使用和不使用ggplot的交互式R Shiny圖

Question

我修改了R Shiny畫廊的交互式R Shiny圖，繪制了交互式標准曲線。 我想在不使用ggplot2庫的情況下繪制交互式繪圖，只使用R基本繪圖函數。

library(ggplot2)

XYdata <- data.frame(cbind(Values = c(91.8, 95.3,   99.8,   123.3,  202.9,  619.8,  1214.2, 1519.1, 1509.2, 1523.3, 1595.2, 1625.1),
                           Concn = c(1000, 300,    100,    30, 10, 3,  1,  0.3,    0.1,    0.03,   0.01,   0)))
ui <- fluidPage(
  fluidRow(
    column(width = 6,
           plotOutput("plot1", height = 350,
                      click = "plot1_click",
                      brush = brushOpts(
                        id = "plot1_brush"
                      )
           ),
           actionButton("exclude_toggle", "Toggle points"),
           actionButton("exclude_reset", "Reset")
    )
  )
)

server <- function(input, output) {
  # For storing which rows have been excluded
  vals <- reactiveValues(
    keeprows = rep(TRUE, nrow(XYdata))
  )
  NonScientific <- function(l) {l <- format(l, scientific = FALSE); parse(text=l)}

  output$plot1 <- renderPlot({
    # Plot the kept and excluded points as two separate data sets

    XYdata <- data.frame(cbind(Values = c(91.8, 95.3,   99.8,   123.3,  202.9,  619.8,  1214.2, 1519.1, 1509.2, 1523.3, 1595.2, 1625.1),
                           Concn = c(1000, 300,    100,    30, 10, 3,  1,  0.3,    0.1,    0.03,   0.01,   0)))
    keep    <- XYdata[ vals$keeprows, , drop = FALSE]
    exclude <- XYdata[!vals$keeprows, , drop = FALSE]
    keep <- subset(keep, Concn > 0)
    exclude <- subset(exclude, Concn > 0)
    nls.fit <- nls(Values ~ (ymax* keep$Concn / (ec50 + keep$Concn)) + Ns*keep$Concn + ymin, data=keep,
                   start=list(ymax=max(keep$Values), ymin = min(keep$Values), ec50 = 3, Ns = 0.2045514))
    keep$nls.pred <- fitted(nls.fit)

    ggplot(keep, aes(y = Values,x = Concn))+geom_point(size = 5,colour="red")+
    geom_smooth(method = "loess",fullrange = F, se = T, aes(Concn, nls.pred),size = 1.5,colour="blue1")+
      geom_point(data = exclude, shape = 21, fill = NA, color = "black",size = 5, alpha = 0.7) +
      xlab('Concentration (nM)')+ ylab('Units')+
      scale_x_log10(labels=NonScientific)+ggtitle("Standard Curve")+theme_classic()+
      theme(panel.background = element_rect(colour = "black", size=1),
            plot.margin = margin(1, 3, 0.5, 1, "cm"), 
            plot.title = element_text(hjust = 0, face="bold",color="#993333", size=16),
            axis.title = element_text(face="bold", color="#993333", size=14),
            axis.text.x = element_text(face="bold", color="#666666", size=12),
            axis.text.y = element_text(face="bold", color="#666666", size=12))
  })

  # Toggle points that are clicked
  observeEvent(input$plot1_click, {
    res <- nearPoints(XYdata, input$plot1_click, allRows = TRUE)

    vals$keeprows <- xor(vals$keeprows, res$selected_)
  })

  # Toggle points that are brushed, when button is clicked
  observeEvent(input$exclude_toggle, {
    res <- brushedPoints(XYdata, input$plot1_brush, allRows = TRUE)

    vals$keeprows <- xor(vals$keeprows, res$selected_)
  })

  # Reset all points
  observeEvent(input$exclude_reset, {
    vals$keeprows <- rep(TRUE, nrow(XYdata))
  })

}

shinyApp(ui, server)

我嘗試用以下內容替換腳本的繪圖部分，但我無法以交互方式繪圖。 我在這做錯了什么？

 plot(Values ~ Concn, keep, subset = Concn > 0, col = 4, cex = 2, log = "x")
 title(main = "XY Std curve")
 lines(predict(nls.fit, new = list(Concn = Concn)) ~ Concn, keep)
 points(Values ~ Concn, exclude, subset = Concn > 0, col = 1, cex = 2, log = "x")

Answer 1

您必須將xvar和yvar參數添加到nearPoints ：

res <- nearPoints(XYdata, input$plot1_click, xvar="Concn", yvar="Values", allRows = TRUE)

Answer 2

工作代碼實現@ HubertL建議像我這樣的人用於交互式繪圖並通過點擊或通過使用鼠標選擇點來淘汰異常值：

XYdata <- data.frame(cbind(Values = c(91.8, 95.3,   99.8,   123.3,  202.9,  619.8,  1214.2, 1519.1, 1509.2, 1523.3, 1595.2, 1625.1),
                           Concn = c(1000, 300, 100,30, 10, 3,  1,  0.3,    0.1, 0.03, 0.01, 0)))
ui <- fluidPage(
  fluidRow(
    column(width = 6,
           plotOutput("plot1", height = 350,click = "plot1_click", brush = brushOpts(id = "plot1_brush")),
           actionButton("exclude_toggle", "Toggle points"),
           actionButton("exclude_reset", "Reset")
    )
  )
)

server <- function(input, output) {
  # For storing which rows have been excluded
  vals <- reactiveValues(
    keeprows = rep(TRUE, nrow(XYdata))
  )
  NonScientific <- function(l) {l <- format(l, scientific = FALSE); parse(text=l)}

  output$plot1 <- renderPlot({
    # Plot the kept and excluded points as two separate data sets

    XYdata <- data.frame(cbind(Values = c(91.8, 95.3,   99.8,   123.3,  202.9,  619.8,  1214.2, 1519.1, 1509.2, 1523.3, 1595.2, 1625.1),
                           Concn = c(1000, 300,    100,    30, 10, 3,  1,  0.3,    0.1,    0.03,   0.01,   0)))
    keep    <- XYdata[ vals$keeprows, , drop = FALSE]
    exclude <- XYdata[!vals$keeprows, , drop = FALSE]
    keep <- subset(keep, Concn > 0)
    exclude <- subset(exclude, Concn > 0)
    o <- order(keep$Concn)
    keep <- keep[o, ]
    fo <- Values ~ (ymax* Concn / (ec50 + Concn)) + Ns * Concn + ymin
    st <- list(ymax=max(keep$Values), ymin = min(keep$Values), ec50 = 3, Ns = 0.2045514)
    nls.fit <- nls(fo, data = keep, start = st)
    plot(Values ~ Concn, keep, subset = Concn > 0, type = 'p',pch = 16,cex = 2, axes = FALSE, frame.plot = TRUE,log = "x")
    title(main = "Interactive Std curve")
    logRange <- with(keep, log(range(Concn[Concn > 0])))
    x <- exp(seq(logRange[1], logRange[2], length = 250))
    lines(x, predict(nls.fit, new = list(Concn = x)))
    points(Values ~ Concn, exclude, subset = Concn > 0, col = 1, cex = 2)
    my.at <- 10^(-2:3)
    axis(1, at = my.at, labels = formatC(my.at, format = "fg"))
    axis(2)
  })

  # Toggle points that are clicked
  observeEvent(input$plot1_click, {

    res <- nearPoints(XYdata, input$plot1_click, xvar="Concn", yvar="Values", allRows = TRUE)
    vals$keeprows <- xor(vals$keeprows, res$selected_)
  })

  # Toggle points that are brushed, when button is clicked
  observeEvent(input$exclude_toggle, {
    res <- brushedPoints(XYdata, input$plot1_brush, allRows = TRUE)

    vals$keeprows <- xor(vals$keeprows, res$selected_)
  })

  # Reset all points
  observeEvent(input$exclude_reset, {
    vals$keeprows <- rep(TRUE, nrow(XYdata))
  })

}

shinyApp(ui, server)