R/mod_about.R

In jennahamlin/Tinsel: An R Shiny Application for annotating outbreak phylogenetic trees

#' about Function
#'
#' @title mod_about_ui mod_about_server
#'
#' @description A shiny Module. This module generates the landing page for the
#' application and provides a link to the github repo where users may file
#' an issue.
#'
#' @rdname mod_about
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#'
#' @keywords internal
#' @importFrom shiny NS tagList
mod_about_ui <- function(id) {
  ns <- NS(id)
  tagList(
    fluidRow(column(12, offset = 0,
                    mainPanel(h1(strong("Getting started with tinselR")),
                              tags$br(),
                              p("tinselR  (pronounced tinsel-er) at its' most
                              basic level is a graphical viewer of newick
                              phylogenetic trees and as a program for producing
                                publication-ready figures.", "The", em("power"),
                                "of tinselR comes with combining a genetic
                                distance matrix for annotating a tree for
                                epidemological outbreak analyses.", "A genetic
                                distance matrix contains the number of snp
                                differences for all pairwise comparisons. Note
                                that the data you upload is only held within
                                the application while launched
                                (i.e. no data is stored.) When you are
                                happy with the way your tree looks scroll to the
                                bottom and press Download."),
                              tags$p("If there is a bug, feature request, or
                                     documentation needed, please file an",
                                     a("issue", href =
                                         "https://github.com/jennahamlin/tinselR/issues"
                                     )),
                              tags$br(),
                              tags$h4(strong("Data Upload")),
                              tags$p("Please click on the 'Data Upload' tab
                              to upload your files. Alternatively, take a look
                              at the 'Example Data' tab to test out the
                              application. A brief description about the
                              example data is provided in the About the Example
                                     Data tab."),
                              tags$br(),
                              tags$p("There is only one differences between the
                              'Example Data' and the 'Data Upload' tabs: the
                              'Example Data' tab has pre-loaded data, while the
                              'Data Upload' tab is where you, the user, can
                              upload your own files (i.e. phylogenetic tree,
                              genetic distance file, and metadata file). By
                              that we mean, in the 'Example Data' tab, the user
                              only has three options to select from - example
                              data 1, example data 2, and example data 3 -
                              displayed in one drop down menu. While in the
                              'Data Upload' tab, there are three drop down menus
                              - 1) tree upload, 2) genetic upload, and 3) meta
                              upload."),
                              tags$br(),
                              tags$p("Both 'Example Data' and 'Data Upload'
                              tabs provide error messages as a user either
                              uploads all three files or selects a data set.
                              Types of file checks that occur inform the user
                              of the correctly selected delimiter, if the tips
                              are concordant across all three files, or if there
                              is a column to use the add heatmap functionality.
                              This file checking happens independently of if the
                              user wants the information. By that, we mean a
                              user can ignore the file check messages if they
                              do not need them and proceed using the
                              application."),
                              tags$br(),
                              tags$p("Beyond that the application is exactly
                              the same between user and example data, thus this
                              is why we highly encourage users to play with the
                              example data first just to familiarize yourself
                              with the application. Below we describe the three
                              types of data files and what can be done within
                              the application  to alter your tree image after
                              they have been uploaded."),
                              tags$br(),
                              tags$h4(strong("Data files to upload")),
                              tags$br(),
                              tags$li(em("1. Phylogenetic Tree"), "- required;
                                      a", a("newick", href =
                                              "https://en.wikipedia.org/wiki/Newick_format"),
                                      "formatted tree"),
                              tags$br(),
                              tags$div(tags$li(em("2. Genetic Distance Data"),
                                               "- optional for use with the
                                               annotation function.",
                                               tags$br(), "A tsv/txt/csv file of
                                      SNP differences. See image below for
                                               example."),
                                       tags$br(),
                                       tags$img(src =
                                                  "www/Slide1.PNG",
                                                height = "100%", width = "100%")
                                       ),
                              tags$br(),
                              tags$div(tags$li(em("3. Meta Data"), "- optional
                              for easy correction of tip labels and addition
                                               of a heatmap;",
                                               tags$br(),
                                               "a tsv/txt/csv file - requires
                                               column headers of Display.labels
                                               and Tip.labels for easy change
                                               of tip labels, while the heatmap
                                               column may be titled whatever you
                                               decide. See image below
                                               for example."),
                                       tags$br(),
                                       tags$img(src = "www/Slide2.PNG",
                                                height = "100%", width = "100%")
                                       ),
                              tags$br(),
                              tags$h4(strong("Ways to alter your tree image")),
                              tags$br(),
                              tags$div(tags$li(tags$em("Once the phylogenetic
                              tree is uploaded you can -")),
                                       "Alter visualization parameters. See
                                       below for a tree with right aligned tip
                                       labels.",
                                       tags$br(),
                                       tags$img(src =
                                                  "www/Slide3.PNG",
                                                height = "100%", width = "100%")
                                       ),
                              tags$br(),
                              tags$div(tags$li(tags$em("Once the genetic
                              distance file is uploaded you can -")), "Add
                              annotation to the visual representation of the
                              tree. If you want to add annotations then
                              highlight the tip labels to their most recent
                                       common ancestor,", tags$a("MRCA", href =
                                                                   "https://evolution.berkeley.edu/evolibrary/article/phylogenetics_02"), "
                                              , and press the 'Add Annotations'
                                              button. Repeat until you are
                                       satisfied.",
                                       tags$br(),
                                       tags$img(src = "www/Slide4.PNG",
                                                height = "100%", width = "100%")
                                       ),
                              tags$br(),
                              tags$div(tags$li(tags$em("If column for heatmap
                                                       included in metadata
                                                       file you can -")), "add
                                       a heatmap with or without annotations",
                                       tags$br(),
                                       tags$img(src =
                                                  "www/Slide5.PNG",
                                                height = "100%", width = "100%")
                                       ),
                              tags$br(),
                              tags$div(tags$li(tags$em("When you are happy
                              with the image, you can download it as a pdf,
                                                       png, or tiff.")),
                                       tags$br(),
                                       tags$img(src = "www/Slide8.PNG",
                                                height = "100%", width = "100%")
                                       ),
                              tags$br()
                    )
    )
    )
  )
}

#' about Server Function
#'
#' @rdname mod_about
mod_about_server <- function(input, output, session) {
  ns <- session$ns
}