From 6a520151634cc09228482babffd40d080fe644c8 Mon Sep 17 00:00:00 2001
From: ssnn-airr <20683719+ssnn-airr@users.noreply.github.com>
Date: Mon, 13 May 2024 12:55:45 +0200
Subject: [PATCH] placeholder help and about

---
 inst/shiny-app/about.md        |  1 +
 inst/shiny-app/help.md         | 25 +++++++++++++++++++++++++
 inst/shiny-app/ui.R            | 14 ++++++++++++--
 inst/shiny-app/www/repcred.css |  2 +-
 4 files changed, 39 insertions(+), 3 deletions(-)
 create mode 100644 inst/shiny-app/about.md
 create mode 100644 inst/shiny-app/help.md

diff --git a/inst/shiny-app/about.md b/inst/shiny-app/about.md
new file mode 100644
index 0000000..c5fd7a3
--- /dev/null
+++ b/inst/shiny-app/about.md
@@ -0,0 +1 @@
+[Software Working Group](https://www.antibodysociety.org/the-airr-community/airr-working-groups/software/)
\ No newline at end of file
diff --git a/inst/shiny-app/help.md b/inst/shiny-app/help.md
new file mode 100644
index 0000000..d55da0a
--- /dev/null
+++ b/inst/shiny-app/help.md
@@ -0,0 +1,25 @@
+Good analysis requires good data, but how can how can a high-quality 
+AIRR dataset be distinguished from a low-quality one? Rep-Cred fills this need 
+by identifying and reporting several key metrics that can be 
+indicators of potential problems. Modeled after fastqc, Rep-Cred provides an
+easily digestible summary that can be used by novices and experts alike.
+
+The only requirement to run Rep-Cred is a file describing IG and/or TCR 
+rearrangements in the [AIRR TSV format](https://docs.airr-community.org/en/stable/datarep/rearrangements.html). 
+By default, all repertoires are randomly down-sampled to XXX rearrangements; 
+we find that this still provides an accurate assessment of repertoire 
+credibility while maintaining a reasonable run time. Finally, if a custom 
+(non-IMGT?) database was used to annotate the rearrangements, this should be 
+provided to Rep-Cred as well, so that SHM and related statistics can be 
+calculated accurately.
+
+[Example repertoire](https://raw.githubusercontent.com/airr-community/rep-cred/master/inst/extdata/ExampleDb.tsv)
+
+To get help or report a bug, please file an issue on Rep-Cred’s github 
+page at [https://github.com/airr-community/rep-cred/issues](https://github.com/airr-community/rep-cred/issues). 
+Although Rep-Cred will not be under active development once the initial release is complete, the program is designed to be modular and accept new functions/metrics with ease. We welcome pull requests 
+(please see [https://github.com/airr-community/airr-standards/blob/master/CONTRIBUTING.rst](https://github.com/airr-community/airr-standards/blob/master/CONTRIBUTING.rst)); 
+all other feature requests will be evaluated and prioritized with respect to our 
+availability to work on adding them.
+
+
diff --git a/inst/shiny-app/ui.R b/inst/shiny-app/ui.R
index a47285d..dad6ee2 100755
--- a/inst/shiny-app/ui.R
+++ b/inst/shiny-app/ui.R
@@ -18,12 +18,14 @@ ui <- fluidPage(
     # App title
     fluidRow(
         id="div-main",
+        style = "width:80%; min-width:500px; height:250px",
         tags$img(src = "logo.svg", width = "100px"),
         tags$h1("Rep-Cred"),
         tags$strong("Credibility of a repertoire"),
         tags$p("Summary statistics and graphical information to quickly asses the quality of a repertoire."),
         tabsetPanel(
             tabPanel("Rep-Cred",
+                     style = "width:100%",
                      br(),
                      # Input
                      fileInput("file1", 
@@ -60,8 +62,16 @@ ui <- fluidPage(
                      uiOutput("openResultsBtn")                     
                      
             ),
-            tabPanel("Help"),
-            tabPanel("About")
+            tabPanel("Help",
+                     style = "width:100%",
+                     br(),
+                     includeMarkdown("help.md")
+                     ),
+            tabPanel("About",
+                     style = "width:100%",
+                     br(),
+                     includeMarkdown("about.md")
+                     )
         )
     )
 )
diff --git a/inst/shiny-app/www/repcred.css b/inst/shiny-app/www/repcred.css
index b106eee..da95697 100644
--- a/inst/shiny-app/www/repcred.css
+++ b/inst/shiny-app/www/repcred.css
@@ -2,7 +2,7 @@
     margin: 0;
     // position: fixed;
     position: absolute;
-    top: calc(50%);
+    top: calc(20%);
     left: calc(50%);
     -ms-transform: translate(-50%, -50%);
     transform: translate(-50%, -50%);