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modified imports in igsva()

pablo-rodr-bio2 authored on 19/04/2021 11:20:20
Showing3 changed files

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@@ -10,7 +10,7 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges,
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          Biobase, SummarizedExperiment, GSEABase, Matrix, parallel,
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          BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray,
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          DelayedMatrixStats, HDF5Array, BiocSingular
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-Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer,
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+Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,
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           genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table,
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           plotly, shinyjs, future, promises, shinybusy, org.Hs.eg.db
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 Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.
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@@ -8,40 +8,41 @@ igsva <- function() {
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     stop(sprintf("Please install the following packages to use the GSVA WebApp:\n\n  %s\n",
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                  paste(shinydeps[!maskshinydeps], collapse=", ")))
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("shiny"))
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-
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("shinythemes"),
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-                      vars="shinytheme")
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-
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("ggplot2"),
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-                      vars="ggplot")
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-
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("data.table"))
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-
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("plotly"),
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-                      vars=c("ggplotly", "event_data", "style"))
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-
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("future"))
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-
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("shinyjs"))
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-
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("shinybusy"))
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-
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-  namespaceImportFrom(self=getNamespace("base"),
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-                      ns=getNamespace("limma"))
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("shiny"))
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+  # 
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("shinythemes"),
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+  #                     vars="shinytheme")
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+  # 
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("ggplot2"),
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+  #                     vars="ggplot")
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+  # 
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("data.table"))
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+  # 
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("plotly"),
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+  #                     vars=c("ggplotly", "event_data", "style"))
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+  # 
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("future"))
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+  # 
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("shinyjs"))
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+  # 
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("shinybusy"))
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+  # 
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+  # namespaceImportFrom(self=getNamespace("base"),
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+  #                     ns=getNamespace("limma"))
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   appDir <- system.file("shinyApp", package="GSVA")
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   if (appDir == "")
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     stop("The GSVA Shiny app cannot be found within the package.")
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-  runWebApp <- get("runApp", mode="function")
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-  runWebApp(appDir)
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+  # runWebApp <- get("runApp", mode="function")
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+  # runWebApp(appDir)
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+  shiny::runApp(appDir)
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 }
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@@ -41,6 +41,8 @@ function(input, output, session) {
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     rv$gs <- NULL
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     rv$dat.t <- NULL
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     rv$p <- NULL
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+    rv$p2 <- NULL
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+    rv$p3 <- NULL
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     rv$errors.gsva = NULL
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     rv$matrix <- isolate(matrix())
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     rv$genesets <- isolate(genesets())