figure_2_c_dorsal_example.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_2_c_dorsal_example_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 2C: Dorsal ChIP-nexus and ChIP-seq at dpp

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

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

``` {r regions_table, results="asis"}
regions.df <- subset(read.csv("internal_data/example_regions.csv", stringsAsFactors=FALSE), figure == "3")
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"))
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")

for(i in 1:length(dl.gr)) {
  dl.i <- gviz_plot_no_exo(genome="dm3", dl.gr[i], dl.bw, dl.nexus, 
                           title=paste0("Dorsal at dpp"))
  
}

```

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