From b7c99ceef878e695e2e3250ba766b9e1f4710af5 Mon Sep 17 00:00:00 2001 From: Daniel Claborne Date: Tue, 6 Aug 2024 15:21:28 -0700 Subject: [PATCH 1/5] fix bad column reference for filter bar plot --- Reactive_Variables/filter_revals.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Reactive_Variables/filter_revals.R b/Reactive_Variables/filter_revals.R index 9d45a3a..e48e867 100644 --- a/Reactive_Variables/filter_revals.R +++ b/Reactive_Variables/filter_revals.R @@ -61,8 +61,8 @@ massfilter_ids <- eventReactive(c(input$massfilter, input$min_mass, input$max_ma if (input$massfilter) { req(length(input$max_mass) > 0, length(input$min_mass) > 0) mass_filter(revals$uploaded_data) %>% - dplyr::filter(!!sym(getMassColName(revals$peakData2)) <= input$max_mass, !!sym(getMassColName(revals$peakData2)) >= input$min_mass) %>% - pluck(getMassColName(revals$peakData2)) + dplyr::filter(`ID__` <= input$max_mass, `ID__` >= input$min_mass) %>% + purrr::pluck('ID__') } else NULL }) From 66365b54e2b506c8a4e5b2927b2758850540feaa Mon Sep 17 00:00:00 2001 From: Daniel Claborne Date: Tue, 6 Aug 2024 15:31:15 -0700 Subject: [PATCH 2/5] change tutorial video url --- ui.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ui.R b/ui.R index 5121430..c680485 100644 --- a/ui.R +++ b/ui.R @@ -28,7 +28,7 @@ ui <- tagList(useShinyjs(), hr(), br(), actionButton('all_tutorials', 'See a playlist of video tutorials', - onclick = "window.open('https://www.youtube.com/watch?v=uU5Q7r_pEGM&list=PLvozcBqO8i7wsMWo5PnOREX0sHSk3mAjE', '_blank')", + onclick = "window.open('https://www.youtube.com/watch?v=k5HLE2kNSBY&list=PLS2sDsRQvdiJEWgnkW8s0CU_ZpubK7z_c&index=1', '_blank')", class="btn btn-info", icon = icon('facetime-video', lib = 'glyphicon')) ), tabPanel(title = "Data Requirements", class = "background_FTICR", value = 'data_requirements', From d369b3c26d768fceed25ee089de22f7db804063e Mon Sep 17 00:00:00 2001 From: Daniel Claborne Date: Thu, 8 Aug 2024 11:59:21 -0700 Subject: [PATCH 3/5] bump version --- DESCRIPTION | 2 +- ui.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4a7787e..8d6302a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FREDA Title: An app for the processing and visualization of Fourier-transform mass spectrometry data. -Version: 1.2.0 +Version: 1.2.1 Authors@R: c(person("Lisa", "Bramer", "lisa.bramer@pnnl.gov", role = "aut", "cre"), person("Daniel", "Claborne", "daniel.claborne@pnnl.gov", role = c("aut"))) Description: A frontend application which exposes functionality of the ftmsRanalysis R package. See diff --git a/ui.R b/ui.R index c680485..907d95e 100644 --- a/ui.R +++ b/ui.R @@ -15,7 +15,7 @@ ui <- tagList(useShinyjs(), ), navbarPage( - title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.0")), + title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.1")), windowTitle = 'FREDA', id = "top_page", theme = "yeti.css", From 46125dc83c6cc4d2349537755a0a1fcfe3be77a0 Mon Sep 17 00:00:00 2001 From: Daniel Claborne Date: Wed, 16 Oct 2024 15:17:38 -0700 Subject: [PATCH 4/5] convert NA columns in categorical tables to the string 'NA' to avoid datatables errors --- Observers/preprocess_observers.R | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Observers/preprocess_observers.R b/Observers/preprocess_observers.R index 59a1bb4..4d02d45 100644 --- a/Observers/preprocess_observers.R +++ b/Observers/preprocess_observers.R @@ -206,6 +206,11 @@ observeEvent(input$preprocess_dismiss, { if (length(revals$preprocess_tables$categorical) > 0) { lapply(1:length(revals$preprocess_tables$categorical), function(i) { + na_cols <- which(is.na(colnames(revals$preprocess_tables$categorical[[i]]))) + if (length(na_cols) > 0) { + colnames(revals$preprocess_tables$categorical[[i]])[na_cols] <- 'NA' + } + output[[paste0('Table_', i)]] <- DT::renderDataTable({revals$preprocess_tables$categorical[[i]]}, options = list(scrollX = TRUE, dom = "t")) Sys.sleep(0.5) }) From 35bdbece7baac0b798733737238a098477a36fe2 Mon Sep 17 00:00:00 2001 From: Daniel Claborne Date: Wed, 16 Oct 2024 15:21:48 -0700 Subject: [PATCH 5/5] update ftmsRanalysis d4c2b9a v1.2.2 --- DESCRIPTION | 2 +- renv.lock | 6 +++--- ui.R | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8d6302a..9527e32 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FREDA Title: An app for the processing and visualization of Fourier-transform mass spectrometry data. -Version: 1.2.1 +Version: 1.2.2 Authors@R: c(person("Lisa", "Bramer", "lisa.bramer@pnnl.gov", role = "aut", "cre"), person("Daniel", "Claborne", "daniel.claborne@pnnl.gov", role = c("aut"))) Description: A frontend application which exposes functionality of the ftmsRanalysis R package. See diff --git a/renv.lock b/renv.lock index 5b560e4..0fca4dd 100644 --- a/renv.lock +++ b/renv.lock @@ -503,8 +503,8 @@ "RemoteHost": "api.github.com", "RemoteRepo": "ftmsRanalysis", "RemoteUsername": "EMSL-Computing", - "RemoteRef": "HEAD", - "RemoteSha": "28581f9adae22637fbbf87992138687b7cdeea5f", + "RemoteRef": "master", + "RemoteSha": "d4c2b9a4ffba2c07126e6732efa62792bc114796", "Requirements": [ "R", "RColorBrewer", @@ -525,7 +525,7 @@ "tidyr", "vegan" ], - "Hash": "1081c4c2bfadf864105ed38ac4f1c06f" + "Hash": "87885633ec68f669a1fca2b32293c18a" }, "generics": { "Package": "generics", diff --git a/ui.R b/ui.R index 907d95e..373849c 100644 --- a/ui.R +++ b/ui.R @@ -15,7 +15,7 @@ ui <- tagList(useShinyjs(), ), navbarPage( - title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.1")), + title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.2")), windowTitle = 'FREDA', id = "top_page", theme = "yeti.css",