# #——回声= FALSE,消息= FALSE ---------------------------------------- 美元knitr: opts_chunk集(崩溃= TRUE,评论= " # > ",整洁= TRUE)图书馆(flowCore)图书馆(flowTime)库(ggplot2 ) ## ------------------------------------------------------------------------ plate1 < -read.flowSet (path =系统。文件(“extdata”、“ss_example”、包=“flowTime”),alter.names = TRUE) #板数字添加到sampleNames sampleNames (plate1) <粘贴(“1 _”,sampleNames (plate1), 9 = " ") dat < -plate1 # # - eval = F ----------------------------------------------------------- # plate2 < -阅读。flowSet(路径=粘贴(实验中,“_2 /”,9月 = ""), # alter.names = TRUE) # sampleNames (plate2) < -粘贴(“2 _ sampleNames (plate2), 9 = " ") # dat < - rbind2 (plate1 plate2 ) ## ------------------------------------------------------------------------ 注释< - read.csv(系统。文件(“extdata”、“ss_example.csv”、包=“flowTime”))头(注释)sampleNames (dat) sampleNames (dat) = =美元注释名称# # - eval = F ----------------------------------------------------------- # 注释< - cbind(注释,“名字”= sampleNames (dat)) # #或#注释< - createAnnotation (yourFlowSet = dat) # write.csv(注释,/ / yourAnnotation.csv文件= '路径 ') ## ------------------------------------------------------------------------ adat < - annotateFlowSet (yourFlowSet = dat annotation_df =注释,mergeBy = '名称')头(rownames (pData(法律)))头(pData(法律 )) ## ---- eval = F ----------------------------------------------------------- # 写。flowSet(adat, outdir = 'your/favorite/directory') # # #读取保存的实验元数据的flowSetflowSet (flowSet文件夹的路径= /流/目录,# phenoData = annotation.txt, alter.names = TRUE ) ## ---- fig.width = 4, fig.height = 4 -------------------------------------- loadGates() #使用默认包含gateSet dat。SS <- steadyState(flowset = adat, ploidy = 'diploid'， only = 'singlets') p <- ggplot(dat。SS, aes(x = as.factor(处理)，y = FL2。A, fill = AFB)) + geom_boxplot(离群值。size = NA) + facet_grid(IAA~AFB) + theme_classic(base_family = 'Arial'， base_size = 16) + ylim(c(-1000,10000)) + xlab(expression(paste('生长素('，mu，'M)'，sep =" "))) + ylab('Fluorescence (AU)') + theme(legend.position="none") p