figure_1_example_regions.Rmd

``` {r setup, echo=FALSE, message=FALSE, include=FALSE, error=FALSE}
library(xtable)
library(Gviz)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
library(BSgenome.Dmelanogaster.UCSC.dm3)
library(rtracklayer)

options(knitr.figure_dir = "figure_1_example_regions_output")

source("shared_code/knitr_common.r")
source("shared_code/samples.r")
source("shared_code/granges_common.r")
source("shared_code/gviz_common.r")
```

# Figure 1: TBP, Dorsal and Twist examples

``` {r header_child, child="child_docs/header_child.Rmd"}
```

## Overview

Examples of TBP, Dorsal and Twist binding at single regions

``` {r load_standard_chip_data, include=FALSE}
dl.bw <- data_path("bigwigs/dmel_embryo_dl_chipseq_01.bw")
tbp.bw <- data_path("bigwigs/hsap_k562_tbp_chipseq_01.bw")
twi.bw <- data_path("bigwigs/dmel_embryo_twi_chipseq_01.bw")
```

``` {r ebox_motifs, include=FALSE}
ebox.gr <- cache("ebox.gr.rds", function() {
  ebox.gr <- vmatchPattern("CANNTG", Dmelanogaster, max.mismatch=0, fixed=FALSE)
  ebox.gr <- ebox.gr[strand(ebox.gr) == "+"]
  mcols(ebox.gr)$feature <- "EBOX"
  mcols(ebox.gr)$id <- substr(as.character(getSeq(Dmelanogaster, ebox.gr)), 3, 4)
  ebox.gr
})

dl_motifs.gr <- cache("dl_motifs.gr.rds", function() {
  dl.motifs <- c("GGGAAAAACAC", 
                 "CGGAATTTCCT",
                 "GGGAAATTCCC",
                 "GGGAAAAGCCCA")
  dl.gr <- do.call(c, lapply(dl.motifs, vmatchPattern, Dmelanogaster, max.mismatch=0, fixed=TRUE))
  strand(dl.gr) <- "*"
  dl.gr <- reduce(dl.gr)
  mcols(dl.gr)$feature <- "dl_motif"
  mcols(dl.gr)$id <- "dl_motif"
  dl.gr
})
 
```

``` {r regions_table, results="asis"}
regions.df <- subset(read.csv("internal_data/example_regions.csv", stringsAsFactors=FALSE), figure == "2")
regions.gr <- with(regions.df, GRanges(ranges=IRanges(start=start, end=end),
                               seqnames=chr, name=name, factor=factor))

regions.df <- subset(regions.df, factor %in% c("dl", "tbp", "twi"))
html_table(regions.df)
```

``` {r set_common_figure_options, include=FALSE}
knitr::opts_chunk$set(dev=c("png", "pdf"), fig.cap="", fig.width=9, fig.height=9)
```

## Dorsal (embryos)

``` {r dl_examples}

dl.gr <- subset(regions.gr, factor == "dl")

dl.nexus <- get_sample_cl("dmel_embryo_dl_chipnexus_01")
dl.exo   <- get_sample_cl("dmel_embryo_dl_chipexo_01")
dl.exo$gr <- c(dl.exo$gr, get_sample_cl("dmel_embryo_dl_chipexo_02")$gr)
dl.exo$pos <- dl.exo$pos + get_sample_cl("dmel_embryo_dl_chipexo_02")$pos
dl.exo$neg <- dl.exo$neg + get_sample_cl("dmel_embryo_dl_chipexo_02")$neg

for(i in 1:length(dl.gr)) {
  dl.i <- gviz_plot_with_exo(genome="dm3", dl.gr[i], dl.bw, dl.nexus, dl.exo, 
                    title=paste0("(no normalization) Dorsal: ", mcols(dl.gr)$name[i]),
                    motifs=dl_motifs.gr)

  dl.i <- gviz_plot_no_exo(genome="dm3", dl.gr[i], dl.bw, dl.nexus, 
                           title=paste0("Dorsal nexus only: ", mcols(dl.gr)$name[i]))
  
}

```

## Twist (embryos)

``` {r twi_examples}

twi.gr <- subset(regions.gr, factor == "twi")

twi.nexus <- get_sample_cl("dmel_embryo_twi_chipnexus_01")
twi.exo   <- get_sample_cl("dmel_embryo_twi_chipexo_01")

for(i in 1:length(twi.gr)) {
  twi.i <- gviz_plot_with_exo(genome="dm3", twi.gr[i], twi.bw, twi.nexus, twi.exo, 
                           title=paste0("(no normalization) Twist: ", mcols(twi.gr)$name[i]),
                           motifs=ebox.gr)
}
```

## TBP (human)

``` {r tbp_examples}

tbp.gr <- subset(regions.gr, factor == "tbp")

tbp.nexus <- get_sample_cl("hsap_k562_tbp_chipnexus_01")
tbp.exo   <- get_sample_cl("hsap_k562_tbp_chipexo_02")

for(i in 1:length(tbp.gr)) {
  tbp.i <- gviz_plot_with_exo(genome="hg19", tbp.gr[i], tbp.bw, tbp.nexus, tbp.exo, 
                                 title=paste0("(downscale ChIP-exo) TBP: ", mcols(tbp.gr)$name[i]),
                                 normalization_method="downscale_exo")

  #tbp.i <- gviz_plot_with_exo(genome="hg19", tbp.gr[i], tbp.bw, tbp.nexus, tbp.exo,
  #                               title=paste0("(zoomed, no normalization) TBP: ", mcols(tbp.gr)$name[i]),
  #                               zoom_to_nexus_scale=TRUE)
}
```

``` {r session_info_child, child="child_docs/session_info_child.Rmd"}
```