---
title: "SDY269: Correlating HAI with Flow Cytometry and ELISPOT Results"
author: "Renan Sauteraud"
date: "`r Sys.Date()`"
output:
  html_vignette:
    toc: true
    number_sections: true
vignette: >
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{SDY269: Correlating HAI with Flow Cytometry and ELISPOT Results}
---

```{r knitr-opts, echo = FALSE, message = FALSE, cache = FALSE}
library(knitr)
opts_chunk$set(cache = FALSE, echo = TRUE, message = FALSE, warning = FALSE,
               fig.width = 7, fig.height = 4, dpi = 100, fig.align = "center")
```

```{r netrc_req, echo = FALSE}
# This chunk is only useful for BioConductor checks and shouldn't affect any other setup
if (!any(file.exists("~/.netrc", "~/_netrc"))) {
    labkey.netrc.file <- ImmuneSpaceR:::.get_env_netrc()
    labkey.url.base <- ImmuneSpaceR:::.get_env_url()
}
```



`ImmuneSpaceR` code produces consistent results, regardless of whether it is being executed from a module or UI based report on the server or on a local machine. This vignette reproduces a report available on <a href="https://datatools.immunespace.org/reports/Studies/SDY269/runReport.view?reportId=module%3ASDY269%2Freports%2Fschemas%2Fhai_flow_elispot.Rmd">the ImmuneSpace portal</a> using the same code.



# Summary

This report investigate the association between the number influenza-specific cells measured by ELISPOT measured at day 7 with the number of plasmablast measured by flow cytometry and day 7 and the HAI response measured at day 28 (log-fold day28/day0). It basically reproduces Figure 1 d-e) of <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140559/" target="_BLANK"> Nakaya et al. (2011)</a> published as part of the original study.



# Load ImmuneSpaceR and other libraries

```{r libraries, cache=FALSE}
library(ImmuneSpaceR)
library(ggplot2)
library(data.table)
```



# Connect to the study and get datasets

```{r connection}
study <- CreateConnection("SDY269")
dt_hai <- study$getDataset("hai", reload = TRUE)
dt_fcs <- study$getDataset("fcs_analyzed_result", reload = TRUE)
dt_elispot <- study$getDataset("elispot", reload = TRUE)
```



# Transform data

```{r data-subset}
# Compute max fold change for HAI, and remove time zero
dt_hai <- dt_hai[, hai_response := value_preferred / value_preferred[study_time_collected == 0],
                 by = "virus,cohort,participant_id"][study_time_collected == 28]
dt_hai <- dt_hai[, list(hai_response = max(hai_response)), by = "cohort,participant_id"]

# Define variable for ELISPOT, keep only the IgG class
dt_elispot <- dt_elispot[, elispot_response := spot_number_reported + 1][study_time_collected == 7 & analyte == "IgG"]

# Compute % plasmablasts
dt_fcs <- dt_fcs[, fcs_response := (as.double(population_cell_number) + 1) /
                   as.double(base_parent_population)][study_time_collected == 7]
```



# Merge data and phenodata

```{r merging}
# Let's key the different datasets
setkeyv(dt_hai, c("participant_id"))
setkeyv(dt_fcs, c("participant_id"))
setkeyv(dt_elispot, c("participant_id"))
dt_all <- dt_hai[dt_fcs, nomatch = 0][dt_elispot, nomatch = 0]
```

The figure below shows the absolute number of plasmablast cells measured by flow cytometry vs. the number of frequency of influenza-specific cells measured by ELISPOT.

```{r plot1, dev='png'}
ggplot(dt_all, aes(x = as.double(fcs_response), y = elispot_response, color = cohort)) +
  geom_point() + 
  scale_y_log10() + 
  scale_x_log10() + 
  geom_smooth(method = "lm") +
  xlab("Total plasmablasts (%)") + 
  ylab("Influenza specific cells\n (per 10^6 PBMCs)") +
  theme_IS()
```

The figure below shows the HAI fold increase over baseline vs. the number of frequency of influenza-specific cells measured by ELISPOT.

```{r plot2, dev='png'}
ggplot(dt_all, aes(x = as.double(hai_response), y = elispot_response, color = cohort)) +
  geom_point() + 
  scale_x_continuous(trans = "log2") + 
  scale_y_log10() +
  geom_smooth(method = "lm") + 
  xlab("HAI fold") +
  ylab("Influenza specific cells\n (per 10^6 PBMCs)") + 
  theme_IS()
```

In each case, we observe good correlations between the different responses, at least for the TIV cohort.