## ---- echo = FALSE, message = FALSE------------------------------------------- knitr::opts_chunk$set(collapse = TRUE, comment = "#>", tidy = TRUE) library(flowCore) library(flowTime) library(ggplot2) ## ----------------------------------------------------------------------------- plate1<-read.flowSet(path=system.file("extdata", "tc_example", package = "flowTime"), alter.names = TRUE) # add plate numbers to the sampleNames, in this example we have already done this # step # sampleNames(plate1)<-paste("1_",sampleNames(plate1),sep="") dat<-plate1 ## ---- eval = F---------------------------------------------------------------- # plate2<-read.flowSet(path = paste(experiment,"_2/",sep=""), alter.names = TRUE) # sampleNames(plate2)<-paste("2_", sampleNames(plate2), sep = "") # dat<-rbind2(plate1, plate2) ## ----------------------------------------------------------------------------- annotation <- read.csv(system.file("extdata", "tc_example.csv", package = "flowTime")) ## ---- eval = F---------------------------------------------------------------- # sampleNames(dat) # view the sample names # sampleNames(dat) == annotation$id # # Replace 'id' with the unique identifier column to test, # # if this column is identical to the sample names of your flowset. # annotation <- cbind(annotation, 'names' = sampleNames(dat)) # # If the sampleNames and unique identifiers are in the correct order # # this command will add the sampleNames as the identifier. ## ----------------------------------------------------------------------------- adat <- annotateFlowSet(dat, annotation) head(rownames(pData(adat))) head(pData(adat)) ## ---- eval = F---------------------------------------------------------------- # write.flowSet(adat, outdir = 'your/favorite/directory') # read.flowSet('flowSet folder', path = 'your/flow/directory', # phenoData = 'annotation.txt', alter.names = TRUE) ## ---- fig.width= 7------------------------------------------------------------ #load the gate set for BD Accuri C6 cytometer loadGates(gatesFile = 'C6Gates.RData', path = system.file("extdata", package = "flowTime")) dat_sum <- summarizeFlow(adat, ploidy = 'diploid', only = 'singlets',channel = 'FL1.A') qplot(x = time, y= FL1.Amean, data = dat_sum, linetype = factor(treatment)) + geom_line() + xlab('Time post Auxin addition (min)') + ylab('Reporter Fluorescence (AU)') + scale_color_discrete(name=expression(paste("Auxin (",mu,"M)",sep = ""))) + theme_classic(base_size = 14, base_family = 'Arial')