diff --git a/inst/DRomicsInterpreter-shiny/server.R b/inst/DRomicsInterpreter-shiny/server.R index 8eccfd1..4be0d69 100644 --- a/inst/DRomicsInterpreter-shiny/server.R +++ b/inst/DRomicsInterpreter-shiny/server.R @@ -469,15 +469,6 @@ server <- function(input, output, session) { shapebyBMDplot <- eventReactive(input$buttonRunStep3, {input$shapebyBMDplot}) colorbyBMDplot <- eventReactive(input$buttonRunStep3, {input$colorbyBMDplot}) - # min doses by default according to the log transformation - xmin_bmdplotwotgradient <- eventReactive(input$BMDlogtransfoBMDplot, { - if(input$doselogtransfoCurvesplot) { - return(round(min(BMD) / 2, 2)) - } else { - return(0) - } - }) - extendedresforBMD <- eventReactive(input$buttonRunStep3, { validate(need(input$annotcheckboxBMDplot, "Please choose at least one annotation")) sortextendedres <- sortextendedres() @@ -488,7 +479,6 @@ server <- function(input, output, session) { "mypathclasslabel" = mypathclasslabel)) }) - output$bmdplot <- renderPlot({ myextendedresforBMD <- extendedresforBMD() @@ -496,7 +486,7 @@ server <- function(input, output, session) { myfacetbyrowsBMDplot <- fnvaluecheckbox(facetbyrowsBMDplot(), myextendedresforBMD$mypathclasslabel) ############ bmdplot plot ############ - use.args <- rep(TRUE, 7) # 7 arguments used in the bmdplot function + use.args <- rep(TRUE, 8) # 8 arguments used in the bmdplot function if(input$nbLevel == 1) {use.args[3] <- FALSE} # use.args[3] = facetby2 if(!isTRUE(shapebyBMDplot())) {use.args[4] <- FALSE} # use.args[4] = shapeby if(!isTRUE(colorbyBMDplot())) {use.args[5] <- FALSE} # use.args[5] = colorby @@ -508,7 +498,8 @@ server <- function(input, output, session) { shapeby = "trend", colorby = "trend", add.label = addlabelBMDplot(), - BMD_log_transfo = BMDlogtransfoBMDplot() + BMD_log_transfo = BMDlogtransfoBMDplot(), + add.CI = addciBMDplot() )[use.args]) mybmdplot <- mybmdplot + ggplot2::theme_bw() + theme(text = element_text(size = 18)) @@ -518,13 +509,12 @@ server <- function(input, output, session) { ) ############ bmdplotwithgradient plot ############ - use.args <- rep(TRUE, 9) # 9 arguments used in the bmdplotwithgradient function - if(input$nbLevel == 1) {use.args[6] <- FALSE} # use.args[6] = facetby2 - if(!isTRUE(shapebyBMDplot())) {use.args[7] <- FALSE} # use.args[7] = shapeby + use.args <- rep(TRUE, 8) # 8 arguments used in the bmdplotwithgradient function + if(input$nbLevel == 1) {use.args[5] <- FALSE} # use.args[5] = facetby2 + if(!isTRUE(shapebyBMDplot())) {use.args[6] <- FALSE} # use.args[6] = shapeby mybmdplotwithgradient <- do.call("bmdplotwithgradient", list( extendedres = myextendedresforBMD$myextendedresforBMD, - xmin = xmin_bmdplotwotgradient(), xmax = maxDoseXScale(), scaling = TRUE, facetby = myfacetbycolumnsBMDplot, @@ -631,7 +621,7 @@ server <- function(input, output, session) { # Update the min and max doses by default according to the log transformation observeEvent(input$doselogtransfoCurvesplot, { if(input$doselogtransfoCurvesplot) { - updateNumericInput(session, "mindoseCurvesplot", value = round(min(BMD) / 2, 2)) + updateNumericInput(session, "mindoseCurvesplot", value = round(min(BMD) * 0.9, 2)) } else { updateNumericInput(session, "mindoseCurvesplot", value = 0) } diff --git a/inst/DRomicsInterpreter-shiny/ui.R b/inst/DRomicsInterpreter-shiny/ui.R index 5b28cd2..e828386 100644 --- a/inst/DRomicsInterpreter-shiny/ui.R +++ b/inst/DRomicsInterpreter-shiny/ui.R @@ -380,7 +380,7 @@ ui <- fluidPage( fixedRow( column(4, splitLayout(cellWidths = c("60%", "40%"), - checkboxInput("doselogtransfoCurvesplot", label = HTML("Dose log transformation"), value = FALSE), + checkboxInput("doselogtransfoCurvesplot", label = HTML("Dose log transformation"), value = TRUE), shinyBS::bsButton("helplabel1step4", label = "", icon = icon("info"), size = "small", style="color:#9c5c16"), shinyBS::bsPopover("helplabel1step4", "", helplabel1step4, placement = "right", trigger = "hover", options = list(container = "body")) ),