From 0700a5011c4595f5776cd72e53f804f9070c9c11 Mon Sep 17 00:00:00 2001 From: mauromiguelm Date: Mon, 27 Feb 2023 12:07:18 +0100 Subject: [PATCH 1/7] fix: remove obj from `plot_expression` --- components/board.dataview/R/dataview_plot_expression.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/board.dataview/R/dataview_plot_expression.R b/components/board.dataview/R/dataview_plot_expression.R index e5ee923e1..a46987f4e 100644 --- a/components/board.dataview/R/dataview_plot_expression.R +++ b/components/board.dataview/R/dataview_plot_expression.R @@ -15,7 +15,7 @@ dataview_plot_expression_ui <- function(id, label = "", height = c(600, 800)) { outputFunc = plotly::plotlyOutput, outputFunc2 = plotly::plotlyOutput, info.text = info_text, - download.fmt = c("png", "pdf", "csv", "obj"), + download.fmt = c("png", "pdf", "csv"), ## width = c("auto","100%"), height = height ) From a97f26f56e75c2b8dfb6b41455285458b87d81ac Mon Sep 17 00:00:00 2001 From: mauromiguelm Date: Mon, 27 Feb 2023 12:32:03 +0100 Subject: [PATCH 2/7] fix: `plot_expression` now works for grouped data --- components/board.dataview/R/dataview_plot_expression.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/components/board.dataview/R/dataview_plot_expression.R b/components/board.dataview/R/dataview_plot_expression.R index a46987f4e..69a879257 100644 --- a/components/board.dataview/R/dataview_plot_expression.R +++ b/components/board.dataview/R/dataview_plot_expression.R @@ -66,7 +66,7 @@ dataview_plot_expression_server <- function(id, } geneplot_type <- "barplot" - geneplot_type <- input$geneplot_type + # geneplot_type <- input$geneplot_type pd <- list( df = data.frame( @@ -85,6 +85,7 @@ dataview_plot_expression_server <- function(id, plot.RENDER.SAVE <- function() { pd <- plot_data() + shiny::req(pd) df <- pd[["df"]] @@ -194,6 +195,7 @@ dataview_plot_expression_server <- function(id, plot.RENDER <- function() { pd <- plot_data() + shiny::req(pd) df <- pd[["df"]] From 1280deb942ed041ce705796338eda9a629f11d6e Mon Sep 17 00:00:00 2001 From: mauromiguelm Date: Mon, 27 Feb 2023 12:36:16 +0100 Subject: [PATCH 3/7] fix: `plot_phenoassociation` now can download data --- components/board.dataview/R/dataview_plot_phenoassociation.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/board.dataview/R/dataview_plot_phenoassociation.R b/components/board.dataview/R/dataview_plot_phenoassociation.R index 675327514..86325cff1 100644 --- a/components/board.dataview/R/dataview_plot_phenoassociation.R +++ b/components/board.dataview/R/dataview_plot_phenoassociation.R @@ -56,7 +56,7 @@ dataview_plot_phenoassociation_server <- function(id, pgx, r.samples, watermark plotlib2 = "base", func = plot.RENDER, func2 = modal_plot.RENDER, - ## csvFunc = plot_data, ## *** downloadable data as CSV + csvFunc = plot_data, ## *** downloadable data as CSV renderFunc = shiny::renderPlot, renderFunc2 = shiny::renderPlot, res = c(100, 170) * 0.85, ## resolution of plots From caafa3baa40b0f40f54868478be54e05e0c997dd Mon Sep 17 00:00:00 2001 From: mauromiguelm Date: Mon, 27 Feb 2023 13:50:26 +0100 Subject: [PATCH 4/7] fix: `plot_correlation_network` has right label --- components/board.wgcna/R/wgcna_plot_correlation_network.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/board.wgcna/R/wgcna_plot_correlation_network.R b/components/board.wgcna/R/wgcna_plot_correlation_network.R index 9aa256c15..db7ba7413 100644 --- a/components/board.wgcna/R/wgcna_plot_correlation_network.R +++ b/components/board.wgcna/R/wgcna_plot_correlation_network.R @@ -11,7 +11,7 @@ wgcna_plot_correlation_network_ui <- function(id, height, width) { PlotModuleUI( ns("plot"), title = "Correlation network", - label = "b", + label = "c", info.text = info_text, height = height, width = width, From 458eeb26e987a3e0b6f045c4a9ff0c717110f180 Mon Sep 17 00:00:00 2001 From: mauromiguelm Date: Mon, 27 Feb 2023 13:51:01 +0100 Subject: [PATCH 5/7] fix: `plot_hm_parcoord` now has option to download data --- .../board.clustering/R/clustering_plot_table_hm_parcoord.R | 1 + 1 file changed, 1 insertion(+) diff --git a/components/board.clustering/R/clustering_plot_table_hm_parcoord.R b/components/board.clustering/R/clustering_plot_table_hm_parcoord.R index 5042fb415..05b2d5ed9 100644 --- a/components/board.clustering/R/clustering_plot_table_hm_parcoord.R +++ b/components/board.clustering/R/clustering_plot_table_hm_parcoord.R @@ -179,6 +179,7 @@ clustering_plot_table_hm_parcoord_server <- function(id, plotlib = "plotly", ## plotlib2 = "plotly", func = hm_parcoord.RENDER, + csvFunc = hm_parcoord.matrix, res = c(90, 170), pdf.width = 8, pdf.height = 8, From 5887490b859493fb329a1424588c253ebde9182e Mon Sep 17 00:00:00 2001 From: mauromiguelm Date: Mon, 27 Feb 2023 13:51:22 +0100 Subject: [PATCH 6/7] fix: `plot_phenoplot` able to download data --- components/board.clustering/R/clustering_plot_phenoplot.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/components/board.clustering/R/clustering_plot_phenoplot.R b/components/board.clustering/R/clustering_plot_phenoplot.R index 42c2c020e..7cc33b9d1 100644 --- a/components/board.clustering/R/clustering_plot_phenoplot.R +++ b/components/board.clustering/R/clustering_plot_phenoplot.R @@ -21,7 +21,7 @@ clustering_plot_phenoplot_ui <- function(id, plotlib = "base", info.text = clust_phenoplot_info, options = clust_phenoplot.opts, - download.fmt = c("png", "pdf", "csv"), + download.fmt = c("png", "pdf"), width = c("auto", "100%"), height = height ) @@ -128,7 +128,7 @@ clustering_plot_phenoplot_server <- function(id, plotlib = "base", ## plotlib2 = "plotly", func = plot.RENDER, - csvFunc = plot_data, ## *** downloadable data as CSV + # csvFunc = plot_data, ## *** downloadable data as CSV ## renderFunc = plotly::renderPlotly, ## renderFunc2 = plotly::renderPlotly, res = c(85), ## resolution of plots From 24b6ef63b3cc5bdc5f2f6facdfad9898fc1368a7 Mon Sep 17 00:00:00 2001 From: mauromiguelm Date: Mon, 27 Feb 2023 13:51:34 +0100 Subject: [PATCH 7/7] fix: `plot_hm_splitmap` able to download data --- components/board.clustering/R/clustering_plot_hm_splitmap.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/components/board.clustering/R/clustering_plot_hm_splitmap.R b/components/board.clustering/R/clustering_plot_hm_splitmap.R index 5a2b61428..b5c4c846f 100644 --- a/components/board.clustering/R/clustering_plot_hm_splitmap.R +++ b/components/board.clustering/R/clustering_plot_hm_splitmap.R @@ -101,7 +101,7 @@ clustering_plot_hm_splitmap_ui <- function(id, plotlib = "plotly", info.text = info_text, options = hm_splitmap_opts, - download.fmt = c("png", "pdf"), + download.fmt = c("png", "pdf", "csv"), width = width, height = height ) @@ -330,7 +330,7 @@ clustering_plot_hm_splitmap_server <- function(id, "pltmod", plotlib = "plotly", func = hm2_splitmap.RENDER, - # csvFunc = + csvFunc = plot_data_hm1, res = c(80, 95), ## resolution of plots pdf.width = 10, pdf.height = 8, add.watermark = watermark