From 0b74801c6de780e9d92ec5a397450fccf222bfe9 Mon Sep 17 00:00:00 2001 From: Kris Sankaran Date: Mon, 20 Nov 2023 14:24:54 -0600 Subject: [PATCH 1/7] add license --- .Rbuildignore | 1 + DESCRIPTION | 2 +- LICENSE.md | 43 +++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 LICENSE.md diff --git a/.Rbuildignore b/.Rbuildignore index 531e115..a3fc3f0 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -2,3 +2,4 @@ ^docs$ ^pkgdown$ ^\.github$ +^LICENSE\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index e8bdbf3..ce32cf6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Authors@R: person("Kaiyan", "Ma", , "kaiiyenma@gmail.com", 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 diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..139c68e --- /dev/null +++ b/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"). + +Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. 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From 5da0f90267b60873545f8232bd17a90f3b4e6baa Mon Sep 17 00:00:00 2001 From: KaiyanM Date: Mon, 20 Nov 2023 14:25:21 -0600 Subject: [PATCH 2/7] . --- NAMESPACE | 2 +- R/gDashboard.R | 2 +- docs/404.html | 4 +- docs/articles/FAQ.html | 4 +- docs/articles/cheese.html | 4 +- .../figure-html/unnamed-chunk-7-1.png | Bin 139209 -> 145101 bytes docs/articles/data_input.html | 28 ++--- docs/articles/index.html | 4 +- docs/articles/navigate.html | 25 ++-- docs/authors.html | 18 +-- docs/index.html | 21 ++-- docs/pkgdown.yml | 2 +- docs/reference/cheese.html | 4 +- docs/reference/color_palettes__.html | 4 +- docs/reference/convert_range.html | 4 +- docs/reference/extend.color__.html | 4 +- docs/reference/figures/dashboard.png | Bin 650056 -> 799393 bytes docs/reference/figures/screen_recording.gif | Bin 10740706 -> 9528027 bytes docs/reference/gAnnotation.html | 4 +- docs/reference/gClusters-1.png | Bin 62857 -> 63248 bytes docs/reference/gClusters.html | 110 +++++++++--------- docs/reference/gDashboard.html | 4 +- docs/reference/gNetwork-1.png | Bin 81498 -> 76833 bytes docs/reference/gNetwork.html | 20 ++-- docs/reference/gNetwork_view.html | 4 +- docs/reference/index.html | 9 +- docs/reference/make_line_plot.html | 4 +- docs/reference/make_stackbar_plot.html | 4 +- docs/reference/make_the_graph.html | 8 +- docs/reference/make_the_table.html | 4 +- docs/reference/mass_produce_lm__.html | 4 +- docs/reference/match_database.html | 4 +- docs/reference/paste_URL.html | 4 +- docs/reference/pre_process.html | 6 +- .../reference/reshape_for_make_functions.html | 4 +- docs/reference/scale_by_row__.html | 4 +- docs/reference/test_data.html | 4 +- docs/reference/transpose_dataframe__.html | 4 +- docs/search.json | 2 +- vignettes/.Rhistory | 30 +++++ 40 files changed, 198 insertions(+), 169 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index bc036c5..f5a8958 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -66,7 +66,7 @@ importFrom(shiny,HTML) importFrom(shiny,brushOpts) importFrom(shiny,column) importFrom(shiny,fluidRow) -importFrom(shiny,h2) +importFrom(shiny,h3) importFrom(shiny,icon) importFrom(shiny,observe) importFrom(shiny,plotOutput) diff --git a/R/gDashboard.R b/R/gDashboard.R index 576653f..d37172b 100644 --- a/R/gDashboard.R +++ b/R/gDashboard.R @@ -25,7 +25,7 @@ #' * 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 runApp fluidRow icon tags HTML column selectInput sliderInput plotOutput brushOpts h3 #' @importFrom DT renderDataTable datatable dataTableOutput #' @export gDashboard <- function(data, cluster, annotation, networkres, diff --git a/docs/404.html b/docs/404.html index ade2e33..0c174e5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -31,7 +31,7 @@ MolPad - 0.0.0.9000 + 1.0.0