Merge branch 'main' into paper

.Rbuildignore

@@ -2,3 +2,4 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^LICENSE\.md$

DESCRIPTION

@@ -5,10 +5,25 @@ Authors@R:
     person("Kaiyan", "Ma", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7355-8924"))
 Description: MolPad offers a visualization dashboard tool designed to enhance our understanding of how molecular co-expression works in the context of multi-omics microbiome data. The approach involves using a cluster network to provide an initial overview of relationships across multiple omics, with the added functionality to interactively zoom in on specific areas of interest. To facilitate this analysis, we've developed a focus-plus-context strategy that seamlessly connects to online curated annotations.
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a license
+License: CC0
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+Imports:
+    DT,
+    dplyr,
+    ggplot2,
+    ggraph,
+    grid,
+    igraph,
+    purrr,
+    randomForest,
+    rlang,
+    shiny,
+    shinydashboard,
+    stringr,
+    tibble,
+    tidyr,
 Suggests: 
     knitr,
     rmarkdown,

LICENSE.md

@@ -0,0 +1,43 @@
+## creative commons
+
+# CC0 1.0 Universal
+
+CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER.
+
+### Statement of Purpose
+
+The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work").
+
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+
+For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights.
+
+1. __Copyright and Related Rights.__ A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following:
+
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+
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+
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+
+    vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof.
+
+2. __Waiver.__ To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose.
+
+3. __Public License Fallback.__ Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose.
+
+4. __Limitations and Disclaimers.__
+
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+    b. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law.
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+
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NAMESPACE

@@ -63,15 +63,16 @@ importFrom(randomForest,importance)
 importFrom(randomForest,randomForest)
 importFrom(rlang,enquo)
 importFrom(shiny,HTML)
+importFrom(shiny,br)
 importFrom(shiny,brushOpts)
 importFrom(shiny,column)
 importFrom(shiny,fluidRow)
-importFrom(shiny,h2)
+importFrom(shiny,h3)
 importFrom(shiny,icon)
 importFrom(shiny,observe)
 importFrom(shiny,plotOutput)
-importFrom(shiny,runApp)
 importFrom(shiny,selectInput)
+importFrom(shiny,shinyApp)
 importFrom(shiny,sliderInput)
 importFrom(shiny,tags)
 importFrom(shinydashboard,box)

R/gDashboard.R

@@ -23,15 +23,15 @@
 #' Please ensure that columns containing external database IDs adhere to the following standards:
 #' * KEGG ID: Begin with 'K' followed by 5 digits, for example, K05685 or K06671.
 #' * GO ID: Begin with 'GO:' followed by 7 digits, such as GO:0003674."
-#' 
+#'
 #' @importFrom shinydashboard dashboardPage dashboardHeader dashboardSidebar sidebarMenu menuItem tabItems tabItem box
-#' @importFrom shiny observe runApp fluidRow icon tags HTML column selectInput sliderInput plotOutput brushOpts h2
+#' @importFrom shiny observe shinyApp fluidRow icon tags HTML column selectInput sliderInput plotOutput brushOpts h3 br
 #' @importFrom DT renderDataTable datatable dataTableOutput
 #' @export
 gDashboard <- function(data, cluster, annotation, networkres,
-                       dashboardtitle = "MolPad Dashboard", 
+                       dashboardtitle = "MolPad Dashboard",
                        id_colname=NULL, id_type=NULL) {
-  
+
   reshaped_df <- reshape_for_make_functions(data, cluster, annotation,id_colname, id_type)
 
   uni_t <- unique(annotation$taxonomic.scope)
@@ -190,5 +190,5 @@ gDashboard <- function(data, cluster, annotation, networkres,
         })
       }
   )
-  runApp(app)
+  do.call(shinyApp, app)
 }

README.md

@@ -5,7 +5,7 @@ An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomi
 
 MolPad offers a visualization dashboard tool designed to enhance our understanding of how molecular co-expression works in the context of microbiome data. The approach involves using a cluster network to provide an initial overview of relationships across multiple omics, with the added functionality to interactively zoom in on specific areas of interest. To facilitate this analysis, we've developed a focus-plus-context strategy that connects to online curated annotations.
 
-Additionally, our package simplifies the entire pipeline for creating the dashboard. This user-friendly design makes it accessible even to students with limited R programming experience.
+Additionally, our package simplifies the entire pipeline for creating the dashboard. This user-friendly design makes it accessible even to people with limited R programming experience. Check out our cheese-data demo [here](https://connect.doit.wisc.edu/molpad-demo/).
 
 <p align="center">
   <img src="/man/figures/screen_recording.gif" width="600" /></a>  
@@ -48,3 +48,4 @@ Remember that it's particularly effective when you can provide a reproducible ex
 ## Contribution
 To contribute to this project, you could use the following workflow: fork the repository --> create your local copy --> submit a pull request.
 
+