Dev

.gitignore

@@ -2,6 +2,8 @@
 # History files
 .Rhistory
 .Rapp.history
+.result_for_antismash.json
+.data_all.csv
 
 # Session Data files
 .RData

DESCRIPTION

@@ -1,10 +1,15 @@
 Package: BGCViz
 Title: BGCViz
-Version: 0.0.0.9000
-Authors@R: person('Pavlo', 'Hrab', email = 'pavlo.hrab@gmail.com', role = c('cre', 'aut'))
-Description: BGCViz is a shiny package, that aims to integrate BGC result from different softwares for same genome sequence.
+Version: 0.99.0
+Authors@R: person('Lev', 'Tsarin', email = 'Tsarinlev@gmail.com', role = c('cre', 'aut'))
+Description: BGCViz is a shiny package, that aims to integrate BGC result 
+    from different softwares for same genome sequence. On top of additional 
+    filtering of GECCO and DeepBGC data and choosing optimal thresholds for them,
+    package allows to form groups of semi-identical BGCs, allowing better 
+    annotation and boundary resolution of each one. The output of BGCViz can 
+    serve as input to clinker software.
 License: MIT + file LICENSE
-biocViews: 
+biocViews: Visualization, MultipleComparison, FunctionalGenomics, ShinyApps
 Imports: 
     BioCircos,
     config (>= 0.3.1),
@@ -28,10 +33,10 @@ Imports:
     sortable,
     stringi,
     stringr,
-    tidyr
+    tidyr,
+    ggtree
 Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 URL: https://github.com/ostash-group/BGCViz
 BugReports: https://github.com/ostash-group/BGCViz/issues
 Suggests: 
@@ -45,4 +50,5 @@ Config/testthat/edition: 3
 Language: en-US
 VignetteBuilder: knitr
 Depends: 
-    R (>= 2.10)
+    R (>= 4.2.0)
+LazyData: true

NAMESPACE

@@ -3,6 +3,7 @@
 export(antismash_to_csv)
 export(arts_to_csv)
 export(get_defaults)
+export(get_dissect_example)
 export(prism_to_csv)
 export(run_app)
 export(sempi_to_csv)

NEWS

@@ -0,0 +1,2 @@
+Changes in version 0.99.0 (2022-06-06)
++ Submitted to Bioconductor

R/app_config.R

@@ -2,15 +2,15 @@
 #'
 #' NOTE: If you manually change your package name in the DESCRIPTION,
 #' don't forget to change it here too, and in the config file.
-#' For a safer name change mechanism, use the `golem::set_golem_name()` 
+#' For a safer name change mechanism, use the `golem::set_golem_name()`
 #' function.
 #'
 #' @param ... character vectors, specifying subdirectory and file(s)
 #' within your package. The default, none, returns the root of the app.
 #'
 #' @noRd
 app_sys <- function(...) {
-  system.file(..., package = "BGCViz")
+    system.file(..., package = "BGCViz")
 }
 
 
@@ -24,18 +24,18 @@ app_sys <- function(...) {
 #' @noRd
 get_golem_config <- function(value,
                              config = Sys.getenv(
-                               "GOLEM_CONFIG_ACTIVE",
-                               Sys.getenv(
-                                 "R_CONFIG_ACTIVE",
-                                 "default"
-                               )
+                                 "GOLEM_CONFIG_ACTIVE",
+                                 Sys.getenv(
+                                     "R_CONFIG_ACTIVE",
+                                     "default"
+                                 )
                              ),
                              use_parent = TRUE) {
-  config::get(
-    value = value,
-    config = config,
-    # Modify this if your config file is somewhere else:
-    file = app_sys("golem-config.yml"),
-    use_parent = use_parent
-  )
+    config::get(
+        value = value,
+        config = config,
+        # Modify this if your config file is somewhere else:
+        file = app_sys("golem-config.yml"),
+        use_parent = use_parent
+    )
 }