From b94e35dd1ce851151cadc3aeed6cea63aca27b0a Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 25 Apr 2018 08:32:42 +0200 Subject: [PATCH 1/5] geneView: do not enable plot until ALL mandatory fields are valid --- R/geneView.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/geneView.R b/R/geneView.R index 55f64c0..6061fdc 100644 --- a/R/geneView.R +++ b/R/geneView.R @@ -306,7 +306,7 @@ geneView <- function(input, output, session, data, metadata, level = NULL, plot. #enable plot button only if plot possible shiny::observe({ - if(is.null(input$genes) | length(selector$selectedColumns()) < 1){ + if(is.null(input$genes) || !shiny::isTruthy(selector$selectedColumns())){ shinyjs::disable("plot") }else if(input$plotType == "violin"){ factor1.levels <- metadata.r()[level == selector$type() & key %in% selector$selectedColumns() & factor1 != ""][, .N, keyby = factor1][["N"]] From 7e5c63c0de286b9198513ba140660a55b66b543f Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 25 Apr 2018 10:49:13 +0200 Subject: [PATCH 2/5] pca: fixed label & sub_label in types parameter --- R/pca.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/pca.R b/R/pca.R index 249af4f..ae49990 100644 --- a/R/pca.R +++ b/R/pca.R @@ -162,11 +162,11 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel = shinyjs::reset("dimB") shinyjs::reset("pointsize") shinyjs::reset("labelsize") - columnSelect <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(types.r()[level %in% levels.r(), c("key", "level"), with = FALSE]), columnTypeLabel = "Column types to choose from") + columnSelect <<- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(types.r()[level %in% levels.r()]), columnTypeLabel = "Column types to choose from") clearPlot(TRUE) }) - columnSelect <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(types.r()[level %in% levels.r(), c("key", "level"), with = FALSE]), columnTypeLabel = "Column types to choose from") + columnSelect <- shiny::callModule(columnSelector, "select", type.columns = shiny::reactive(types.r()[level %in% levels.r()]), columnTypeLabel = "Column types to choose from") output$datalevel <- shiny::renderUI({ shiny::selectInput(session$ns("select"), label = "select data level", choices = unique(levels.r())) From bad82bbed039ed06ac3dfc3c7f6a00fdced5d876 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 25 Apr 2018 14:20:00 +0200 Subject: [PATCH 3/5] pca: fixed wrong variable name --- R/pca.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/pca.R b/R/pca.R index ae49990..8d4d166 100644 --- a/R/pca.R +++ b/R/pca.R @@ -111,7 +111,7 @@ pca <- function(input, output, session, data, types, levels = NULL, entryLabel = }) levels.r <- shiny::reactive({ if(is.null(levels)){ - metadata.r()[["level"]] + types.r()[["level"]] }else{ if(shiny::is.reactive(levels)){ levels() From 0f0bd8249dfab59b43fc3dc3965f7cbdde07eb4d Mon Sep 17 00:00:00 2001 From: Carsten Kuenne Date: Thu, 24 May 2018 15:09:16 +0200 Subject: [PATCH 4/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index cc7941f..37ce5e6 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ CLARION: generiC fiLe formAt foR quantItative cOmparsions of high throughput scr CLARION is a data format especially developed to be used with WIlsON, which relies on a tab-delimited table with a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes) with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq, ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible without having to modify the code of WIlsON for each specific experiment. -Please check the following link for details considering the [CLARION format](https://github.molgen.mpg.de/loosolab/wilson-apps/blob/master/wilson-basic/introduction/format.md). +Please check the following link for details considering the [CLARION format](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format). ## How to cite *Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M, Looso M*. WIlsON: Webbased Interactive Omics VisualizatioN. (2018), doi: https://XY From 4c0dd37b0921a7cd7a7da967172b23d9e9006c34 Mon Sep 17 00:00:00 2001 From: Carsten Kuenne Date: Mon, 28 May 2018 11:19:03 +0200 Subject: [PATCH 5/5] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 37ce5e6..d17ed20 100644 --- a/README.md +++ b/README.md @@ -13,9 +13,11 @@ The WIlsON R package includes a toolbox of R Shiny modules that can be used to c ## Availability All components of the WIlsON R package have been implemented in an integrated web application that is available for download from the Github repository [wilson-apps](https://github.molgen.mpg.de/loosolab/wilson-apps) and can be tested on our [official demonstration server](http://loosolab.mpi-bn.mpg.de/apps/wilson/). +Usage instructions can be found in the extensive [documentation](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki). + Get a Docker container [here](https://hub.docker.com/r/loosolab/wilson/). -Please make sure to check our other projects at http://loosolab.mpi-bn.mpg.de/. +Please make sure to check our other projects at [loosolab](http://loosolab.mpi-bn.mpg.de/). ## Organization and Philosophy Visualizations are organized hierarchically as Shiny modules, such that larger visualizations are built from small, general, and reusable components.