diff --git a/R/barplot.R b/R/barplot.R index 3aa074e0..c039896d 100644 --- a/R/barplot.R +++ b/R/barplot.R @@ -193,7 +193,7 @@ srv_g_barplot <- function(id, "\nFacetting Variable:", input$`facet-sample_var`, "\nGenes Selected:", - paste0(input$`x-genes`, collapse = ", "), + paste0(x()$get_gene_labels(), collapse = ", "), "\nGene Summary:", input$`x-fun_name`, "\nQuantiles:", diff --git a/R/boxplot.R b/R/boxplot.R index 0a45f8fc..d949ce53 100644 --- a/R/boxplot.R +++ b/R/boxplot.R @@ -190,7 +190,7 @@ srv_g_boxplot <- function(id, "\nFacetting Variable:", input$`facet-sample_var`, "\nGenes Selected:", - paste0(input$`genes-genes`, collapse = ", "), + paste0(genes()$get_gene_labels(), collapse = ", "), "\nGene Summary:", input$`genes-fun_name`, "\nJitter:", diff --git a/R/forestplot.R b/R/forestplot.R index 916bd953..0e326bf5 100644 --- a/R/forestplot.R +++ b/R/forestplot.R @@ -19,8 +19,8 @@ #' dataset( #' "ADTTE", #' adtte, -#' code = 'adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte %>% -#' dplyr::mutate(is_event = (.data$CNSR == 0))' +#' code = "adtte <- scda::synthetic_cdisc_data('rcd_2021_07_07')$adtte %>% +#' dplyr::mutate(is_event = (.data$CNSR == 0))" #' ), #' dataset("MAE", mae) #' ) @@ -236,7 +236,7 @@ srv_g_forest_tte <- function(id, "\nAssay:", input$`assay-name`, "\nGenes Selected:", - paste0(input$`genes-genes`, collapse = ", "), + paste0(genes()$get_gene_labels(), collapse = ", "), "\nGene Summary:", input$`genes-fun_name`, "\nEndpoint:", diff --git a/R/km.R b/R/km.R index b17dda8e..42b57d48 100644 --- a/R/km.R +++ b/R/km.R @@ -20,8 +20,8 @@ #' dataset( #' "ADTTE", #' adtte, -#' code = 'adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte %>% -#' dplyr::mutate(is_event = (.data$CNSR == 0))' +#' code = "adtte <- scda::synthetic_cdisc_data('rcd_2021_07_07')$adtte %>% +#' dplyr::mutate(is_event = (.data$CNSR == 0))" #' ), #' dataset("MAE", mae) #' ) @@ -224,7 +224,7 @@ srv_g_km <- function(id, "\nAssay:", input$`assay-name`, "\nGenes Selected:", - paste0(input$`genes-genes`, collapse = ", "), + paste0(genes()$get_gene_labels(), collapse = ", "), "\nGene Summary:", input$`genes-fun_name`, "\nEndpoint:", diff --git a/R/scatterplot.R b/R/scatterplot.R index 229d20e0..a2ec5dad 100644 --- a/R/scatterplot.R +++ b/R/scatterplot.R @@ -187,11 +187,11 @@ srv_g_scatterplot <- function(id, "\nAssay:", input$`assay-name`, "\nX Genes Selected:", - paste0(input$`x_spec-genes`, collapse = ", "), + paste0(x_spec()$get_gene_labels(), collapse = ", "), "\nX Genes Summary:", input$`x_spec-fun_name`, "\nY Genes Selected:", - paste0(input$`y_spec-genes`, collapse = ", "), + paste0(y_spec()$get_gene_labels(), collapse = ", "), "\nY Genes Summary:", input$`y_spec-fun_name`, "\nOptional Color Variable:", diff --git a/R/volcanoplot.R b/R/volcanoplot.R index 10a6eaa5..4f0f1a97 100644 --- a/R/volcanoplot.R +++ b/R/volcanoplot.R @@ -200,8 +200,8 @@ srv_g_volcanoplot <- function(id, if (with_reporter) { card_fun <- function(comment) { card <- teal.reporter::TealReportCard$new() - card$set_name("Scatter Plot") - card$append_text("Scatter Plot", "header2") + card$set_name("Volcano Plot") + card$append_text("Volcano Plot", "header2") card$append_fs(datasets$get_filter_state()) card$append_text("Selected Options", "header3") encodings_list <- list( diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd index 4c1ec569..3ff91bbd 100644 --- a/man/tm_g_forest_tte.Rd +++ b/man/tm_g_forest_tte.Rd @@ -124,8 +124,8 @@ data <- teal_data( dataset( "ADTTE", adtte, - code = 'adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte \%>\% - dplyr::mutate(is_event = (.data$CNSR == 0))' + code = "adtte <- scda::synthetic_cdisc_data('rcd_2021_07_07')$adtte \%>\% + dplyr::mutate(is_event = (.data$CNSR == 0))" ), dataset("MAE", mae) ) diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd index ed7c1434..81cdd000 100644 --- a/man/tm_g_km.Rd +++ b/man/tm_g_km.Rd @@ -115,8 +115,8 @@ data <- teal_data( dataset( "ADTTE", adtte, - code = 'adtte <- scda::synthetic_cdisc_data("rcd_2021_07_07")$adtte \%>\% - dplyr::mutate(is_event = (.data$CNSR == 0))' + code = "adtte <- scda::synthetic_cdisc_data('rcd_2021_07_07')$adtte \%>\% + dplyr::mutate(is_event = (.data$CNSR == 0))" ), dataset("MAE", mae) )