---

title: "Part 16"

output:

  BiocStyle::html_document

---

```{r, message=FALSE, include=!exists(".standalone"), eval=!exists(".standalone")}

library("BloodCancerMultiOmics2017")

library("ggplot2")

library("dplyr")

library("gridExtra")

```

```{r echo=FALSE}

plotDir = ifelse(exists(".standalone"), "", "part16/")

if(plotDir!="") if(!file.exists(plotDir)) dir.create(plotDir)

```

# Response to cytokines in CLL

In order to find out whether the cytokines have pro-survival effect on patient cells the drug sreen was performed.

`r length(unique(cytokineViab$Patient))` patient samples were exposed to 6 different cytokines. The viability of the treated cells were normalized by untreated controls.

Load the drug response dataset.

```{r}

data("cytokineViab")

```

Plot the drug response curves.

```{r cytokinesC0, fig.width=8, fig.height=6, warning=FALSE, fig.path=plotDir, dev=c("png", "pdf")}

cond <- c("IL-2", "IL-4", "IL-10", "IL-21", "LPS", "IgM")

for (i in cond){  

  plot = ggplot(

    filter(cytokineViab, Duplicate%in%c("1"), Stimulation==i, Timepoint=="48h"),

    aes(x=as.factor(Cytokine_Concentration2), y=Normalized_DMSO, colour=mtor,

        group=interaction(Patient))) +

    ylab("viability") + xlab("c(stimulation)") + ylim(c(0.8, 1.4)) +

    geom_line() + geom_point() + ggtitle(i) + theme_bw() + guides(color="none")

    assign(paste0("p",i), plot)

}

grid.arrange(`pIL-2`,`pIL-10`,`pIL-4`,`pIL-21`,pLPS, pIgM, nrow=2)

```

IL-10 had a pro-survival effect on the majority of samples, but not on those in the mTOR group.

IL-4 and IL-21 had pro-survival effects on most samples, including the mTOR group.

```{r, include=!exists(".standalone"), eval=!exists(".standalone")}

sessionInfo()

```

```{r, message=FALSE, warning=FALSE, include=FALSE}

rm(list=ls())

```