## ----- echo = false，消息= false --------------------------------------------------------------------------------------------- knitr::opts_chunk$set(collapse = TRUE, comment = "#>", tidy = TRUE) library(flowCore) library(flowTime) library(ggplot2) ## --------------------------------------------------------------------------------------------------------------- plate1<-read.flowSet(path=system.file("extdata", "ss_example", package = "flowTime"), alter.names = true）＃将板号添加到Samplenames Samplenames（plate1）<-aspe（“ 1_”，Samplenames（plate1），sep =“”）dat <-plate1 ## -----------------------------------------------------------------------------------------------------------------------------------------＃plate2 < - read.flowset（路径=粘贴（实验，“ _2/”，sep =“”），＃alter.names = true）＃samplenames（plate2）< -粘贴（“ 2_”，Samplenames（plate2），sep =“”）＃dat <-rbind2（plate1，plate2）## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------注释< - read.csv（system.file（“ extdata”，“ ss_example.csv”，package =“ flowtime”））head（注释）samplenames（dat）samplenames（dat）== annOtation $ NAME ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # annotation <- cbind(annotation, 'name' = sampleNames(dat)) # # or # annotation <-createAnnotation（yourflowset = dat）＃write.csv（注释，file ='path/to/yourannotation.csv'）## ------------------------------------------------------------------------------------------------------------------------------------------------------------------- adat <-AntotateFlowset（yourflowset = dat，annotation_df = notation，mergeby ='name'）head（rownames（pdata（adat）））head（pdata（adat））## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # write.flowSet(adat, outdir = 'your/favorite/directory') # # # Read the flowSet with the saved experimental meta data # read.flowSet('flowSet folder', path = 'your/flow/directory', # phenoData = 'annotation.txt', alter.names = TRUE) ## ---- fig.width = 4, fig.height = 4------------------------------------------- loadGates() # use the default included gateSet dat.SS <- steadyState(flowset = adat, ploidy = 'diploid', only = 'singlets') p <- ggplot(dat.SS, aes(x = as.factor(treatment), y = FL2.A, fill = AFB)) + geom_boxplot(outlier.shape = NA) + facet_grid(IAA~AFB) + theme_classic(base_family = 'Arial', base_size = 16) + ylim(c(-1000,10000)) + xlab(expression(paste('Auxin (',mu,'M)',sep = ""))) + ylab('Fluorescence (AU)') + theme(legend.position="none") p