Interactive R Shiny plot with and without using ggplot

Question

I modified the interactive R Shiny plot from the R Shiny gallery to plot an interactive standard curve. I would like to plot the interactive plot without using ggplot2 library with just using R base plotting functions.

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)

I tried replacing the plotting portion of the script with the following but I am not able to interactively plot. What am I doing wrong here?

 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")

HubertL · Accepted Answer · 2017-03-28 22:19:20Z

3

You have to add xvarand yvar parameters to nearPoints:

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

answered Mar 28, 2017 at 22:19

HubertL

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2 Comments

RanonKahn Over a year ago

Hi @HubertL, Your suggestion worked. The only issue I am facing now is I am not able to override the axis title with a more detailed one. Can you please have a look at the code below? Whatever I do it writes over the "Concn" and "Values" causing chaos. Any suggestions please?

HubertL Over a year ago

just add these parameters to the plot call ylab="", xlab=""

RanonKahn · Accepted Answer · 2019-09-16 00:48:45Z

The working code implementing @HubertL's suggestion for someone like me to use for interactive plotting and to knockout outliers by clicking on or by selecting the point(s) using mouse:

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_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_)
  })

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

shinyApp(ui, server)

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