FigureS12_expression_quantification.Rmd

---
title: "Figure S12 Reporter-ChIP-nexus expression quantification"
author: "Wanqing Shao(was@stowers.org) "
output:
  pdf_document:
    toc: yes
header-includes:
- \usepackage{fancyhdr}
- \usepackage{lipsum}
- \pagestyle{fancy}
- \fancypagestyle{plain}{\pagestyle{fancy}}
---

# Enviroment setup

``` {r setup, message=FALSE, error=FALSE}
library(GenomicRanges, warn.conflicts=F)
library(magrittr)
library(Rmisc)
library(reshape2)

setwd("/data/analysis_code")
options(knitr.figure_dir = 
          "FigureS12_expression_quantification")

source("shared_code/knitr_common.r")
source("shared_code/ggplot_common.r")
source("shared_code/granges_common.r")
source("shared_code/metapeak_common.r")
```

# Analysis

```{r, fig.height= 5, fig.width=7}
expression <- read.csv("expression_quantification.csv")

prepare_expression_df <- function(genes){
  downstream_exp <- subset(expression, gene %in% genes) %>% 
    melt(., id.vars = "gene", na.rm = T)
  summary <- summarySE(downstream_exp, measurevar="value", groupvars="gene")
  summary$gene <- factor(summary$gene, levels = genes)
  summary
}

downstream <- c("pepck", "act5c", "pepck-pk", "pepck-dve", "act5c-pk")
tata <- c("pk", "comm2", "dve", 
          "act5c_up_pk", "act5c_up_comm2", "act5c_up_dve",
          "tata_pk", "tata_comm2", "tata_dve")
inr <- c("dve", "act5c_up_dve", "act5c_dve_down", "dve_act5c_inr")
inr_2 <- c("dve", "pk", "scp", "dve-inr-T", "dve-inr-A", "pk-inr-T", "scp-inr-T")

sample_list <- list(downstream = downstream,tata=tata, inr= inr, inr2= inr_2)

expression_df <- lapply(sample_list, prepare_expression_df)

plotting_expression <- function(exp_df){
  x <- ggplot(exp_df, aes(x=gene, y=value)) + 
        geom_bar(stat= "identity", position = "dodge", 
                fill =  "#EBBD77") + 
        geom_errorbar(aes(ymin=value-se, ymax=value+se), 
                     width=.1, position=position_dodge(.9)) +
        ylab("Normalized signal") +
        xlab("")+ 
        ggtitle("Expression")+
        geom_hline(yintercept = 1, lty = 4) +
        theme(axis.text.x = element_text(size=14, angle = 60, hjust = 1)) 
  print(x)
}

nothing <- lapply(expression_df, plotting_expression)
```

# Session Info

This analysis was performed with the following R/Bioconductor session:

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