## ----knitr-opts, echo = FALSE, message = FALSE, cache = FALSE------------
library(knitr)
opts_chunk$set(cache=FALSE, echo=TRUE, message=FALSE, warning=FALSE,
               fig.width=10, fig.height=14, dpi=100, fig.align="center")

## ----netrc_req, echo = FALSE---------------------------------------------
# This chunk is only useful for BioConductor checks and shouldn't affect any other setup
ISR_login <- Sys.getenv("ISR_login")
ISR_pwd <- Sys.getenv("ISR_pwd")
if(ISR_login != ""  &  ISR_pwd != ""){
  netrc_file <- tempfile("ImmuneSpaceR_tmp_netrc")
  netrc_string <- paste("machine www.immunespace.org login", ISR_login, "password", ISR_pwd)
  write(x = netrc_string, file = netrc_file)
  labkey.netrc.file <- netrc_file
}

## ----libraries, cache=FALSE----------------------------------------------
library(ImmuneSpaceR)
library(ggplot2)
library(data.table)

## ----connection----------------------------------------------------------
study <- CreateConnection(c("SDY180"))
dt_fcs <- study$getDataset("fcs_analyzed_result", reload=TRUE)

## ----data-subset---------------------------------------------------------
dt_fcs19 <- dt_fcs[population_name_reported%like%"Plasma"]
dt_fcs19 <- dt_fcs19[,cohort:=gsub("Study g", "G", cohort),]

## ----data-summary--------------------------------------------------------
dt_fcs19_median <- dt_fcs19[, .(median_cell_reported = median(as.double(population_cell_number) + 1,
                   na.rm=TRUE)), by = .(cohort,study_time_collected,population_name_reported)]

## ---- dev='png'----------------------------------------------------------
ggplot(dt_fcs19, aes(x = as.factor(study_time_collected), y = as.double(population_cell_number) + 1)) +
  geom_boxplot() + geom_jitter() + scale_y_log10() + facet_grid(cohort~population_name_reported, 
  scale = "free") + xlab("Time") + ylab(expression(paste("Number of cells/", mu, "l"))) + 
  geom_line(data = dt_fcs19_median, aes(x = as.factor(study_time_collected), y = as.double(median_cell_reported),
  group = 1), color = "black", size = 1.2) + labs(title = "Plasma cell abundance after vaccination") + theme_IS()