R/loadAboutTab.R

In SRHilz/GliomaAtlas3D: A 3D Map of Tumor-Wide Genetic and Microenvironmental Heterogeneity Present Across Adult Diffuse Glioma

#' UI-elements for about tab
#'
#' @import shiny
#' @export 

loadAboutTab <- function(){
  addResourcePath('www',system.file('shinyApp/www',package = "GliomaAtlas3D"))  
  version <- paste0('GliomaAtlas3D ',as.character(packageVersion(.packageName)))
  aboutTab <- tabPanel(title = 'About', id = 'about', 
           titlePanel("The 3D Glioma Atlas"),
           sidebarLayout(
             sidebarPanel(
               h4("Version Information"),
               a(version, href = "https://github.com/SRHilz/GliomaAtlas3D"),
               h4("Citation Information"),
               p("For more information about the data in our app, please check out our publication:"),
               em("Stephanie Hilz, Chibo Hong, Llewellyn E. Jalbert, Robert K. Hu, Tali Mazor, Anupam Kumar, Ivan V. Smirnov, Andrew McKinney, Samuel J. Shelton, Patrick Schupp, Michael Y. Zhang, Michael Martin, Stephen T. Magill, Karen H.K. Wong, Josie L. Hayes, Yao Yu, Matthew R. Grimmer, Tracy Luks, Marram P. Olson, Marisa Lafontaine, Anny Shai, Henrik Bengtsson, Adam Olshen, Annette M. Molinaro, Michael W. McDermott, Manish K. Aghi, Edward F. Chang, Shawn L. Hervey-Jumper, Mitchel S. Berger, Daniel A. Lim, Aaron Diaz, Janine M. Lupo, Joanna J. Phillips, Susan M. Chang, Sarah J. Nelson, Michael C. Oldham, Joseph F. Costello. "),
                  strong(em("A three-dimensional atlas of whole tumors reveals principles of glioma growth.")),
                  em("In review"),
               br(),
               br(),
               p("Please cite us if you use any data from our app in your own work."),
               p("If you use ATAC-seq data, please also cite:"),
               em("Radhika Mathur, Qixuan Wang, Sriranga Iyyanki, Stephanie Hilz, Chibo Hong, Joanna Phillips, Susan Chang, Feng Yue, Joseph Costello. "),
                  strong(em("EPCO-31. EPIGENOMIC INTRATUMORAL HETEROGENEITY OF GLIOBLASTOMA IN THREE-DIMENSIONAL SPACE.")), 
                  em("Neuro-Oncology, Volume 22, Issue Supplement_2, November 2020, Page ii76, https://doi.org/10.1093/neuonc/noaa215.310"),
               br(),
               br(),
               "The 3D Glioma Atlas was built by Stephanie Hilz, Henrik Bengtsson, and Robert Hu using ", 
               a("R", 
                 href = "https://www.r-project.org/about.html"),
               " and ",
               a("Shiny", 
                 href = "http://shiny.rstudio.com")
             ),
             mainPanel(
               h1("Introducing a spatial approach to cancer genomics"),
               br(),
               img(src = "www/concept.png", height="90%", width="90%", align="center"),
               br(),
               br(),
               p("To create the 3D Glioma Atlas, we maximally sampled the anatomical diversity present in each patient's tumor, registering the physical location of each sample to a preoperative magnetic resonance image (MRI). This allowed us to analyze genomic and histologic information from each sample in relation to other samples and the tumor as a whole."),
               br(),
               h4("How do I use the Atlas?"),
               br(),
               p("Using the Atlas is simple. Select a patient and you will see all tumors available for that patient. After selecting a tumor, you will see the available data types. Some of these will have additional inputs, such as gene names for RNAseq data, that you can additionally select. A 3D heatmap of samples shaded by that data type will then appear on the right."),
               br(),
               h4("Why 3D?"),
               br(),
               p("ITH is thought to be a major reason for targeted treatment failure. Previous studies have been restricted in their ability to provide a comprehensive understanding of ITH in solid tumors due to insufficient sampling, typically just one biopsy per patient, and a lack of knowledge of where within the tumor the sample was taken. "),
               br(),
               h4("Available data types"),
               br(),
               strong("- Tumor cell proportion: "),
               p("The proportion of cells in the sample that are tumor, based on whole exome sequencing data"),
               strong("- Cell Types: "),
               p("The enrichment score for the abundance of different cell types estimated from RNAseq-based coexpression network analysis"),
               strong("- Cancer Processes: "),
               p("The enrichment score for 14 different cancer-associated processes estimated from RNAseq data using CancerSEA"),
               strong("- Expansion Events: "),
               p("The mean variant allele frequency (VAF) for predicted tumor cell clonal expansion events"),
               strong("- RNAseq: "),
               p("The transcript level of a given gene, based on RNA sequencing"),
               strong("- Gene Promoter Accessibility: "),
	       p("The chromatin accessibility of a given gene's promotor, as measured by ATAC-Seq relative enrichment"),
	       strong("- Gene Enhancer Accessibility: "),
	       p("The chromatin accessibility of a given gene's enhancer, as measured by ATAC-Seq relative enrichment"),
	       strong("- Copy Number: "),
               p("The number of copies per gene, based on whole exome data"),
               strong("- Amplification: "),
               p("Whether or not a gene is amplified at a given threshold, based on whole exome data"),
               strong("- Percent Necrosis: "),
               p("The percent of tissue estimated to be necrotic, based on histology"),
               strong("- BV Hyperplasia: "),
               p("A score indicating the extent of abnormal blood vessles, based on histology")
          
               
               
             )
           )
  )
  invisible(aboutTab)
}