## ---- knitr，回声=假--------------------------------------------1111echo = false ----------------------------------------＃块仅适用于生物导体检查，不应影响任何其他设置ISR_Login < - sys.getenv（“isr_login”）ISR_PWD < - sys.getEnv（ISR_Login！=“”“＆ISR_PWD！=”“）{netrc_file < - tempfile（“免疫缺省函数_tmp_netrc”）netrc_string < - paste（“machine www.immunespace.org登录”，ISR_Login，“密码”，ISR_PWD）Write（x = netrc_string，file = netrc_file）labkey.netrc.file <- netrc_file} ## -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Con < - CreateConnection（“SDY144”）流< - con $ getdataset（“fcs_analyzed_result”）hai < - con $ getdataset（“hai”）vn < - con$ getd.ataset（“neut_ab_titer”）## ----子集---------------------------------------------------------- Pb < - 流量[plation_name_reported％c％c（“等离子体细胞，频率。of，b lym cd27 +“，”plasmablast，freq。 of,Q3: CD19+, CD20-")] pb <- pb[, population_cell_number := as.numeric(population_cell_number)] pb <- pb[study_time_collected == 7 & study_time_collected_unit == "Days"] #13 subjects pb <- pb[, list(participant_id, population_cell_number, population_name_reported)] ## ----FC------------------------------------------------------------------ # HAI hai <- hai[,response:=value_reported/value_reported[study_time_collected==0], by="virus,cohort,participant_id"][study_time_collected==30] hai <- hai[, list(participant_id, virus, response)] dat_hai <- merge(hai, pb, by = "participant_id", allow.cartesian = TRUE) # VN vn <- vn[, response:=value_reported/value_reported[study_time_collected==0], by="virus,cohort,participant_id"][study_time_collected==30] vn <- vn[, list(participant_id, virus, response)] dat_vn <- merge(vn, pb, by = "participant_id", allow.cartesian = TRUE) ## ----HAI, dev='png'------------------------------------------------------ ggplot(dat_hai, aes(x = population_cell_number, y = response)) + geom_point() + geom_smooth(method = "lm") + facet_grid(virus~population_name_reported, scale = "free") + xlab("Number of cells") + ylab("HI fold-increase Day 30 vs. baseline") + theme_IS() ## ----VN, dev='png'------------------------------------------------------- ggplot(dat_vn, aes(x = population_cell_number, y = response)) + geom_point() + geom_smooth(method = "lm") + facet_grid(virus~population_name_reported, scale = "free") + xlab("Number of cells") + ylab("VN fold-increase Day 30 vs. baseline") + theme_IS()