Version 1.3.0

ShinyFabio · Mar 17, 2023 · dc8d7a7 · dc8d7a7
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,5 +1,8 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^dev
-^\.github$
+^\.github$
+^deploy$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,102 +1,94 @@
 Package: ADViSELipidomics
 Title: Shinyapp for the acquisition and the analysis of lipidomics data
-Version: 1.2.0
-Authors@R: c(person("Eugenio", "Del Prete", email = "[email protected]",
-                 role = "aut", comment = c(ORCID = "0000-0003-3214-9021")),
-            person("Fabio", "Della Rocca", email = "[email protected]",
-                 role = c("aut","cre"), comment = c(ORCID = "0000-0002-8003-2648")),
-            person("Ana Margarida", "Campos", email = "[email protected]",
-                 role = c("ctb","dtc"), comment = c(ORCID = "0000-0002-8832-7686")),
-            person("Carmela", "Gallo", email = "[email protected]",
-                 role = "dtc", comment = c(ORCID = "0000-0002-1665-2615")),
-            person("Genoveffa", "Nuzzo", email = "[email protected]",
-                 role = c("ctb","dtc"), comment = c(ORCID = "0000-0001-7065-2379")),
-            person("Angelo", "Fontana", email = "[email protected]",
-                 role = c("dtc", "fnd"), comment = c(ORCID = "0000-0002-5453-461X")),
-            person("Claudia", "Angelini", email = "[email protected]",
-                 role = c("ctb","fnd"), comment = c(ORCID = "0000-0001-8350-8464"))
-            )
-Description: ADViSELipidomics is suitable for the acquisition of LipidSearch and LIQUID files, the computation
-             of the recovery percentages, the creation of the feature matrix (lipid species 
-             concentration) and the statistical analysis of the feature matrix.
+Version: 1.3.0
+Authors@R: c(
+    person("Eugenio", "Del Prete", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0003-3214-9021")),
+    person("Fabio", "Della Rocca", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-8003-2648")),
+    person("Ana Margarida", "Campos", , "[email protected]", role = c("ctb", "dtc"),
+           comment = c(ORCID = "0000-0002-8832-7686")),
+    person("Carmela", "Gallo", , "[email protected]", role = "dtc",
+           comment = c(ORCID = "0000-0002-1665-2615")),
+    person("Genoveffa", "Nuzzo", , "[email protected]", role = c("ctb", "dtc"),
+           comment = c(ORCID = "0000-0001-7065-2379")),
+    person("Angelo", "Fontana", , "[email protected]", role = c("dtc", "fnd"),
+           comment = c(ORCID = "0000-0002-5453-461X")),
+    person("Claudia", "Angelini", , "[email protected]", role = c("ctb", "fnd"),
+           comment = c(ORCID = "0000-0001-8350-8464"))
+  )
+Description: ADViSELipidomics is suitable for the acquisition of
+    LipidSearch and LIQUID files, the computation of the recovery
+    percentages, the creation of the feature matrix (lipid species
+    concentration) and the statistical analysis of the feature matrix.
 License: MIT + file LICENSE
+URL: https://github.com/ShinyFabio/ADViSELipidomics
+BugReports: https://github.com/ShinyFabio/ADViSELipidomics/issues
 Depends:
-    shinyBS,
     shiny (>= 1.6.0),
-    shinyWidgets,
-    shinydashboard
+    shinyBS,
+    shinydashboard,
+    shinyWidgets
 Imports: 
-    attempt,
+    bsplus,
+    cicerone,
+    circlize,
+    cluster,
+    ComplexHeatmap,
     config (>= 0.3.1),
-    DT,
-    glue,
-    golem (>= 0.3.1),
-    htmltools,
-    shinyFiles,
-    shinyjs,
-    shinycssloaders,
+    crayon,
     dashboardthemes,
-    SummarizedExperiment,
-    purrr,
-    fs,
-    readr,
-    readxl,
-    dplyr,
-    MASS,
-    reshape2,
-    lubridate,
+    data.table,
     DataEditR,
-    miniUI,
-    bsplus,
-    ggplot2,
-    plotly,
-    BiocManager,
-    VIM,
-    ggfortify,
-    grDevices,
-    RColorBrewer,
+    dendextend,
+    dplyr,
+    DT,
+    factoextra,
+    fgsea,
     fmsb,
-    stringr,
-    imputeMissings,
-    stringi,
     forcats,
-    tidyr,
-    cicerone,
-    statmod,
+    fs,
+    ggfortify,
+    ggplot2,
+    ggpubr,
     ggrepel,
-    ComplexHeatmap,
-    InteractiveComplexHeatmap,
-    circlize,
-    grid,
-    dendextend,
     ggVennDiagram,
-    sva,
-    ggpubr,
-    fgsea,
-    mixOmics,
-    factoextra,
-    cluster,
+    golem (>= 0.3.1),
+    graphics,
+    grDevices,
+    grid,
     gridExtra,
+    InteractiveComplexHeatmap,
+    knitr,
     limma,
+    lubridate,
+    MASS,
     metabolomicsWorkbenchR,
+    miniUI,
+    mixOmics,
     openxlsx,
-    crayon,
-    data.table,
-    knitr,
-    tibble,
+    plotly,
+    purrr,
+    RColorBrewer,
+    readr,
+    reshape2,
+    S4Vectors,
     scales,
-    S4Vectors
-biocViews:
+    shinycssloaders,
+    shinyFiles,
+    shinyjs,
+    statmod,
+    stats,
+    stringr,
     SummarizedExperiment,
-    limma,
     sva,
-    fgsea,
-    mixOmics,
-    metabolomicsWorkbenchR,
-    ComplexHeatmap,
-    InteractiveComplexHeatmap
+    tibble,
+    tidyr,
+    tools,
+    utils,
+    VIM
+biocViews:SummarizedExperiment, limma, sva, fgsea, mixOmics,
+    metabolomicsWorkbenchR, ComplexHeatmap, InteractiveComplexHeatmap
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
-URL: https://github.com/ShinyFabio/ADViSELipidomics
-BugReports: https://github.com/ShinyFabio/ADViSELipidomics/issues
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,7 +2,6 @@
 
 export(caliblist_advise_lipidomics)
 export(calibplot_advise_lipidomics)
-export(comparison_advise_lipidomics)
 export(diffexp_advise_lipidomics)
 export(enrichment_advise_lipidomics)
 export(expdesign_advise_lipidomics)
@@ -20,8 +19,6 @@ import(dplyr)
 import(ggVennDiagram)
 import(ggfortify)
 import(ggplot2, except = last_plot)
-import(ggplot2, except = last_plot)
-
 import(limma)
 import(plotly, except = rename)
 import(scales)
@@ -121,6 +118,7 @@ importFrom(mixOmics,plotVar)
 importFrom(mixOmics,plsda)
 importFrom(mixOmics,splsda)
 importFrom(mixOmics,tune.splsda)
+importFrom(openxlsx,read.xlsx)
 importFrom(openxlsx,write.xlsx)
 importFrom(purrr,flatten)
 importFrom(purrr,map)
@@ -130,7 +128,6 @@ importFrom(readr,parse_number)
 importFrom(readr,read_csv)
 importFrom(readr,read_delim)
 importFrom(readr,write_excel_csv)
-importFrom(readxl,read_xlsx)
 importFrom(reshape2,dcast)
 importFrom(reshape2,melt)
 importFrom(shiny,NS)
@@ -154,7 +151,6 @@ importFrom(stats,kmeans)
 importFrom(stats,lm)
 importFrom(stats,prcomp)
 importFrom(stats,setNames)
-importFrom(stringi,stri_list2matrix)
 importFrom(stringr,str_count)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_replace)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# ADViSELipidomics 1.3.0
+* Graphical improvements
+* ADViSELipidomics now can perform DA with more than two design variables uploading a txt file with the contrasts. For 1 or 2 design variables it is still possible to easily write the contrasts inside the shinyapp as before.
+* Removed two package dependencies (readxl and stringi)
+* Added other tooltips
+* Added a docker version of ADViSELipidomics
+
+
 # ADViSELipidomics 1.2.0
 
 * Added check for the LipidSearch version.