# #——回声= FALSE -------------------------------------------------------------- 库(knitr) opts_chunk美元集(消息= FALSE,警告= FALSE, fig.height = 2, fig.width = 3, fig.show = " ") ## ----------------------------------------------------------------------------- 库(flowCore)库(flowWorkspace)图书馆(openCyto)图书馆(ggcyto) gs < - load_gs(系统。文件(“extdata / gs_bcell_auto”,包= " flowWorkspaceData ")) ## ----------------------------------------------------------------------------- fr < - gh_pop_get_data (gs[[2]],“住”,returnType =“flowFrame”)chnl < - CD3“g < - openCyto:::。mindensity (fr、通道= chnl) autoplot (fr, chnl) + geom_gate (g) autoplot (fr, chnl SSC-A) + geom_gate (g ) ## ----------------------------------------------------------------------------- fr < - gh_pop_get_data (gs[[1]],“边界”,returnType =“flowFrame”)chnl < -“FSC-A”g < - openCyto:::。mindensity (fr、通道= chnl) mylimits < - ggcyto_par_set(限制=“仪器”)p < - autoplot (fr, chnl) + mylimits p + geom_gate (g) autoplot (fr, chnl SSC-A) + geom_gate (g ) ## ----------------------------------------------------------------------------- g < - openCyto:::。mindensity (fr,渠道= chnl gate_range = c (7 e4, 1 e5),调整= 1.5)p + geom_gate (g) autoplot (fr, chnl SSC-A) + geom_gate (g ) ## ----------------------------------------------------------------------------- g < - openCyto:::。mindensity (fr,渠道= chnl min = 7 e4, max = 1 e5) p + geom_gate (g ) ## ----------------------------------------------------------------------------- fr < - gh_pop_get_data (gs[[1]],“淋巴returnType =“flowFrame”)chnl < -“活”g < - openCyto:::。后挡板(fr,渠道= chnl tol = 0.05) p < - autoplot (fr, chnl) + mylimits p + geom_gate (g) autoplot (fr, chnl SSC-A) + geom_gate (g ) ## ----------------------------------------------------------------------------- g < - openCyto:::。quantileGate (fr,渠道= chnl,聚合氯化铝= 0.99)p < - autoplot (fr, chnl) + mylimits p + geom_gate (g) autoplot (fr, chnl SSC-A) + geom_gate (g ) ## ----------------------------------------------------------------------------- fr < - gh_pop_get_data (gs[[1]],“根”,returnType =“flowFrame”)chnl < - c(“FSC-A”、“SSC-A”)g < - openCyto:::。边界(fr,渠道= chnl min = c (0, 0), max = c (2.5 e5, 2.5 e5)) p < - autoplot (fr, x = chnl [1], y = chnl [2]) p + geom_gate (g ) ## ----------------------------------------------------------------------------- fr < - read.FCS(执行(“extdata / CytoTrol_CytoTrol_1。fcs"， package = "flowWorkspaceData")) chnl <- c("FSC-A"， "FSC-H") g <- openCyto:::。singletGate (fr、通道= chnl) p < - autoplot (fr, x = chnl [1], y = chnl [2]) p + geom_gate (g ) ## ----------------------------------------------------------------------------- fr < - gh_pop_get_data (gs[[1]],“nonDebris returnType =“flowFrame”)chnl < - c(“FSC-A”、“SSC-A”)g < - openCyto::: .flowClust。2 d (fr,渠道= chnl K = 2,目标= c (1 e5、5 e4)分位数= 0.95)p < - autoplot (fr, x = chnl [1], y = chnl [2]) + mylimits p + geom_gate (g ) ## ----------------------------------------------------------------------------- fr < - gh_pop_get_data (gs[[1]],“CD19andCD20 returnType =“flowFrame”)chnl < - c(“CD38”、“CD24”)g < - openCyto::: .flowClust。2 d (fr,渠道= chnl K = 6,过渡= TRUE,目标= c (3.5 e3, 3.5 e3)分位数= 0.95,翻译= 0.15,pp_res = NULL) p < - autoplot (fr, x = chnl [1], y = chnl [2]) + mylimits p + geom_gate (g ) ## ----------------------------------------------------------------------------- gs < load_gs(系统。file("extdata/gs_DC_auto"， package = "flowWorkspaceData")) fr <- gh_pop_get_data(gs[[2]]， "HLADR+"， returnType = "flowFrame") chnl <- c("CD11c"， "CD123") p <- autoplot(fr, chnl[1]， chnl[2]) g <- openCyto:::. quadgate。tmix(fr, channels = chnl, K = 3, usprior = "no") p + geom_gate(g)