---
title: "My Rmd Document"
output: 
  html_document:
    self_contained: false
---
  
```{r safety, echo = FALSE}
library(knitr)
# Calling knit_meta() here is just a safety protocol.
# knit_print.animint uses knitr's meta-data to efficiently place JS scripts.
# If this meta-data isn't clear when a document is knit, the result won't be rendered properly
knit_meta() 
```
  
  
```{r plot-1-top}
library(ggplot2) 
library(animint)
dat <- data.frame(x = 1:10, y = 1:10, label = rep(c("a178", "b934"), 5))
q2 <- list(q = qplot(x, y, data = dat, colour = label, 
                     xlab = "first plot with color legend"))
structure(q2, class = "animint")
```

Clicking on the plot above should not affect the plot below.

```{r plot.1.bottom}
q1 <- list(q = qplot(x, y, data = dat, colour = label, 
                     xlab = "second plot with color legend"))
structure(q1, class = "animint")
```

The plot below has no interactive features.

```{r boring}
boring <- list(q = qplot(rnorm(100), xlab = "non-interactive plot"))
structure(boring, class = "animint")
```

The next data viz consists of two plots, one of which should have
common chunk data files. 

```{r breakpoints}
data(breakpoints)
only.error <- subset(breakpoints$error,type=="E")
only.segments <- subset(only.error,bases.per.probe==bases.per.probe[1])
signal.colors <- c(estimate="#0adb0a",
                   latent="#0098ef")
breakpointError <- 
  list(signal=ggplot()+
         geom_point(aes(position, signal, showSelected=bases.per.probe),
                    data=breakpoints$signals)+
         geom_line(aes(position, signal), colour=signal.colors[["latent"]],
                   data=breakpoints$imprecision)+
         geom_segment(aes(first.base, mean, xend=last.base, yend=mean,
                          showSelected=segments,
                          showSelected2=bases.per.probe),
                      colour=signal.colors[["estimate"]],
                      data=breakpoints$segments)+
         geom_vline(aes(xintercept=base,
                        showSelected=segments,
                        showSelected2=bases.per.probe),
                    colour=signal.colors[["estimate"]],
                    linetype="dashed",
                    data=breakpoints$breaks),
       error=ggplot()+
         geom_vline(aes(xintercept=segments, clickSelects=segments),
                    data=only.segments, lwd=17, alpha=1/2)+
         geom_line(aes(segments, error, group=bases.per.probe,
                       clickSelects=bases.per.probe),
                   data=only.error, lwd=4),
       first=list(segments=6))
structure(breakpointError, class="animint")
```