First version of app to display atlas

app.R

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+library(shiny)
+library(dplyr)
+library(magrittr)
+library(DT)
+
+if(!exists("mi_atlas")){
+  mi_atlas <- read.table("mi-atlas.tsv", header = TRUE, sep = "\t",
+                         stringsAsFactors = FALSE, row.names = 1)
+}
+
+# Define UI
+ui <- fluidPage(
+  lang = "en", 
+  title = "mi-atlas",
+  fluidRow(column(width = 12, align = "center",
+                  h1("An interactive and evolving microbial interactions catalog"))),
+  fluidRow(
+    column(
+      imageOutput("logo"),
+      align = "center", alt = "Logo of mi-atlas", width = 1),
+    column(width = 2),
+    column(width = 6,
+           h2("About", align = "center"),
+           p("Here is the list of interactions occuring between microorganisms that are documented",
+             "in the versioned catalog (see website).", "This classification is based on a framework",
+             "suggested by", a(href="https://doi.org/10.1093/femsle/fnz125", 
+                               target = "_blank", rel = "noreferrer noopener",
+                               # open in new tab w/ protection
+                               "(Pacheco and Segrè, 2019)."), align = "left"),
+           p("List of the microbial interactions in the catalog."),
+           helpText("Details on the column names can be found",
+                    a(href="https://github.com/cpauvert/mi-atlas/blob/main/README.md#attributes-of-microbial-interactions", 
+                      target = "_blank", rel = "noreferrer noopener",
+                      # open in new tab w/ protection
+                      "here."))
+    ),
+    column(width = 2),
+    column(align = "center", width = 1,
+      a(href="https://cpauvert.github.io/mi-atlas/framework.html",
+        target = "_blank", rel = "noreferrer noopener",
+        icon("book-open")), br(),
+      a(href="https://cpauvert.github.io/mi-atlas/framework.html",
+        target = "_blank", rel = "noreferrer noopener", "Framework"), br(),
+      a(href="https://cpauvert.github.io/mi-atlas",
+        target = "_blank", rel = "noreferrer noopener", icon("globe")), br(),
+      a(href="https://cpauvert.github.io/mi-atlas",
+        target = "_blank", rel = "noreferrer noopener", "Website"), br(),
+      a(href="https://github.com/cpauvert/mi-atlas/blob/main/CONTRIBUTING.md",
+        target = "_blank", rel = "noreferrer noopener", icon("github")), br(),
+      a(href="https://github.com/cpauvert/mi-atlas/blob/main/CONTRIBUTING.md",
+        target = "_blank", rel = "noreferrer noopener", "Contribute")
+      )
+  ),
+  fluidRow(
+    column(width = 2),
+    column(width = 8, DT::dataTableOutput("table")),
+    column(width = 2)
+  )
+)
+
+# Define server logic
+server <- function(input, output, session) {
+  output$logo <- renderImage({
+    list(src="docs/content/extra/logo.png",
+         # align="left", width="155", height="179",
+         align="left", width="77.5", height="89.5",
+         alt = "Logo of mi-atlas")
+  }, deleteFile = FALSE)
+  preview_atlas <- reactive({
+    mi_atlas %>% select(Interaction_name,
+                        Participant_1, Participant_2, Participant_3)
+  })
+  output$table <- DT::renderDataTable(preview_atlas(),
+                                      extensions = 'Responsive',
+                                      selection = 'single', 
+                                      options = list(
+                                        autoWidth = TRUE
+                                        )
+  )
+  output$wd<-renderText(getwd())
+}
+
+# Run the application 
+shinyApp(ui = ui, server = server)
+