require(shiny)
require(shinyjs)
require(d3Toolbox)
require(GSVA)
require(Rtsne)
require(RColorBrewer)
require(limma)
require(SummarizedExperiment)
ui <- navbarPage(title = "tSNEfier",
tabPanel(title = "File loading",
fluidRow(
includeCSS(system.file('www','tSNEfier',package='tSNEfier')),
column(6,
fileInput("eSet_file",
"Load gene expression data (.rds)",
accept = c(".rds",".RDS")),
fileInput("gmt_file",
"Load gene set file (.gmt)",
accept = c(".gmt")),
actionButton("runGSVA", "Run GSVA")
),
column(6,
fileInput("state_file",
"Load a saved state (.rds)",
accept = c(".rds",".RDS")),
downloadButton("SaveStateButton", "Save current state")
)
)
),
tabPanel(title = "Display panel",
fluidRow(
column(6,
d3ScatterOutput("scatter", width = "100%", height = "600"),
fluidRow(
column(4,
selectizeInput("gene_color",
label = h5("Select gene"),
choices = NULL)
),
column(4,
selectizeInput("pathway_color",
label = h5("Select pathway"),
choices = NULL)
),
column(4,
selectizeInput("covariate_color",
label = h5("Select covariate"),
choices = NULL)
)
),
actionButton("runtSNE", "Run tSNE"),
selectizeInput("gene_filter",
label = h5("Select gene space for the filter"),
choices = NULL)
),
column(6,
actionButton("diffGenes", "Differential Genes"),
actionButton("diffPathways", "Differential Pathways"),
dataTableOutput('diffTable')
)
)
)
)
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