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"))
),