## ----setup, echo=FALSE--------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  fig.width = 7,
  fig.height = 3,
  fig.align = "center",
  comment = "#>"
)

## -----------------------------------------------------------------------------
sim.seg <- function(seg.mean, size.mean=15){
  seg.size <- rpois(1, size.mean)
  rpois(seg.size, seg.mean)
}
set.seed(1)
seg.mean.vec <- c(1.5, 3.5, 0.5, 4.5, 2.5)
z.list <- lapply(seg.mean.vec, sim.seg)
(z.rep.vec <- unlist(z.list))

## ----ggcount------------------------------------------------------------------
count.df <- data.frame(
  chrom="chrUnknown",
  chromStart=0:(length(z.rep.vec)-1),
  chromEnd=1:length(z.rep.vec),
  count=z.rep.vec)
if(require(ggplot2)){
gg.count <- ggplot()+
  xlab("position")+
  geom_point(aes(
    chromEnd, count),
    shape=1,
    data=count.df)
gg.count
}

## -----------------------------------------------------------------------------
n.segs <- length(seg.mean.vec)
seg.size.vec <- sapply(z.list, length)
seg.end.vec <- cumsum(seg.size.vec)
change.vec <- seg.end.vec[-n.segs]+0.5
change.df <- data.frame(
  changepoint=change.vec)
if(require(ggplot2)){
gg.change <- gg.count+
  geom_vline(aes(
    xintercept=changepoint, color=model),
    data=data.frame(change.df, model="simulation"))+
  scale_color_manual(
    values=c(
      simulation="black",
      fitted="green"))
gg.change
}

## -----------------------------------------------------------------------------
fit <- list()
(fit$vec <- PeakSegDisk::PeakSegFPOP_vec(z.rep.vec, 10.5))

## -----------------------------------------------------------------------------
gg.change+
  geom_segment(aes(
    chromStart+0.5, mean, xend=chromEnd+0.5, yend=mean, color=model),
    data=data.frame(fit$vec$segments, model="fitted"))

## -----------------------------------------------------------------------------
plot(fit$vec)

## -----------------------------------------------------------------------------
(fit$df <- PeakSegDisk::PeakSegFPOP_df(count.df, 10.5))

## -----------------------------------------------------------------------------
z.rle.vec <- rle(z.rep.vec)
chromEnd <- cumsum(z.rle.vec$lengths)
rle.df <- data.frame(
  chrom="chrUnknown",
  chromStart=c(0L, chromEnd[-length(chromEnd)]),
  chromEnd,
  count=z.rle.vec$values)
if(require(ggplot2)){
gg.rle <- ggplot()+
  geom_segment(aes(
    chromStart+0.5, count, xend=chromEnd+0.5, yend=count),
    data=rle.df)+
  geom_point(aes(
    chromEnd, count),
    shape=1,
    data=rle.df)+
  geom_vline(aes(
    xintercept=changepoint, color=model),
    data=data.frame(change.df, model="simulation"))+
  scale_color_manual(
    values=c(
      simulation="black",
      fitted="green"))+
  xlab("position")
gg.rle
}

## -----------------------------------------------------------------------------
(fit$rle <- PeakSegDisk::PeakSegFPOP_df(rle.df, 10.5))
if(require(ggplot2)){
gg.rle+
  geom_segment(aes(
    chromStart+0.5, mean, xend=chromEnd+0.5, yend=mean, color=model),
    data=data.frame(fit$rle$segments, model="fitted"))
}

## -----------------------------------------------------------------------------
data.dir <- file.path(
  tempfile(),
  with(rle.df, sprintf(
    "%s-%d-%d", chrom[1], min(chromStart), max(chromEnd))))
dir.create(data.dir, showWarnings=FALSE, recursive=TRUE)
coverage.bedGraph <- file.path(data.dir, "coverage.bedGraph")
write.table(
  rle.df, coverage.bedGraph,
  sep="\t", row.names=FALSE, col.names=FALSE)

## -----------------------------------------------------------------------------
(fit$dir <- PeakSegDisk::PeakSegFPOP_dir(data.dir, 10.5))

## -----------------------------------------------------------------------------
if(interactive() && requireNamespace("future"))future::plan("multisession")
(fit$search <- PeakSegDisk::sequentialSearch_dir(data.dir, 2L, verbose=1))

## -----------------------------------------------------------------------------
lossDF <- function(L)data.frame(L$loss)[, names(fit$dir$loss)]
do.call(rbind, lapply(fit, lossDF))

## -----------------------------------------------------------------------------
four.peaks <- PeakSegDisk::sequentialSearch_dir(data.dir, 4L)
four.peaks$others[, .(iteration, penalty, peaks)]