inst/shinyApp/ui/uitab3.R
In Mathelab/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)
tabItem3 <- shinydashboard::tabItem(
tabName = "pathFromMeta",
shinydashboard::tabBox(width = 12, id = "tabset3",
shiny::tabPanel(
title = strong("Input analyte one by one"),
label ="sub_tab_1_TAB3",
#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.")
)),
#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 compound name or source id')),
helpText("Given a gene/metabolite name or ID,retrieve pathways in which the compound is involved in."),
textInput("compName","",placeholder = "Input compound name or source id"),
radioButtons("NameOrId","Search by common names or source IDs?",
choices = c("Names" = "names", "Source ID" = "ids"),selected = "ids"),
selectInput("KW_synonym", "Select from list", choices = NULL),
actionButton("submit_compName","Submit"),
br(),
br(),
shinydashboard::infoBoxOutput("statusbox_tab3_subtab1", width = NULL)
),
shiny::mainPanel(
width = 6,
h4(strong('Summary')),
textOutput("summary_path"),
br(),
downloadButton("comp_report","Download Results")
),
shiny::mainPanel(
width=12,
h4(strong('Query Result')),
fluidRow(
div(style = "width:100%;height:100%;align:center;",
helpText("Preview of output only display first 20 items."),
DT::dataTableOutput("result3")
)
)
))
),
# end tabPanel
shiny::tabPanel(
title = strong("Input multiple analytes (batch query)"),
label = "sub_tab_2_TAB3",
#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("1.Query Analytes"),
shiny::mainPanel(
width=6,
h4(strong('Input a list of metabolites, one per line')),
textAreaInput("input_mul_tab3",label = "",
placeholder = "Input list of metabolites, one per line"),
radioButtons("NameOrSourcemult","Search by names or source IDs?",
choices = c("Names" = "names", "Source ID" = "ids"),selected = "ids"),
h4(strong('Input a list of genes, one per line')),
textAreaInput("input_mul_tab3_genes",label = "",
placeholder = "Input list of genes, one per line"),
radioButtons("NameOrSourcemult_genes","Search by names or source IDs?",
choices = c("Names" = "names", "Source ID" = "ids"),selected = "ids"),
actionButton("sub_mul_tab3",label = "Submit Query"),
br(),
br(),
shinydashboard::infoBoxOutput("statusbox_tab3_subtab2", width = NULL)
),
shiny::mainPanel(
width=6,
h4(strong("Summary")),
textOutput("summary_path_tab2"),
p("The following number of names/ids were mapped:"),
textOutput("num_mapped_namesids"),
p("The query returned the following number of pathways per query gene/metabolite:"),
DT::dataTableOutput("summary_mulpath_out"),
p("Query results should be visible here"),
br(),
br(),
downloadButton("tab3_mul_report",label = "Download Results")
),
shiny::mainPanel(
width = 12,
HTML("<div id='database-group-output'>"),
h4(strong("Query Result")),
helpText("Table output display"),
div(style = 'width:100%;height:100%;align:center;',
DT::dataTableOutput("preview_multi_names")),
HTML("</div>")
)),
#Box for Pathway Enrichment Analysis
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = FALSE,
status = "primary",
title = strong("2.Run Pathway Enrichment Analysis"),
shiny::mainPanel(
width = 12,
h4(strong("Set Pathway Enrichment Parameters")),
tags$head(tags$style(type="text/css", "
#loadmessage {
position: fixed;
top: 0px;
left: 0px;
width: 100%;
padding: 5px 0px 5px 0px;
text-align: center;
font-weight: bold;
font-size: 100%;
color: #000000;
background-color: #FFA500;
z-index: 105;
}
")),
conditionalPanel(condition="$('html').hasClass('shiny-busy')",
tags$div("Processing request...",id="loadmessage")),
actionButton("runFisher","Run Pathway Enrichment (please be patient!)"),
HTML("<br>"),
HTML("<br>"),
textOutput("FisherTestResultWithoutFilter_AnalyteType"),
HTML("<br>"),
dataTableOutput("FisherTestResultWithoutFilter_fishresults"),
textOutput("fishersProgress")
),
shiny::mainPanel(
width = 12
# h4(strong("Results of Pathway Enrichment Analysis")),
# column(width = 6,
# selectInput("show_cluster","Display pathways in cluster:",choices = 1),
# textOutput("cluster_summary_text")
# ), # end columnb
# column(width = 6,
# plotOutput("cluster_summary_plot",height = "300px")
# ), # end column
# DT::dataTableOutput("results_fisher",width = '100%')
)),
#Box for Filter and Cluster pathways
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = FALSE,
status = "primary",
title = strong("3.Filter and cluster Pathways"),
shiny::mainPanel(
width = 12,
h4(strong("Set Filtering/Clustering Parameters")),
numericInput("p_holmadj_cutoff",
"Select cutoff for Holm Adjusted p-values (will only return pathways with Holm adj p-values < cutoff)",
value = 0.01,
min=0,max=1,
width = "80%"),
h4("Clustering Parameters:"),
numericInput("perc_analyte_overlap", "Overlap threshold (0-1) for pathways to be considered similar (for medoid establishment):",min = 0.01, max = 1, value = 0.2, step = 0.01),
numericInput("min_pathway_tocluster", "Number of similar neighbors required (for medoid establishment):",min = 1, max = 100, value = 2, step = 1),
numericInput("perc_pathway_overlap", "Overlap threshold (0-1) for pathways to be clustered:",min = 0.01, max = 1, value = 0.75, step = 0.01),
actionButton("runClustering","Filter and Cluster Results"),
h4(strong("Results of Pathway Enrichment Analysis")),
column(width = 12,
selectInput("show_cluster","Display pathways in cluster:",choices = 1),
textOutput("cluster_summary_text")
), # end columnb
br(),
br(),
column(width = 12,
shinydashboard::infoBoxOutput("results_status", width = NULL)
),
# end column
textOutput("filterStatus"),
DT::dataTableOutput("results_fisher",width = '100%'),
column(width = 6,
plotOutput("cluster_summary_plot",height = "300px")
)
)),
#Box for Download Results.
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = FALSE,
status = "primary",
title = strong("4.Download Results"),
shiny::mainPanel(
p("Significant pathways are returned under 'Results of Pathway Enrichment Analysis' and can be downloaded by clicking 'Download Results'"),
p("Note that only pathways that contain at least 3 analytes from the user input will be output"),
#textOutput("summary_Fisher"),
p("The following number of pathways per database were processed:"),
DT::dataTableOutput("summary_fisher",width = '80%'),
downloadButton("fisher_stats_report",label = "Download Results")
))
)#end tabpanel
) # end Tab Box
) # end Tabitem
Mathelab/RaMP-DB documentation built on April 24, 2021, 3:11 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
tabItem3 <- shinydashboard::tabItem(
tabName = "pathFromMeta",
shinydashboard::tabBox(width = 12, id = "tabset3",
shiny::tabPanel(
title = strong("Input analyte one by one"),
label ="sub_tab_1_TAB3",
#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.")
)),
#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 compound name or source id')),
helpText("Given a gene/metabolite name or ID,retrieve pathways in which the compound is involved in."),
textInput("compName","",placeholder = "Input compound name or source id"),
radioButtons("NameOrId","Search by common names or source IDs?",
choices = c("Names" = "names", "Source ID" = "ids"),selected = "ids"),
selectInput("KW_synonym", "Select from list", choices = NULL),
actionButton("submit_compName","Submit"),
br(),
br(),
shinydashboard::infoBoxOutput("statusbox_tab3_subtab1", width = NULL)
),
shiny::mainPanel(
width = 6,
h4(strong('Summary')),
textOutput("summary_path"),
br(),
downloadButton("comp_report","Download Results")
),
shiny::mainPanel(
width=12,
h4(strong('Query Result')),
fluidRow(
div(style = "width:100%;height:100%;align:center;",
helpText("Preview of output only display first 20 items."),
DT::dataTableOutput("result3")
)
)
))
),
# end tabPanel
shiny::tabPanel(
title = strong("Input multiple analytes (batch query)"),
label = "sub_tab_2_TAB3",
#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("1.Query Analytes"),
shiny::mainPanel(
width=6,
h4(strong('Input a list of metabolites, one per line')),
textAreaInput("input_mul_tab3",label = "",
placeholder = "Input list of metabolites, one per line"),
radioButtons("NameOrSourcemult","Search by names or source IDs?",
choices = c("Names" = "names", "Source ID" = "ids"),selected = "ids"),
h4(strong('Input a list of genes, one per line')),
textAreaInput("input_mul_tab3_genes",label = "",
placeholder = "Input list of genes, one per line"),
radioButtons("NameOrSourcemult_genes","Search by names or source IDs?",
choices = c("Names" = "names", "Source ID" = "ids"),selected = "ids"),
actionButton("sub_mul_tab3",label = "Submit Query"),
br(),
br(),
shinydashboard::infoBoxOutput("statusbox_tab3_subtab2", width = NULL)
),
shiny::mainPanel(
width=6,
h4(strong("Summary")),
textOutput("summary_path_tab2"),
p("The following number of names/ids were mapped:"),
textOutput("num_mapped_namesids"),
p("The query returned the following number of pathways per query gene/metabolite:"),
DT::dataTableOutput("summary_mulpath_out"),
p("Query results should be visible here"),
br(),
br(),
downloadButton("tab3_mul_report",label = "Download Results")
),
shiny::mainPanel(
width = 12,
HTML("<div id='database-group-output'>"),
h4(strong("Query Result")),
helpText("Table output display"),
div(style = 'width:100%;height:100%;align:center;',
DT::dataTableOutput("preview_multi_names")),
HTML("</div>")
)),
#Box for Pathway Enrichment Analysis
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = FALSE,
status = "primary",
title = strong("2.Run Pathway Enrichment Analysis"),
shiny::mainPanel(
width = 12,
h4(strong("Set Pathway Enrichment Parameters")),
tags$head(tags$style(type="text/css", "
#loadmessage {
position: fixed;
top: 0px;
left: 0px;
width: 100%;
padding: 5px 0px 5px 0px;
text-align: center;
font-weight: bold;
font-size: 100%;
color: #000000;
background-color: #FFA500;
z-index: 105;
}
")),
conditionalPanel(condition="$('html').hasClass('shiny-busy')",
tags$div("Processing request...",id="loadmessage")),
actionButton("runFisher","Run Pathway Enrichment (please be patient!)"),
HTML("<br>"),
HTML("<br>"),
textOutput("FisherTestResultWithoutFilter_AnalyteType"),
HTML("<br>"),
dataTableOutput("FisherTestResultWithoutFilter_fishresults"),
textOutput("fishersProgress")
),
shiny::mainPanel(
width = 12
# h4(strong("Results of Pathway Enrichment Analysis")),
# column(width = 6,
# selectInput("show_cluster","Display pathways in cluster:",choices = 1),
# textOutput("cluster_summary_text")
# ), # end columnb
# column(width = 6,
# plotOutput("cluster_summary_plot",height = "300px")
# ), # end column
# DT::dataTableOutput("results_fisher",width = '100%')
)),
#Box for Filter and Cluster pathways
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = FALSE,
status = "primary",
title = strong("3.Filter and cluster Pathways"),
shiny::mainPanel(
width = 12,
h4(strong("Set Filtering/Clustering Parameters")),
numericInput("p_holmadj_cutoff",
"Select cutoff for Holm Adjusted p-values (will only return pathways with Holm adj p-values < cutoff)",
value = 0.01,
min=0,max=1,
width = "80%"),
h4("Clustering Parameters:"),
numericInput("perc_analyte_overlap", "Overlap threshold (0-1) for pathways to be considered similar (for medoid establishment):",min = 0.01, max = 1, value = 0.2, step = 0.01),
numericInput("min_pathway_tocluster", "Number of similar neighbors required (for medoid establishment):",min = 1, max = 100, value = 2, step = 1),
numericInput("perc_pathway_overlap", "Overlap threshold (0-1) for pathways to be clustered:",min = 0.01, max = 1, value = 0.75, step = 0.01),
actionButton("runClustering","Filter and Cluster Results"),
h4(strong("Results of Pathway Enrichment Analysis")),
column(width = 12,
selectInput("show_cluster","Display pathways in cluster:",choices = 1),
textOutput("cluster_summary_text")
), # end columnb
br(),
br(),
column(width = 12,
shinydashboard::infoBoxOutput("results_status", width = NULL)
),
# end column
textOutput("filterStatus"),
DT::dataTableOutput("results_fisher",width = '100%'),
column(width = 6,
plotOutput("cluster_summary_plot",height = "300px")
)
)),
#Box for Download Results.
shinydashboard::box(width = 12,
solidHeader = T,
collapsible = TRUE,
collapsed = FALSE,
status = "primary",
title = strong("4.Download Results"),
shiny::mainPanel(
p("Significant pathways are returned under 'Results of Pathway Enrichment Analysis' and can be downloaded by clicking 'Download Results'"),
p("Note that only pathways that contain at least 3 analytes from the user input will be output"),
#textOutput("summary_Fisher"),
p("The following number of pathways per database were processed:"),
DT::dataTableOutput("summary_fisher",width = '80%'),
downloadButton("fisher_stats_report",label = "Download Results")
))
)#end tabpanel
) # end Tab Box
) # end Tabitem
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Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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