound '16737' must be searched by 'chebi:16737'.")
)),
#box for Query Analytes,Summary and Results
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = FALSE,
status = "primary",
title = strong("Query Analytes"),
shiny::mainPanel(
width = 6,
h4(strong('Input metabolite or gene')),
helpText("If a compound is input, all genes that catalyze reactions involving the compound are returned."),
helpText("Conversely, if a gene is input, all compounds in reactions that are catalyzed by that gene are returned"),
textInput("CataInput","", placeholder = "Input compound name or id"),
radioButtons('CataInput_choices',label = 'Search by name or source id',
choices = c('Names' = 'names','Source ID' = 'ids')),
selectInput("KW_cata", "Select from list", choices = NULL),
actionButton("subText_cata","Submit"),
br(),
br(),
shinydashboard::infoBoxOutput("statusbox_tab4_subtab1", width = NULL)
),
shiny::mainPanel(
width = 6,
h4(strong('Summary')),
textOutput("summary_cata"),
br(),
downloadButton("report_cata","Download Results")
),
shiny::mainPanel(
width = 12,
h4(strong('Query Result')),
helpText("Table output display"),
fluidRow(
DT::dataTableOutput("result_cata")
)
)),
#box for interaction network display
shinydashboard::box(width = 12,
solidHeader = T,
status = "primary",
collapsible = T,
collapsed = F,
title = strong("Visuazlize gene-metabolite interaction network"),
shiny::mainPanel(
width=12,
fluidRow(
visNetwork::visNetworkOutput("network",height = '1000px')
) # end box
)
)
),#end tabpanel
shiny::tabPanel(
title = strong("Input a list of genes or metabolites"),
"",
#box for Important note
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = TRUE,
status = "primary",
title = strong("IMPORTANT NOTE/INSTRUCTIONS"),
shiny::mainPanel(
width = 12,
h5("When inputting source IDs, it is important to add a prefix to denote the id type. This is important because it is possible for two different metabolites to have the same IDs, although each ID may be from a different database source."),
h5("Metabolites can be searched with the following ID types: CAS, chebi, chemspider, hmdb, kegg, LIPIDMAPS, and pubchem. To search for a metabolite, the ID type must be added as a prefix. For example, the compound 'HMDB0000562' must be searched by 'hmdb:HMDB0000562', the compound '16737' must be searched by 'chebi:16737'."),
h5("Genes can be searched with the following ID types: enzymeNomenclature, ensembl, entrez, hmdb, kegg, uniprot. Similar to metabolites, prefix ID types must be added to the ID for searching."),
h5(strong("Only one type of ID can be input: either source ID or name, not both"))
)),
#box for Query Analytes,Summary and Results
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = FALSE,
status = "primary",
title = strong("Query Analytes"),
shiny::mainPanel(
width = 6,
h4(strong('Input a list of genes or metabolites')),
textAreaInput("input_mul_tab4",label = "",
placeholder = "Input list of genes or metabolites, one per line"),
radioButtons('input_mul_tab4_choices',label = 'Search by source id or name?',
choices = c('Name' = 'names','Source ID' = 'ids')),
actionButton("sub_mul_tab4",label = "Submit"),
br(),
br(),
shinydashboard::infoBoxOutput("statusbox_tab4_subtab2", width = NULL)
),
shiny::mainPanel(
width = 6,
h4(strong('Summary')),
textOutput("summary_cata_tab2"),
br(),
downloadButton("tab4_mul_report",label = "Download Results")
),
shiny::mainPanel(
width = 12,
h4(strong('Query Result')),
helpText("Table output display"),
fluidRow(
DT::dataTableOutput("preview_multi_names_tab4")
)
)),
#box for interaction network display
shinydashboard::box(width = 12,
solidHeader = T,
status = "primary",
collapsible = T,
collapsed = F,
title = strong("Visuazlize gene-metabolite interaction network"),
shiny::mainPanel(
width = 12,
fluidRow(
visNetwork::visNetworkOutput("networkmulti",height = '1000px')
)
)
)
)#end tabpanel
)# end tabBox
)# end tabItem
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