In RGLab/ImmPortR: An R wrapper Around the ImmPort API

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.height = 12,
  dpi = 100,
  fig.align = "center"
)

Summary

This report investigate the abundance of plasmablast (and other B cell subsets) over time after vaccination with Pneumovax, Fluzone, or no vaccination (saline control group). It can be seen on the figure below that the plasmablast subset peaks at day 7 in both vaccine groups, with a stronger and more durable response with Pneumovax. As expected, there is no clear peak in the saline group. These results are similar to those reported in Figure 6B of Obermoser et al. (2013) published as part of the original study. This vignette reproduces a report available on the ImmuneSpace portal using ImmPortR.

Load ImmPortR and other libraries

library(ImmPortR)
library(ggplot2)
library(dplyr)

Reterieve the flow cytometry analyzed results

fcsAnalyzed <- query_dataset("SDY180", "fcsAnalyzed")

Subset the population of interest

fcsAnalyzed <- fcsAnalyzed %>% 
  filter(grepl("Plasma", populationNameReported)) %>% 
  mutate(
    cohort = gsub("Study g", "G", armName),
    populationStatisticReported = as.double(populationStatisticReported),
    studyTimeCollected = as.factor(studyTimeCollected),
    populationStatisticReported = as.double(populationStatisticReported)
  )

Compute the median

fcsAnalyzedMedian <- fcsAnalyzed %>% 
  group_by(cohort, studyTimeCollected, populationNameReported) %>% 
  summarise(medianCellReported = median(populationStatisticReported + 1, na.rm = TRUE))

Abundance of plasmablasts measured by multi-parameter flow cytometry

ggplot(fcsAnalyzed, aes(x = studyTimeCollected, y = populationStatisticReported + 1)) +
  geom_boxplot() +
  geom_jitter() +
  scale_y_log10() +
  facet_grid(cohort ~ populationNameReported, scale = "free") +
  xlab("Time") +
  ylab(expression(paste("Number of cells/", mu, "l"))) +
  geom_line(data = fcsAnalyzedMedian, aes(
    x = studyTimeCollected, y = medianCellReported,
    group = 1
  ), color = "black", size = 1.2) +
  labs(title = "Plasma cell abundance after vaccination")