inst/app/tabs.R
In BimberLab/geneSetVis: Gene set visualization
tab_info <- shinydashboard::tabItem(
tabName = 'appInfo',
fluidRow(
shinydashboard::box(
title = tagList(p('App Information', style = "padding-right: 5px; display: inline")),
side = 'right',
status = 'primary',
solidHeader = TRUE,
height = NULL,
width = 16,
uiOutput('app_info')
)
)
)
tab_load_data <- shinydashboard::tabItem(
tabName = 'loadData',
fluidRow(
#column = 6,
shinydashboard::box(
title = 'Input Gene List',
status = 'primary',
solidHeader = TRUE,
height = '800px',
textAreaInput(
inputId = 'areaInput',
label = tagList(
'Enter Gene-sets:',
div(style = "display:inline-block", em('Example')),
div(style = "display:inline-block", actionLink('demo1', '#1')),
div(style = "display:inline-block", actionLink('demo2', '#2'))
),
height = '150px',
width = NULL,
value = NULL,
cols = NULL,
rows = NULL,
placeholder = NULL,
resize = NULL
),
fileInput(
'fileInput',
label = tagList(
'or Upload Gene-sets:',
div(style = "font-weight:10px; font-size:12px;", em("Enter column headers in file. If p_val column present, will filter out >0.5")),
div(style = "display:inline-block; font-weight:normal; font-size:12px;", textInput("file_geneCol", label = NULL, value = "gene")),
div(style = "display:inline-block; font-weight:normal; font-size:12px;", textInput("file_avgLogFCcol", label = NULL, value = "avg_logFC")),
div(style = "display:inline-block; font-weight:normal; font-size:12px;", textInput("file_pvaladjCol", label = NULL, value = "p_val_adj")),
),
multiple = F,
accept = c(".xlsx", ".xls", "csv")
),
radioButtons("inputType",
label = "Input Type:",
choices = list("Gene only", "Gene & avg. LogFC"),
selected = 'Gene & avg. LogFC'),
radioButtons("geneIdType",
label = "Select Gene ID Type:",
choices = list("Ensembl" = "Ensembl",
"Symbol" = "Symbol"),
selected = 'Symbol'),
withBusyIndicatorUI(actionButton('submit', 'Submit')),
),
shinydashboard::box(
title = 'Parsed Genes',
status = 'primary',
solidHeader = TRUE,
height = '800px',
DT::dataTableOutput('inputTable')
)
)
)
if (exists('gsvis_package')) {
stringdbSpecies <- read.csv(file = system.file('app/intdata/stringdb_species.v10.txt', package = 'geneSetVis'), header = T, stringsAsFactors = F, check.names = F, quote = "", sep = "\t")
} else {
stringdbSpecies <- read.csv(file = 'intdata/stringdb_species.v10.txt', header = T, stringsAsFactors = F, check.names = F, quote = "", sep = "\t")
}
tab_stringdb <- shinydashboard::tabItem(
tabName = 'stringdb',
shinydashboard::box(
title = tagList(p('Run STRINGdb', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "stringdb_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(
selectInput(
inputId = 'stringdb_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'stringdb_refSpecies_input',
label = 'Reference species:',
selected = 'Homo sapiens',
choices = stringdbSpecies$official_name_NCBI
),
numericInput(
inputId = 'stringdb_maxHitsToPlot_input',
label = 'Max. number of hits to plot:',
value = 200
),
numericInput(
inputId = 'stringdb_scoreThreshold_input',
label = 'Score threshold:',
value = 0
)
),
withBusyIndicatorUI(actionButton('runstringdb_button', 'Run'))
),
#browser(),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('stringdb_map_stats'))
),
# shinydashboard::tabBox(
# title = NULL,
# side = 'right',
# height = NULL,
# selected = 'Network (PNG)',
# width = 16,
# tabPanel( 'Network (PNG)', imageOutput('stringdb_network_png'))
# ),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'GO',
width = 16,
tabPanel('GO', DT::dataTableOutput('stringdb_GO')),
tabPanel('KEGG', DT::dataTableOutput('stringdb_KEGG'))
)
)
if (exists('gsvis_package')) {
msigdbCategories <- read.table(file = system.file('app/intdata/msigdb_categories.txt', package = 'geneSetVis'), sep = '\t', header = T, stringsAsFactors = FALSE)
} else {
msigdbCategories <- read.table(file = 'intdata/msigdb_categories.txt', sep = '\t', header = T, stringsAsFactors = FALSE)
}
msigdbCategories <- unique(msigdbCategories[c('Category', 'CategoryLabel')])
msigdbCategories$CategoryLabel <- paste0(msigdbCategories$Category, ': ', msigdbCategories$CategoryLabel)
msigdb_categories <- msigdbCategories$Category
names(msigdb_categories) <- msigdbCategories$CategoryLabel
rm(msigdbCategories)
tab_msigdb <- shinydashboard::tabItem(
tabName = 'msigdb',
shinydashboard::box(
title = tagList(p('Run MSigDB', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "msigdb_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
HTML('<a href="https://www.gsea-msigdb.org/gsea/msigdb/index.jsp" target="_blank" style="font-weight: bold;">Click here for more information on available MSigDB collections</a><br><br>'),
flowLayout(
selectInput(
inputId = 'msigdb_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'msigdb_species_input',
label = 'Reference species',
selected = 'Homo sapiens',
choices = sort(msigdbr::msigdbr_species()$species_name)
),
selectInput(
inputId = 'msigdb_category_input',
label = 'Select category (optional):',
selected = '',
choices = c('', msigdb_categories)
),
selectInput(
inputId = 'msigdb_subcategory_input',
label = 'Select subcategory (optional):',
selected = '',
choices = NULL
)
),
withBusyIndicatorUI(actionButton('runmsigdb_button', 'Run'))
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('msigdb_map_stats'))
),
makeTabBox(title = 'Enricher', key = 'enricher'),
makeTabBox(title = 'FGSEA', key = 'fgsea')
)
tab_reactome <- shinydashboard::tabItem(
tabName = 'reactome',
shinydashboard::box(
title = tagList(p('Run Reactome', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "reactome_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(selectInput(
inputId = 'reactome_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'reactome_OrgDB_input',
label = 'OrgDB:',
selected = 'org.Hs.eg.db',
#choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db')
choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db')
)
),
withBusyIndicatorUI(actionButton('runreactome_button', 'Run')),
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('reactome_map_stats'))
),
makeTabBox(title = 'Reactome', key = 'reactome')
)
tab_dose <- shinydashboard::tabItem(
tabName = 'dose',
shinydashboard::box(
title = tagList(p('Run DOSE', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "dose_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(
selectInput(
inputId = 'dose_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'dose_OrgDB_input',
label = 'OrgDB:',
selected = 'org.Hs.eg.db',
#choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db')
choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db')
)
),
withBusyIndicatorUI(actionButton('rundose_button', 'Run')),
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('dose_map_stats'))
),
makeTabBox(title = 'DOSE', key = 'dose')
#sliderInput('pvalueCutoff', label = 'p Value cutoff:', min = 0, max = 1, value = 0.5)
)
tab_ncg <- shinydashboard::tabItem(
tabName = 'ncg',
shinydashboard::box(
title = tagList(p('Run NCG', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "ncg_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(
selectInput(
inputId = 'ncg_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'ncg_OrgDB_input',
label = 'OrgDB:',
selected = 'org.Hs.eg.db',
#choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db')
choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db')
)
),
withBusyIndicatorUI(actionButton('runncg_button', 'Run')),
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('ncg_map_stats'))
),
makeTabBox(title = 'NCG', key = 'ncg')
)
tab_dgn <- shinydashboard::tabItem(
tabName = 'dgn',
shinydashboard::box(
title = tagList(p('Run DisGeNET', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "dgn_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(
selectInput(
inputId = 'dgn_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'dgn_OrgDB_input',
label = 'OrgDB:',
selected = 'org.Hs.eg.db',
#choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db')
choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db')
)
),
withBusyIndicatorUI(actionButton('rundgn_button', 'Run')),
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('dgn_map_stats'))
),
makeTabBox(title = 'DisGeNET', key = 'dgn')
)
tab_enrichr <- shinydashboard::tabItem(
tabName = 'enrichr',
shinydashboard::box(
title = tagList(p('Run enrichR', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "enrichr_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
HTML('<a href="https://amp.pharm.mssm.edu/Enrichr/#stats" target="_blank" style="font-weight: bold;">Click here for more information on available enrichR databases/libraries</a><br><br>'),
flowLayout(
selectInput(
inputId = 'enrichr_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
shinyWidgets::pickerInput(inputId = "enrichr_db",
label = 'Select database(s) to query:',
choices = c('', enrichR::listEnrichrDbs()$libraryName),
options = list(`actions-box` = TRUE),
multiple = T)
),
withBusyIndicatorUI(actionButton('runenrichr_button', 'Run'))
),
selectInput(
inputId = 'enrichr_selectQuery',
label = 'Select query result to view:',
choices = ''
),
#uiOutput('enrichrResults_selected_ui'),
#dataTableOutput('enrichrResults_selected_table'),
# ),
# shinydashboard::tabBox(
# title = NULL,
# side = 'right',
# height = NULL,
# selected = 'Mapped',
# width = 16,
# tabPanel('Mapped', uiOutput('enrichr_map_stats'))
# ),
makeTabBox(title = 'enrichR', key = 'enrichr')
)
BimberLab/geneSetVis documentation built on Feb. 21, 2022, 4:21 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
tab_info <- shinydashboard::tabItem(
tabName = 'appInfo',
fluidRow(
shinydashboard::box(
title = tagList(p('App Information', style = "padding-right: 5px; display: inline")),
side = 'right',
status = 'primary',
solidHeader = TRUE,
height = NULL,
width = 16,
uiOutput('app_info')
)
)
)
tab_load_data <- shinydashboard::tabItem(
tabName = 'loadData',
fluidRow(
#column = 6,
shinydashboard::box(
title = 'Input Gene List',
status = 'primary',
solidHeader = TRUE,
height = '800px',
textAreaInput(
inputId = 'areaInput',
label = tagList(
'Enter Gene-sets:',
div(style = "display:inline-block", em('Example')),
div(style = "display:inline-block", actionLink('demo1', '#1')),
div(style = "display:inline-block", actionLink('demo2', '#2'))
),
height = '150px',
width = NULL,
value = NULL,
cols = NULL,
rows = NULL,
placeholder = NULL,
resize = NULL
),
fileInput(
'fileInput',
label = tagList(
'or Upload Gene-sets:',
div(style = "font-weight:10px; font-size:12px;", em("Enter column headers in file. If p_val column present, will filter out >0.5")),
div(style = "display:inline-block; font-weight:normal; font-size:12px;", textInput("file_geneCol", label = NULL, value = "gene")),
div(style = "display:inline-block; font-weight:normal; font-size:12px;", textInput("file_avgLogFCcol", label = NULL, value = "avg_logFC")),
div(style = "display:inline-block; font-weight:normal; font-size:12px;", textInput("file_pvaladjCol", label = NULL, value = "p_val_adj")),
),
multiple = F,
accept = c(".xlsx", ".xls", "csv")
),
radioButtons("inputType",
label = "Input Type:",
choices = list("Gene only", "Gene & avg. LogFC"),
selected = 'Gene & avg. LogFC'),
radioButtons("geneIdType",
label = "Select Gene ID Type:",
choices = list("Ensembl" = "Ensembl",
"Symbol" = "Symbol"),
selected = 'Symbol'),
withBusyIndicatorUI(actionButton('submit', 'Submit')),
),
shinydashboard::box(
title = 'Parsed Genes',
status = 'primary',
solidHeader = TRUE,
height = '800px',
DT::dataTableOutput('inputTable')
)
)
)
if (exists('gsvis_package')) {
stringdbSpecies <- read.csv(file = system.file('app/intdata/stringdb_species.v10.txt', package = 'geneSetVis'), header = T, stringsAsFactors = F, check.names = F, quote = "", sep = "\t")
} else {
stringdbSpecies <- read.csv(file = 'intdata/stringdb_species.v10.txt', header = T, stringsAsFactors = F, check.names = F, quote = "", sep = "\t")
}
tab_stringdb <- shinydashboard::tabItem(
tabName = 'stringdb',
shinydashboard::box(
title = tagList(p('Run STRINGdb', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "stringdb_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(
selectInput(
inputId = 'stringdb_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'stringdb_refSpecies_input',
label = 'Reference species:',
selected = 'Homo sapiens',
choices = stringdbSpecies$official_name_NCBI
),
numericInput(
inputId = 'stringdb_maxHitsToPlot_input',
label = 'Max. number of hits to plot:',
value = 200
),
numericInput(
inputId = 'stringdb_scoreThreshold_input',
label = 'Score threshold:',
value = 0
)
),
withBusyIndicatorUI(actionButton('runstringdb_button', 'Run'))
),
#browser(),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('stringdb_map_stats'))
),
# shinydashboard::tabBox(
# title = NULL,
# side = 'right',
# height = NULL,
# selected = 'Network (PNG)',
# width = 16,
# tabPanel( 'Network (PNG)', imageOutput('stringdb_network_png'))
# ),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'GO',
width = 16,
tabPanel('GO', DT::dataTableOutput('stringdb_GO')),
tabPanel('KEGG', DT::dataTableOutput('stringdb_KEGG'))
)
)
if (exists('gsvis_package')) {
msigdbCategories <- read.table(file = system.file('app/intdata/msigdb_categories.txt', package = 'geneSetVis'), sep = '\t', header = T, stringsAsFactors = FALSE)
} else {
msigdbCategories <- read.table(file = 'intdata/msigdb_categories.txt', sep = '\t', header = T, stringsAsFactors = FALSE)
}
msigdbCategories <- unique(msigdbCategories[c('Category', 'CategoryLabel')])
msigdbCategories$CategoryLabel <- paste0(msigdbCategories$Category, ': ', msigdbCategories$CategoryLabel)
msigdb_categories <- msigdbCategories$Category
names(msigdb_categories) <- msigdbCategories$CategoryLabel
rm(msigdbCategories)
tab_msigdb <- shinydashboard::tabItem(
tabName = 'msigdb',
shinydashboard::box(
title = tagList(p('Run MSigDB', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "msigdb_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
HTML('<a href="https://www.gsea-msigdb.org/gsea/msigdb/index.jsp" target="_blank" style="font-weight: bold;">Click here for more information on available MSigDB collections</a><br><br>'),
flowLayout(
selectInput(
inputId = 'msigdb_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'msigdb_species_input',
label = 'Reference species',
selected = 'Homo sapiens',
choices = sort(msigdbr::msigdbr_species()$species_name)
),
selectInput(
inputId = 'msigdb_category_input',
label = 'Select category (optional):',
selected = '',
choices = c('', msigdb_categories)
),
selectInput(
inputId = 'msigdb_subcategory_input',
label = 'Select subcategory (optional):',
selected = '',
choices = NULL
)
),
withBusyIndicatorUI(actionButton('runmsigdb_button', 'Run'))
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('msigdb_map_stats'))
),
makeTabBox(title = 'Enricher', key = 'enricher'),
makeTabBox(title = 'FGSEA', key = 'fgsea')
)
tab_reactome <- shinydashboard::tabItem(
tabName = 'reactome',
shinydashboard::box(
title = tagList(p('Run Reactome', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "reactome_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(selectInput(
inputId = 'reactome_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'reactome_OrgDB_input',
label = 'OrgDB:',
selected = 'org.Hs.eg.db',
#choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db')
choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db')
)
),
withBusyIndicatorUI(actionButton('runreactome_button', 'Run')),
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('reactome_map_stats'))
),
makeTabBox(title = 'Reactome', key = 'reactome')
)
tab_dose <- shinydashboard::tabItem(
tabName = 'dose',
shinydashboard::box(
title = tagList(p('Run DOSE', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "dose_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(
selectInput(
inputId = 'dose_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'dose_OrgDB_input',
label = 'OrgDB:',
selected = 'org.Hs.eg.db',
#choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db')
choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db')
)
),
withBusyIndicatorUI(actionButton('rundose_button', 'Run')),
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('dose_map_stats'))
),
makeTabBox(title = 'DOSE', key = 'dose')
#sliderInput('pvalueCutoff', label = 'p Value cutoff:', min = 0, max = 1, value = 0.5)
)
tab_ncg <- shinydashboard::tabItem(
tabName = 'ncg',
shinydashboard::box(
title = tagList(p('Run NCG', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "ncg_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(
selectInput(
inputId = 'ncg_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'ncg_OrgDB_input',
label = 'OrgDB:',
selected = 'org.Hs.eg.db',
#choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db')
choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db')
)
),
withBusyIndicatorUI(actionButton('runncg_button', 'Run')),
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('ncg_map_stats'))
),
makeTabBox(title = 'NCG', key = 'ncg')
)
tab_dgn <- shinydashboard::tabItem(
tabName = 'dgn',
shinydashboard::box(
title = tagList(p('Run DisGeNET', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "dgn_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
flowLayout(
selectInput(
inputId = 'dgn_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
selectInput(
inputId = 'dgn_OrgDB_input',
label = 'OrgDB:',
selected = 'org.Hs.eg.db',
#choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db')
choices = c('org.Hs.eg.db', 'org.Mmu.eg.db', 'org.Mm.eg.db')
)
),
withBusyIndicatorUI(actionButton('rundgn_button', 'Run')),
),
shinydashboard::tabBox(
title = NULL,
side = 'right',
height = NULL,
selected = 'Mapped',
width = 16,
tabPanel('Mapped', uiOutput('dgn_map_stats'))
),
makeTabBox(title = 'DisGeNET', key = 'dgn')
)
tab_enrichr <- shinydashboard::tabItem(
tabName = 'enrichr',
shinydashboard::box(
title = tagList(p('Run enrichR', style = "padding-right: 5px; display: inline"),
actionButton(
inputId = "enrichr_resource_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information.."
)),
status = 'primary',
solidHeader = TRUE,
width = 16,
collapsible = TRUE,
HTML('<a href="https://amp.pharm.mssm.edu/Enrichr/#stats" target="_blank" style="font-weight: bold;">Click here for more information on available enrichR databases/libraries</a><br><br>'),
flowLayout(
selectInput(
inputId = 'enrichr_selectGeneCol',
label = 'Select gene column to use:',
selected = 'gene',
choices = ''
),
shinyWidgets::pickerInput(inputId = "enrichr_db",
label = 'Select database(s) to query:',
choices = c('', enrichR::listEnrichrDbs()$libraryName),
options = list(`actions-box` = TRUE),
multiple = T)
),
withBusyIndicatorUI(actionButton('runenrichr_button', 'Run'))
),
selectInput(
inputId = 'enrichr_selectQuery',
label = 'Select query result to view:',
choices = ''
),
#uiOutput('enrichrResults_selected_ui'),
#dataTableOutput('enrichrResults_selected_table'),
# ),
# shinydashboard::tabBox(
# title = NULL,
# side = 'right',
# height = NULL,
# selected = 'Mapped',
# width = 16,
# tabPanel('Mapped', uiOutput('enrichr_map_stats'))
# ),
makeTabBox(title = 'enrichR', key = 'enrichr')
)
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