From 1b8609ed12863c4213a33ca3344fd06b613de4c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Tue, 8 Jul 2025 15:02:38 +0200 Subject: [PATCH 1/5] Rename to match convention --- R/{quality.R => tm_g_quality.R} | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) rename R/{quality.R => tm_g_quality.R} (97%) diff --git a/R/quality.R b/R/tm_g_quality.R similarity index 97% rename from R/quality.R rename to R/tm_g_quality.R index 1bda4ff9..f8ab162d 100644 --- a/R/quality.R +++ b/R/tm_g_quality.R @@ -65,6 +65,7 @@ heatmap_plot <- function(object, assay_name) { #' @return Shiny module to be used in the teal app. #' #' @export +#' @inheritSection teal::example_module Reporting #' #' @examples #' data <- teal_data(MAE = hermes::multi_assay_experiment) @@ -124,9 +125,6 @@ ui_g_quality <- function(id, ns <- NS(id) teal.widgets::standard_layout( encoding = tags$div( - ### Reporter - teal.reporter::simple_reporter_ui(ns("simple_reporter")), - ### tags$label("Encodings", class = "text-primary"), helpText("Analysis of MAE:", tags$code(mae_name)), uiOutput(ns("experiment_ui")), @@ -201,13 +199,9 @@ ui_g_quality <- function(id, #' @export srv_g_quality <- function(id, data, - filter_panel_api, - reporter, mae_name, exclude_assays, .test = FALSE) { - with_reporter <- !missing(reporter) && inherits(reporter, "Reporter") - assert_class(filter_panel_api, "FilterPanelAPI") checkmate::assert_class(data, "reactive") checkmate::assert_class(shiny::isolate(data()), "teal_data") @@ -374,6 +368,11 @@ srv_g_quality <- function(id, output$table <- renderPrint(table()) } + joined_qenvs <- reactive({ + req(plot_r(), table()) + c(plot_r(), table()) + }) + ### REPORTER if (with_reporter) { card_fun <- function(comment, label) { @@ -429,6 +428,7 @@ srv_g_quality <- function(id, teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun) } ### + joined_qenvs }) } From 51616eb841a7d5ef490f32f9c4ddfc9be5af156c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Tue, 8 Jul 2025 15:06:58 +0200 Subject: [PATCH 2/5] Undo some changes for the report --- R/tm_g_quality.R | 7 ------- 1 file changed, 7 deletions(-) diff --git a/R/tm_g_quality.R b/R/tm_g_quality.R index f8ab162d..2ea76d63 100644 --- a/R/tm_g_quality.R +++ b/R/tm_g_quality.R @@ -65,7 +65,6 @@ heatmap_plot <- function(object, assay_name) { #' @return Shiny module to be used in the teal app. #' #' @export -#' @inheritSection teal::example_module Reporting #' #' @examples #' data <- teal_data(MAE = hermes::multi_assay_experiment) @@ -368,11 +367,6 @@ srv_g_quality <- function(id, output$table <- renderPrint(table()) } - joined_qenvs <- reactive({ - req(plot_r(), table()) - c(plot_r(), table()) - }) - ### REPORTER if (with_reporter) { card_fun <- function(comment, label) { @@ -428,7 +422,6 @@ srv_g_quality <- function(id, teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun) } ### - joined_qenvs }) } From bd38d1e3ca3d14fe4c2c7d1ed0d6e8ded7177641 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Tue, 8 Jul 2025 15:08:41 +0200 Subject: [PATCH 3/5] Add back some removed code --- R/tm_g_quality.R | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/R/tm_g_quality.R b/R/tm_g_quality.R index 2ea76d63..1bda4ff9 100644 --- a/R/tm_g_quality.R +++ b/R/tm_g_quality.R @@ -124,6 +124,9 @@ ui_g_quality <- function(id, ns <- NS(id) teal.widgets::standard_layout( encoding = tags$div( + ### Reporter + teal.reporter::simple_reporter_ui(ns("simple_reporter")), + ### tags$label("Encodings", class = "text-primary"), helpText("Analysis of MAE:", tags$code(mae_name)), uiOutput(ns("experiment_ui")), @@ -198,9 +201,13 @@ ui_g_quality <- function(id, #' @export srv_g_quality <- function(id, data, + filter_panel_api, + reporter, mae_name, exclude_assays, .test = FALSE) { + with_reporter <- !missing(reporter) && inherits(reporter, "Reporter") + assert_class(filter_panel_api, "FilterPanelAPI") checkmate::assert_class(data, "reactive") checkmate::assert_class(shiny::isolate(data()), "teal_data") From 13b8b9a07a833cd4bea3b5dd8d6e75d0bb1d63eb Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 8 Jul 2025 13:30:17 +0000 Subject: [PATCH 4/5] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/heatmap_plot.Rd | 2 +- man/tm_g_quality.Rd | 2 +- man/top_gene_plot.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/man/heatmap_plot.Rd b/man/heatmap_plot.Rd index df4455b7..0ca9bd80 100644 --- a/man/heatmap_plot.Rd +++ b/man/heatmap_plot.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/quality.R +% Please edit documentation in R/tm_g_quality.R \name{heatmap_plot} \alias{heatmap_plot} \title{Correlation Heatmap Plot} diff --git a/man/tm_g_quality.Rd b/man/tm_g_quality.Rd index 48fb7388..17fbde32 100644 --- a/man/tm_g_quality.Rd +++ b/man/tm_g_quality.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/quality.R +% Please edit documentation in R/tm_g_quality.R \name{tm_g_quality} \alias{tm_g_quality} \alias{ui_g_quality} diff --git a/man/top_gene_plot.Rd b/man/top_gene_plot.Rd index 79edae21..81dea891 100644 --- a/man/top_gene_plot.Rd +++ b/man/top_gene_plot.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/quality.R +% Please edit documentation in R/tm_g_quality.R \name{top_gene_plot} \alias{top_gene_plot} \title{Most Expressed Genes Plot} From 064d4bb96c8515492b5c4e7989bbe6a0a4a08591 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Tue, 8 Jul 2025 15:41:56 +0200 Subject: [PATCH 5/5] Update the comment with the original file --- man/heatmap_plot.Rd | 2 +- man/tm_g_quality.Rd | 2 +- man/top_gene_plot.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/man/heatmap_plot.Rd b/man/heatmap_plot.Rd index df4455b7..0ca9bd80 100644 --- a/man/heatmap_plot.Rd +++ b/man/heatmap_plot.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/quality.R +% Please edit documentation in R/tm_g_quality.R \name{heatmap_plot} \alias{heatmap_plot} \title{Correlation Heatmap Plot} diff --git a/man/tm_g_quality.Rd b/man/tm_g_quality.Rd index 48fb7388..17fbde32 100644 --- a/man/tm_g_quality.Rd +++ b/man/tm_g_quality.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/quality.R +% Please edit documentation in R/tm_g_quality.R \name{tm_g_quality} \alias{tm_g_quality} \alias{ui_g_quality} diff --git a/man/top_gene_plot.Rd b/man/top_gene_plot.Rd index 79edae21..81dea891 100644 --- a/man/top_gene_plot.Rd +++ b/man/top_gene_plot.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/quality.R +% Please edit documentation in R/tm_g_quality.R \name{top_gene_plot} \alias{top_gene_plot} \title{Most Expressed Genes Plot}