Afatinib_targets.Rmd

---
title: "Afatinib targets"
author: "Britta Velten"
date: "15 April 2020"
output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 3
params: 
    today: 200415
---

Investigate RNAseq data for potential Afatinib targets.
```{r}
library(BloodCancerMultiOmics2017)
library(DESeq2)
library(reshape2)
library(tidyverse)
```

```{r}
outdir <- "out"
today <- params$today
figdir = paste0("figs", today, "/figuresAfatinib/")
if(!dir.exists(figdir)) dir.create(figdir)
knitr::opts_chunk$set(dev = c("png", "pdf"), fig.path = figdir)
```


```{r}
load(file.path(outdir, paste0("OmicsData",today,".RData")))
vst <- varianceStabilizingTransformation(eData)
pot_targets <- c("EGFR", "ERBB2", "ERBB3", "ERBB4", "GAK", "BLK",
                 "IRAK1", "EPHA6", "HIPK4", "PHKG2", "MAPK9",
                 "MAPK14", "ABCG2") # list by Sascha
rownames(vst) <- rowData(eData)$symbol
colnames(vst) <- colData(eData)$PatID
target_expr <- vst[pot_targets]
target_expr <- assay(target_expr) 
target_expr <- melt(t(target_expr), varnames = c("PatID", "gene"))
```

```{r expr_Afatinibtargets}
ggplot(target_expr, aes(x= gene, y= value)) +
    ggbeeswarm::geom_beeswarm(cex=0.15, size=1, col = "black", alpha =0.7)  +
    geom_violin(fill = "forestgreen", alpha =0.4)+
    # geom_boxplot()+
    ylab("Normalized gene expression") +
    theme_bw(base_size = 16) +
    theme(axis.text.x = element_text(angle=60, hjust=1, vjust=1))
```

```{r}
sessionInfo()
```