Merge pull request #98 from selkamand/80-add-acknowledgements-+-updat…

…e-license-ahead-of-release 80 add acknowledgements + update license ahead of release
selkamand · Jun 17, 2024 · ea55d07 · ea55d07
2 parents 70d2d29 + bbf24e7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -5,7 +5,7 @@ Version: 0.1.0
 Authors@R:
   person(given = "Sam",
   family = "El-Kamand",
-  role = c("aut", "cre", "cph"),
+  role = c("aut", "cre"),
   email = "[email protected]",
   comment = c(ORCID = "0000-0003-2270-8088"))
 Description: Generate oncoplots from tabular mutational data. 

diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2022
-COPYRIGHT HOLDER: ggoncoplot authors
+YEAR: 2024
+COPYRIGHT HOLDER: Children's Cancer Institute
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022 ggoncoplot authors
+Copyright (c) 2024 Children's Cancer Institute
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.Rmd b/README.Rmd
@@ -98,11 +98,22 @@ gbm_df |>
    col_samples = "Tumor_Sample_Barcode",
    col_mutation_type = "Variant_Classification",
    metadata = gbm_clinical_df,
-   cols_to_plot_metadata = c('gender', 'histological_type', 'prior_glioma', 'tumor_tissue_site'), 
+   cols_to_plot_metadata = c('gender', 'histological_type', 'prior_glioma', 'tumor_tissue_site'),
    draw_tmb_barplot = TRUE, 
    draw_gene_barplot = TRUE, 
    show_all_samples = TRUE,
    interactive = FALSE
   )
 ```
 
+
+## Acknowledgements
+
+We acknowledge the developers and contributors whose packages and efforts were integral to the development of ggoncoplot:
+
+- **David Gohel** for the `ggiraph` package, which enables the interactivity of ggoncoplot.
+- **Thomas Lin Pedersen** for his contributions to the `patchwork` package and the maintenance of `ggplot2`.
+- **Hadley Wickham** and all contributors to the `ggplot2` package, which provides a robust foundation for data visualization in R.
+
+Additionally, we thank **Dr. Marion Mateos** for her insightful feedback during the early stages of ggoncoplot development.
+
diff --git a/README.md b/README.md
@@ -116,7 +116,7 @@ gbm_df |>
    col_samples = "Tumor_Sample_Barcode",
    col_mutation_type = "Variant_Classification",
    metadata = gbm_clinical_df,
-   cols_to_plot_metadata = c('gender', 'histological_type', 'prior_glioma', 'tumor_tissue_site'), 
+   cols_to_plot_metadata = c('gender', 'histological_type', 'prior_glioma', 'tumor_tissue_site'),
    draw_tmb_barplot = TRUE, 
    draw_gene_barplot = TRUE, 
    show_all_samples = TRUE,
@@ -139,3 +139,18 @@ gbm_df |>
 ```
 
 <img src="man/figures/README-unnamed-chunk-4-1.png" width="100%" />
+
+## Acknowledgements
+
+We acknowledge the developers and contributors whose packages and
+efforts were integral to the development of ggoncoplot:
+
+- **David Gohel** for the `ggiraph` package, which enables the
+  interactivity of ggoncoplot.
+- **Thomas Lin Pedersen** for his contributions to the `patchwork`
+  package and the maintenance of `ggplot2`.
+- **Hadley Wickham** and all contributors to the `ggplot2` package,
+  which provides a robust foundation for data visualization in R.
+
+Additionally, we thank **Dr. Marion Mateos** for her insightful feedback
+during the early stages of ggoncoplot development.
diff --git a/vignettes/quick_start.Rmd → vignettes/manual.Rmd b/vignettes/quick_start.Rmd → vignettes/manual.Rmd
@@ -1,8 +1,8 @@
 ---
-title: "Usage"
+title: "Manual"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{quick_start}
+  %\VignetteIndexEntry{manual}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---