mmollina · Cristianetaniguti · Feb 28, 2025 · Oct 10, 2024 · Feb 28, 2025 · Feb 28, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,83 +1,83 @@
-Package: viewpoly
-Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
-Version: 0.4.1
-Authors@R: c(
-           person(given = "Cristiane",
-                  family = "Taniguti",
-                  role = c("aut", "cre"),
-                  email = "chtaniguti@tamu.edu"),
-           person(given = "Gabriel",
-                  family = "de Siqueira Gesteira",
-                  role = c("aut"),
-                  email = "gdesiqu@ncsu.edu"),
-           person(given = "Jeekin",
-                  family = "Lau",
-                  role = c("aut")),
-           person(given = "Olivia",
-                  family = "Angelin-Bonnet",
-                  role = c("aut")),
-           person(given = "Susan",
-                  family = "Thomson",
-                  role = c("ctb")),
-           person(given = "Guilherme",
-                  family = "da Silva Pereira",
-                  role = c("ctb")),
-           person(given = "David",
-                  family = "Byrne",
-                  role = c("ctb")),
-           person(given = "Zhao-Bang",
-                  family = "Zeng",
-                  role = c("ctb")),   
-           person(given = "Oscar",
-                  family = "Riera-Lizarazu",
-                  role = c("ctb")),
-           person(given = "Marcelo",
-                  family = "Mollinari",
-                  role = c("aut"),
-                  email = "mmollin@ncsu.edu")
-           )
-Maintainer: Cristiane Taniguti <chtaniguti@tamu.edu>
-Description: Provides a graphical user interface to integrate, visualize and explore results 
-            from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid 
-            species. The app is meant for interactive use and allows users to optionally upload different sources 
-            of information, including  gene annotation and alignment files, enabling the exploitation and search for 
-            candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 
-            'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages. 
-License: GPL (>= 3)
-Depends:
-    R (>= 4.0)
-Imports: 
-    shiny (>= 1.6.0),
-    shinyjs,
-    shinythemes,
-    shinyWidgets,
-    shinydashboard,
-    config (>= 0.3.1),
-    golem (>= 0.3.1),
-    JBrowseR,
-    dplyr,
-    tidyr,
-    DT,
-    ggplot2,
-    ggpubr,
-    plotly,
-    vroom,
-    abind,
-    reshape2,
-    markdown,
-    stats,
-    hidecan,
-    purrr
-URL: https://github.com/mmollina/viewpoly
-BugReports: https://github.com/mmollina/viewpoly/issues
-Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.2.3
-Suggests: 
-    testthat (>= 3.0.0),
-    shinytest,
-    rlang,
-    pkgload,
-    vdiffr
-Config/testthat/edition: 3
-Language: en-US
+Package: viewpoly
+Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
+Version: 0.4.2
+Authors@R: c(
+           person(given = "Cristiane",
+                  family = "Taniguti",
+                  role = c("aut", "cre"),
+                  email = "chtaniguti@tamu.edu"),
+           person(given = "Gabriel",
+                  family = "de Siqueira Gesteira",
+                  role = c("aut"),
+                  email = "gdesiqu@ncsu.edu"),
+           person(given = "Jeekin",
+                  family = "Lau",
+                  role = c("aut")),
+           person(given = "Olivia",
+                  family = "Angelin-Bonnet",
+                  role = c("aut")),
+           person(given = "Susan",
+                  family = "Thomson",
+                  role = c("ctb")),
+           person(given = "Guilherme",
+                  family = "da Silva Pereira",
+                  role = c("ctb")),
+           person(given = "David",
+                  family = "Byrne",
+                  role = c("ctb")),
+           person(given = "Zhao-Bang",
+                  family = "Zeng",
+                  role = c("ctb")),   
+           person(given = "Oscar",
+                  family = "Riera-Lizarazu",
+                  role = c("ctb")),
+           person(given = "Marcelo",
+                  family = "Mollinari",
+                  role = c("aut"),
+                  email = "mmollin@ncsu.edu")
+           )
+Maintainer: Cristiane Taniguti <chtaniguti@tamu.edu>
+Description: Provides a graphical user interface to integrate, visualize and explore results 
+            from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid 
+            species. The app is meant for interactive use and allows users to optionally upload different sources 
+            of information, including  gene annotation and alignment files, enabling the exploitation and search for 
+            candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 
+            'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages. 
+License: GPL (>= 3)
+Depends:
+    R (>= 4.0)
+Imports: 
+    shiny (>= 1.6.0),
+    shinyjs,
+    shinythemes,
+    shinyWidgets,
+    shinydashboard,
+    config (>= 0.3.1),
+    golem (>= 0.3.1),
+    JBrowseR,
+    dplyr,
+    tidyr,
+    DT,
+    ggplot2,
+    ggpubr,
+    plotly,
+    vroom,
+    abind,
+    reshape2,
+    markdown,
+    stats,
+    hidecan,
+    purrr
+URL: https://github.com/mmollina/viewpoly
+BugReports: https://github.com/mmollina/viewpoly/issues
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.3.2
+Suggests: 
+    testthat (>= 3.0.0),
+    shinytest,
+    rlang,
+    pkgload,
+    vdiffr
+Config/testthat/edition: 3
+Language: en-US
diff --git a/NEWS.md b/NEWS.md
@@ -1,46 +1,56 @@
-# viewpoly 0.1.0
-
-* Added a `NEWS.md` file to track changes to the package.
-
-# viewpoly 0.1.1
-
-* Bug fixed in VIEWgenome module
-* Add GitHub link in DESCRIPTION
-* Add tutorial video link
-* Update README.md
-
-
-# viewpoly 0.2.0
-
-Main modifications made during JOSS review:
-
-* Fix broken links
-* Fix download of the images with .tiff format
-* Remove warnings and error messages displayed in the console during app execution
-* Improve error messages
-* Improve function documentation
-* Aesthetic improvements
-* App is also available on shinyapps.io: https://cris-taniguti.shinyapps.io/viewpoly/
-* Functional testing added
-* Disable the download buttons when image parameters are not reliable
-* Title of boxes are now also collapsible
-
-# viewpoly 0.3.0
-
-* Support for diaQTL multi-population evaluation
-* User-defined parents names in effects graphics
-* Download of plots with RData format
-* Docker image available
-* Allow to exclude haplotypes from haplotypes probability view in VIEWqtl module
-* Bug fixed to upload genome through genome link
-* Bug fixed to upload viewpoly object
-
-# viewpoly 0.3.1
-
-* Avoid errors if user has not internet connection
-* Inform number and ID of individuals selected by haplotypes
-* README updated to include new vignette for server version (available at brach publishing_data)
-
-# viewpoly 0.3.2
-
-* CRAN version without all testthat tests
+# viewpoly 0.1.0
+
+* Added a `NEWS.md` file to track changes to the package.
+
+# viewpoly 0.1.1
+
+* Bug fixed in VIEWgenome module
+* Add GitHub link in DESCRIPTION
+* Add tutorial video link
+* Update README.md
+
+
+# viewpoly 0.2.0
+
+Main modifications made during JOSS review:
+
+* Fix broken links
+* Fix download of the images with .tiff format
+* Remove warnings and error messages displayed in the console during app execution
+* Improve error messages
+* Improve function documentation
+* Aesthetic improvements
+* App is also available on shinyapps.io: https://cris-taniguti.shinyapps.io/viewpoly/
+* Functional testing added
+* Disable the download buttons when image parameters are not reliable
+* Title of boxes are now also collapsible
+
+# viewpoly 0.3.0
+
+* Support for diaQTL multi-population evaluation
+* User-defined parents names in effects graphics
+* Download of plots with RData format
+* Docker image available
+* Allow to exclude haplotypes from haplotypes probability view in VIEWqtl module
+* Bug fixed to upload genome through genome link
+* Bug fixed to upload viewpoly object
+
+# viewpoly 0.3.1
+
+* Avoid errors if user has not internet connection
+* Inform number and ID of individuals selected by haplotypes
+* README updated to include new vignette for server version (available at brach publishing_data)
+
+# viewpoly 0.3.2
+
+* CRAN version without all testthat tests
+
+# viewpoly 0.4.0
+
+* All testthat back
+* Add HIDECAN module
+
+# viewpoly 0.4.2
+
+* HIDECAN module now supports multiple GWASpoly output files
+* Support for diploid QTL results in the QTL module