Rename to geposanui and update README

DESCRIPTION

@@ -1,15 +1,17 @@
-Package: tpeold
+Package: geposanui
-Title: Interface for Finding TPE-OLD Candidates
+Title: Graphical user interface for geposan
 Version: 0.0.0.9000
 Authors@R:
     person(
         "Elias",
         "Projahn",
         email = "elias@johrpan.de",
-        role = c("aut", "cre")
+        role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0002-4153-4071")
     )
-Description: This package provides a Shiny interface for analyzing genes and
+Description: This package provides a graphical user interface for analyzing
-    finding TPE-OLD candidates based on known TPE-OLD genes.
+    genes based on position data across species. It is a frontend for the
+    R package "geposan".
 License: AGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

R/preset_editor.R

@@ -51,16 +51,17 @@ preset_editor_ui <- function(id, options) {
             )
         },
         if (options$locked) {
-            HTML(
+            HTML(paste0(
                 "This instance prohibits performing custom analyses ",
                 "to reduce resource usage. Normally, it is possible ",
                 "to use this web application for analyzing any set of ",
                 "reference genes to find patterns in their ",
                 "chromosomal positions. If you would like to apply ",
                 "this method for your own research, see ",
-                "<a href=\"https://code.johrpan.de/johrpan/tpeold\"",
+                "<a href=\"https://code.johrpan.de/johrpan/geposanui/src/",
-                "target=\"_blank\">this page</a> for more information."
+                "branch/main/README.md\" target=\"_blank\">this page</a> for ",
-            )
+                "more information."
+            ))
         }
     )
 }

README.md

@@ -1,21 +1,56 @@
-# tpeold
+# geposanui
 
-Tpeold provides a Shiny interface for analyzing genes and finding TPE-OLD
+This package provides a graphical user interface for analyzing genes based on
-candidates based on known TPE-OLD genes.
+position data across species. It is a frontend for the R package
+[`geposan`](https://code.johrpan.de/johrpan/geposan). You can visit an example
+instance of the application [here](https://tpe-old.uni-rostock.de) where the
+method is used to find new
+[TPE-OLD](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233240/) candidate
+genes based on the currently known ones.
 
 ## Installation
 
-You can install the development version of tpeold using:
+You can install the development version of `geposanui` using:
 
 ```r
 # install.packages("remotes")
 remotes::install_github("dreamRs/shinyvs")
-remotes::install_git("https://code.johrpan.de/johrpan/tpeold.git")
+remotes::install_git("https://code.johrpan.de/johrpan/geposanui.git")
 ```
 
 See [this page](https://remotes.r-lib.org/reference/install_git.html) for more
 information on this command.
 
+## Usage
+
+The main entry point is the `run_app()` function that is provided by the
+package. It will setup the initial analysis and provide the interactive user
+interface. You have to provide at least one gene set for the application to
+work. The following minimal example shows how to do that:
+
+```r
+# Ten random genes from Ensembl.
+my_interesting_genes <- c(
+    "ENSG00000142347",
+    "ENSG00000186174",
+    "ENSG00000143553",
+    "ENSG00000240972",
+    "ENSG00000105357",
+    "ENSG00000159251",
+    "ENSG00000258643",
+    "ENSG00000147873",
+    "ENSG00000158270",
+    "ENSG00000197616"
+)
+
+# Choose a name for your gene set.
+geposanui::run_app(list("Interesting genes" = my_interesting_genes))
+```
+
+This will run the application which you can reach using your favorite browser.
+For more information on the options provided by the function, take a look at the
+built-in documentation (`?geposanui::run_app`).
+
 ## License
 
 This program is free software: you can redistribute it and/or modify it under