## ---- eval=FALSE---------------------------------------------------------
## source("https://bioconductor.org/biocLite.R")
## biocLite()

## ---- eval=FALSE---------------------------------------------------------
## biocLite("flowPloidy")

## ---- eval=FALSE---------------------------------------------------------
## biocLite("flowPloidyData")

## ---- eval = FALSE-------------------------------------------------------
## install.packages("devtools", dependencies = TRUE)
## library("devtools")
## install_github("plantarum/flowPloidy")

## ------------------------------------------------------------------------
library(flowPloidy)
library(flowPloidyData)

## ---- output = "hold"----------------------------------------------------
viewFlowChannels(flowPloidyFiles[1])

## ------------------------------------------------------------------------
fh1 <- FlowHist(file = flowPloidyFiles[1], channel = "FL3.INT.LIN",
                analyze = FALSE)

## ----simplePlot, fig.cap = "FCS Histogram"-------------------------------
plot(fh1)

## ----initialValues, fig.cap = "Histogram with Initial Values"------------
plot(fh1, init = TRUE)

## ------------------------------------------------------------------------
fh1 <- fhAnalyze(fh1)

## ----simpleAnalysis, fig.cap = "Histogram with Fitted Model"-------------
plot(fh1)

## ---- output = "hold"----------------------------------------------------
fh1

## ----noisyData, fig.cap = "Histogram with Bad Initial Values"------------
fh2 <- FlowHist(file = flowPloidyFiles["734.LMD"], channel = "FL3.INT.LIN")
plot(fh2, init = TRUE)

## ---- eval = FALSE-------------------------------------------------------
## fh2 <- pickInit(fh2)

## ----fakingInteraction, echo = FALSE, fig.cap = "Histogram with Manually Selected Peaks"----
## This stuff is automatically done by the interactive function pickInit,
## which we can't actually use in the automated vignette.
## Using internal functions here, not intended for use by users

fh2 <- flowPloidy:::resetFlowHist(fh2)
flowPloidy:::fhPeaks(fh2) <-
  structure(c(50.2623811329645, 139.061074258603, 258.242164238835,
              178.771283080744), .Dim = c(2L, 2L),
                          .Dimnames = list(NULL, c("mean", "height")))

fh2 <- flowPloidy:::addComponents(fh2)
fh2 <- flowPloidy:::makeModel(fh2)
fh2 <- flowPloidy:::getInit(fh2)

plot(fh2)
points(flowPloidy:::fhInit(fh2)$Ma, 255, col = 2, cex = 3)
points(flowPloidy:::fhInit(fh2)$Mb, 175, col = 3, cex = 3)

## ----initPick, fig.cap = "Histogram with Corrected Initial Values"-------
plot(fh2, init = TRUE)

## ----correctedAnalysis, fig.cap = "Histogram with Fitted Model"----------
fh2 <- fhAnalyze(fh2)
plot(fh2)
fh2

## ----multi-cut model-----------------------------------------------------
fh2MC <- updateFlowHist(fh2, debris = "MC")
plot(fh2MC)

## ----FlowHist multi-cut, eval = FALSE------------------------------------
## fh2MC <- FlowHist(file = flowPloidyFiles["734.LMD"],
##                   channel = "FL3.INT.LIN", debris = "MC")

## ------------------------------------------------------------------------
tabulateFlowHist(fh1)

## ------------------------------------------------------------------------
tabulateFlowHist(list(fh1, fh2))

## ---- eval = FALSE-------------------------------------------------------
## tabulateFlowHist(list(fh1, fh2), file = "flow-results.csv")

## ---- eval = FALSE-------------------------------------------------------
## my.files <- list.files("datadir/", full.names = TRUE)

## ---- eval = FALSE-------------------------------------------------------
## my.files <- list.files("datadir/", pattern = ".LMD", full.names = TRUE)

## ---- eval = FALSE-------------------------------------------------------
## my.files <- list.files("datadir1/", full.names = TRUE)
## my.files <- c(my.files, list.files("datadir2/", full.names = TRUE))

## ----histBatch-----------------------------------------------------------
batch1 <- batchFlowHist(flowPloidyFiles, channel = "FL3.INT.LIN")

## ------------------------------------------------------------------------
tabulateFlowHist(batch1)

## ---- eval = FALSE-------------------------------------------------------
## parOld <- par(ask = TRUE)
## lapply(batch1, FUN = plot)
## ## press enter to scroll through your files!
## par(parOld)

## ----browseFlowHist, eval = FALSE----------------------------------------
## batch1 <- browseFlowHist(batch1)

## ----flowShiny-output, eval = FALSE--------------------------------------
## plot(batch1[["240+S.LMD"]])

## ----flowShiny-export, eval = FALSE--------------------------------------
## tabulateFlowHist(batch1)

## ---- eval = FALSE-------------------------------------------------------
## tabulateFlowHist(batch1, file = "my-analysis-output.csv")