inst/app/code/ui/demoOmicsTable.R

In chemokine/OmicsSBGN: Overlay omics data onto SBGN pathway diagram

fluidPage(
    sidebarLayout(
        # Sidebar panel for inputs ----
        sidebarPanel(
            # selectInput("preData",
            #                label = NULL,
            #                c("IFNg"
            #                 ,"cancer" 
            #                 )
            # ),
            downloadButton("Example", "Download Example Table")
            ,conditionalPanel(
                # condition = "input.preData == 'IFNg'"
                condition = "input.usePathways == 'userSBGN'"
                ,p(
                    "This table includes the gene expression fold change data of an RNA-Seq experiment comparing two groups:
                    ",br(),"
                    IFNg KO mice and wild type mice.
                    ",br(),
                HTML("<ol>",
                        "<li>
                            Species: mouse (KEGG code: 'mmu')
                        </li>
                         ",
                        "<li> 
                            Molecule ID type: ENSEMBL GENE
                        </li>",
                    "</ol>"),
                   
                    "
                    The experiment and data processing was described in this work: Greer, Renee L., Xiaoxi Dong, et al.
                    'Akkermansia muciniphila mediates negative effects of IFNG on glucose metabolism.'
                    Nature communications 7 (2016): 13329. " 
                    ) 
            ),
            conditionalPanel( 
                # condition = "input.preData == 'cancer'"
                condition = "input.usePathways == 'UsePrePathways'"
                ,p( 
                    "This is a fold change table from a breast cancer study (Emery et al, 2009)
                    downloaded from Gene Expression Omnibus (GEO).
                    ",br(),"
                    The Dataset is pre-processed using FARMS method and includes 3 patient cases,
                    each with HN (histologically normal) and DCIS (ductal carcinoma in situ) RMA samples.
                    ",br(),"
                    The three columns are gene expression fold changes of three pairs of 
                    cancer (DCIS) vs normal (HN) samples from three patients, respectively." 
                    ,HTML("<ol>",
                            "<li>
                                Species: human (KEGG code: 'hsa')
                            </li>
                             ",
                            "<li> 
                                Molecule ID type: ENTREZ GENE ID
                            </li>",
                        "</ol>")
                   
                    )
                
            )
        ),
        mainPanel(
            # Output: Data file ----
            # tableOutput("contents")
            div(style = "padding-left: 15px;color: var(--neutral2);",
            DT::dataTableOutput("demoDataTable")
            )
            
        )
    )
)