Interactive R Shiny plot with and without using ggplot - r

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")

Answer 1

You have to add xvarand yvar parameters to nearPoints:
res <- nearPoints(XYdata, input$plot1_click, xvar="Concn", yvar="Values", allRows = TRUE)

Answer 2

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)