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

## ----biocLite1, eval=FALSE-----------------------------------------------
#  biocLite("flowPloidy")

## ----biocLite2, eval=FALSE-----------------------------------------------
#  biocLite("flowPloidyData")

## ----bioconductor2, eval=FALSE-------------------------------------------
#  source("https://bioconductor.org/biocLite.R")
#  biocLite()

## ----bioc-dependencies, eval = FALSE-------------------------------------
#  biocLite("flowCore")
#  biocLite("flowPloidyData")

## ----devtools, eval = FALSE----------------------------------------------
#  install.packages("devtools", dependencies = TRUE)

## ----github, eval = FALSE------------------------------------------------
#  library("devtools")
#  install_github("plantarum/flowPloidy", dependencies = TRUE,
#                 build_vignettes = TRUE)

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

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

## ----list.files1, eval = FALSE-------------------------------------------
#  my.files <- list.files("~/flow/data", full.names = TRUE)

## ----list.files2, eval = FALSE-------------------------------------------
#  my.files <- list.files("~/flow/data", full.names = TRUE, pattern = ".LMD")

## ----viewFlowChannel, output = "hold"------------------------------------
viewFlowChannels(flowPloidyFiles[1])
## or viewFlowcChannels("my-flow-file.LMD")

## ----batchFlowHist, message = 1:10, collapse = TRUE, cache = TRUE--------
batch1 <- batchFlowHist(flowPloidyFiles, channel = "FL3.INT.LIN")

## ----browseFlowHist, eval = FALSE----------------------------------------
#  batch1 <- browseFlowHist(batch1) ## update the histograms in batch1

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse1.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse2.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse2c.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse3.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse3b.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse3c.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse11.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse11b.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_browse11c.png")

## ----tabulateFlowHist----------------------------------------------------
tabulateFlowHist(batch1)[1:4, ]

## ----tabulateFlowHist2, eval = FALSE-------------------------------------
#  results <- tabulateFlowHist(batch1)

## ----tabulateFlowHist3, eval = FALSE-------------------------------------
#  results <- tabulateFlowHist(batch1, file = "FCMresults.csv")

## ----saving FlowHist objects, eval = FALSE-------------------------------
#  save(batch1, file = "my-FCM-analyses.Rdata")

## ----setting standards, eval = FALSE-------------------------------------
#  batch1 <- batchFlowHist(flowPloidyFiles, channel = "FL3.INT.LIN",
#                          standards = 1.11)

## ----multiple standards, eval = FALSE------------------------------------
#  batch1 <- batchFlowHist(flowPloidyFiles, channel = "FL3.INT.LIN",
#                          standards = c(1.11, 9.09))

## ----vac channel---------------------------------------------------------
viewFlowChannels(fpVac)

## ----read vac------------------------------------------------------------
vac <- batchFlowHist(fpVac, channel = "FL2.A")

## ----view vac, eval = FALSE----------------------------------------------
#  vac <- browseFlowHist(vac)

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("vac1.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gate_ui.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_gate.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gs_gate_zoom2.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("draw_gate.png")

## ---- echo = FALSE, out.width = "100%"-----------------------------------
knitr::include_graphics("gated_analysis.png")