使用和不使用 ggplot 的交互式 R Shiny 绘图
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【中文标题】使用和不使用 ggplot 的交互式 R Shiny 绘图【英文标题】：Interactive R Shiny plot with and without using ggplot 【发布时间】：2017-08-22 04:37:41 【问题描述】：我修改了 R Shiny 库中的交互式 R Shiny 图以绘制交互式标准曲线。我想在不使用 ggplot2 库的情况下仅使用 R 基础绘图函数来绘制交互式绘图。
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$keeprows <- rep(TRUE, nrow(XYdata))
)
shinyApp(ui, server)
我尝试用以下内容替换脚本的绘图部分，但我无法交互式绘图。我在这里做错了什么？
plot(Values ~ Concn, keep, subset = Concn > 0, col = 4, cex = 2, log = "x")
title(main = "XY Std curve")
lines(predict(nls.fit, new = list(Concn = Concn)) ~ Concn, keep)
points(Values ~ Concn, exclude, subset = Concn > 0, col = 1, cex = 2, log = "x")
【问题讨论】：
【参考方案1】：您必须将xvar和yvar参数添加到nearPoints：
res <- nearPoints(XYdata, input$plot1_click, xvar="Concn", yvar="Values", allRows = TRUE)
【讨论】：
嗨@HubertL，你的建议奏效了。我现在面临的唯一问题是我无法用更详细的标题覆盖轴标题。你能看看下面的代码吗？无论我做什么，它都会覆盖“Concn”和“Values”，造成混乱。请问有什么建议吗？ 只需将这些参数添加到绘图调用ylab="", xlab=""【参考方案2】：
实现@HubertL 对像我这样的人的建议的工作代码用于交互式绘图并通过单击或使用鼠标选择点来剔除异常值：
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_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)
【讨论】：
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