diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 65a51f9..ed58530 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -52,9 +52,9 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: 'devel', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } - - { os: macOS-latest, r: 'devel', bioc: '3.20'} - - { os: windows-latest, r: 'devel', bioc: '3.20'} + - { os: ubuntu-latest, r: 'devel', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } + - { os: macOS-latest, r: 'devel', bioc: '3.21'} + - { os: windows-latest, r: 'devel', bioc: '3.21'} ## Check https://github.com/r-lib/actions/tree/master/examples ## for examples using the http-user-agent env: @@ -191,7 +191,7 @@ jobs: gha_repos <- if( .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin" ) c( - "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.20/bioc", + "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.21/bioc", BiocManager::repositories() ) else BiocManager::repositories() diff --git a/NAMESPACE b/NAMESPACE index e254d09..b99f390 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,10 +3,12 @@ export(SampleIdentificationCenter) exportClasses(SampleIdentificationCenter) exportMethods(.createObservers) +exportMethods(.defineDataInterface) exportMethods(.defineOutput) exportMethods(.definePanelTour) exportMethods(.fullName) exportMethods(.generateOutput) +exportMethods(.multiSelectionResponsive) exportMethods(.panelColor) exportMethods(.renderOutput) exportMethods(initialize) @@ -19,10 +21,13 @@ importClassesFrom(iSEE,Panel) importFrom(iSEE,.emptyDefault) importFrom(methods,callNextMethod) importFrom(methods,new) +importFrom(shiny,HTML) importFrom(shiny,nearPoints) importFrom(shiny,renderPlot) importFrom(shiny,renderUI) +importFrom(shiny,span) importFrom(shiny,tagList) +importFrom(shiny,textInput) importFrom(shiny,uiOutput) importFrom(shiny,wellPanel) importFrom(shinyAce,aceEditor) diff --git a/R/panel_SampleIdentificationCenter.R b/R/panel_SampleIdentificationCenter.R index bcac779..f64b3e2 100644 --- a/R/panel_SampleIdentificationCenter.R +++ b/R/panel_SampleIdentificationCenter.R @@ -119,7 +119,7 @@ setMethod("initialize", "SampleIdentificationCenter", function(.Object, ...) { # TODO - placeholder #' @export -#' @importFrom shiny tagList +#' @importFrom shiny tagList textInput span HTML setMethod(".defineDataInterface", "SampleIdentificationCenter", function(x) { panel_name <- .getEncodedName(x) @@ -246,11 +246,8 @@ setMethod(".renderOutput", "SampleIdentificationCenter", function(x, se, output, # Transmission ----------------------------------------------------------------- #' @export -setMethods(".multiSelectionResponsive", "SampleIdentificationCenter", function(x, dims = character(0)){ - if ("column" %in% dims) { - return(TRUE) - } - return(FALSE) +setMethod(".multiSelectionResponsive", "SampleIdentificationCenter", function(x, dim = character(0)) { + dim == "column" }) # Tour definition -------------------------------------------------------------- diff --git a/man/SampleIdentificationCenter-class.Rd b/man/SampleIdentificationCenter-class.Rd index 220a88c..785d031 100644 --- a/man/SampleIdentificationCenter-class.Rd +++ b/man/SampleIdentificationCenter-class.Rd @@ -43,11 +43,11 @@ library(iSEE) library(scRNAseq) # Example data ---- -sce <- ReprocessedAllenData(assays="tophat_counts") +sce <- ReprocessedAllenData(assays = "tophat_counts") class(sce) library(scater) -sce <- logNormCounts(sce, exprs_values="tophat_counts") +sce <- logNormCounts(sce, exprs_values = "tophat_counts") sce <- runPCA(sce, ncomponents=4) sce <- runTSNE(sce) @@ -57,7 +57,7 @@ rowData(sce)$n_cells <- rowSums(assay(sce, "tophat_counts") > 0) # launch the app itself ---- if (interactive()) { - iSEE(sce, initial=list( + iSEE(sce, initial = list( ReducedDimensionPlot(), SampleIdentificationCenter( ColumnSelectionSource = "ReducedDimensionPlot1"