## ----bioconductor, eval=FALSE-------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") ## ----install1, eval=FALSE------------------------------------------------ # BiocManager::install("flowPloidy") ## ----install2, eval=FALSE------------------------------------------------ # BiocManager::install("flowPloidyData") ## ----bioconductor2, eval=FALSE------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install() ## ----bioc-dependencies, eval = FALSE------------------------------------- # BiocManager::install("flowCore") # BiocManager::install("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("gsFigs/gs_browse1.png") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gs_browse2.png") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gs_browse2c.png") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gs_browse3.png") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gs_browse3b.png") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gs_browse11.png") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gs_browse11b.png") ## ---- echo = FALSE, out.width = "100%", fig.cap = "Annotating a Failed Histogram"---- knitr::include_graphics("gsFigs/gs_Fail.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("gsFigs/vac1.png") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gate_ui.png") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gs_gate.jpg") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gs_gate_zoom2.jpg") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/draw_gate.jpg") ## ---- echo = FALSE, out.width = "100%"----------------------------------- knitr::include_graphics("gsFigs/gated_analysis.jpg")