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chipnexus_single_enhancer_example.Rmd
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chipnexus_single_enhancer_example.Rmd
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``` {r setup, echo=FALSE, message=FALSE, include=FALSE, error=FALSE}
library(GenomicRanges, warn.conflicts=F)
library(magrittr)
library(parallel)
library(ggplot2)
library(Gviz)
library(BSgenome.Dmelanogaster.UCSC.dm6)
library(TxDb.Dmelanogaster.UCSC.dm6.ensGene)
setwd("/papagianni_PNAS_2017/analysis/")
options(knitr.figure_dir = "chipnexus_single_enhancer_example")
source("shared_code/knitr_common.r")
source("shared_code/granges_common.r")
source("shared_code/ggplot_common.r")
source("shared_code/metapeak_common.r")
source("shared_code/sample_common.r")
```
# ChIP-nexus single enhancer example
**Author:** [Wanqing Shao](mailto:[email protected])
**Generated:** `r format(Sys.time(), "%a %b %d %Y, %I:%M %p")`
ChIP-nexus single gene example. Both zoomed in and zoomed out version will be included.
```{r single_gene_zoomed, fig.height=8}
enhancer <- read.csv("region_of_interests.csv", header= T, stringsAsFactors = F)
enhancer_gr <- makeGRangesFromDataFrame(enhancer, keep.extra.columns = T)
enhancer_zoomed <- enhancer_gr[enhancer_gr$type == "zoomed"]
enhancer_whole <- enhancer_gr[enhancer_gr$type == "whole"]
motif_gr_list <- list(dl_2mm = readRDS("rdata/dl_motif_GGRWWTTCC_2_mm_cl.rds")$gr,
cic_0mm = readRDS("rdata/cic_motif_TSAATGAA_no_mm_cl.rds")$gr,
cic_1mm = readRDS("rdata/cic_motif_TSAATGAA_1_mm_only_cl.rds")$gr)
samples <- list(tl_dl = load_bigwig("tl_dl_nexus"),
tl_cic = load_bigwig("tl_cic_nexus"),
gd_cic = load_bigwig("gd_cic_nexus"))
build_nexus_track <- function(data, name, chr, start, end, ylim, pos_col, neg_col){
data_track <- DataTrack(data=data,
start=start:end, width=0,
chromosome=chr,
genome="dm6",
name=name,
type="histogram",
groups=c("pos", "neg"),
ylim=c(-ylim, ylim),
legend=FALSE,
col=c(pos_col, neg_col),
col.histogram ="transparent",
background.title = "white")
data_track
}
build_gene_track <- function(chr, start, end){
gtrack <- GeneRegionTrack(range=TxDb.Dmelanogaster.UCSC.dm6.ensGene,
genome="dm6",
chromosome=chr,
name="Genes",
showId=TRUE,
geneSymbol=TRUE,
fill="gray60",
background.title = "white",
start=start, end=end,
collapseTranscripts=FALSE)
gtrack
}
build_motif_track <- function(motif_gr,chr, start, end, name, col){
motif_gr <- motif_gr[seqnames(motif_gr) == chr &
start(motif_gr) >= start - 10 &
end(motif_gr) <= end + 10 ]
motif_track <- GeneRegionTrack(range=motif_gr,
genome="dm6",
chromosome=chr,
start = start, end = end,
name=name,
fill=col,
col=col, col.grid=col,
background.title = "white",
collapseTranscripts=FALSE)
}
cic_nexus_col <- rev(c("#c6331d", "#D05947"))
dl_nexus_col <- rev(c("#27679C", "#3C76A5"))
motif_colors <- c(dl_1mm = "#276599",
cic_0mm = "#D02309",
cic_1mm = "#F98978")
build_track_plot<- function(region.gr, nexus_sample_list, motif_list = NULL) {
r_chr <- as.character(seqnames(region.gr))
r_start <- start(region.gr)
r_end <- end(region.gr)
gtrack <- build_gene_track(r_chr, r_start, r_end)
nexus_data <- mclapply(nexus_sample_list, function(x){
exo_matrix <- exo_metapeak_matrix(resize(region.gr, 1, "start"), x, upstream=0, downstream = width(region.gr))
exo_matrix_t <- rbind(exo_matrix$pos,-1 * exo_matrix$neg)
exo_matrix_t}, mc.cores =1)
dl_ylim <- max(abs(nexus_data$tl_dl))
cic_ylim <- c(nexus_data$tl_cic, nexus_data$tl_cic) %>% abs %>% max
nexus_track_list <- mapply(build_nexus_track,
nexus_data, c("dl Toll10b", "cic Toll10b", "cic gd7"),
list(r_chr), list(r_start), list(r_end),
list(dl_ylim,cic_ylim,cic_ylim ),
c(dl_nexus_col[1], cic_nexus_col[1], cic_nexus_col[1]),
c(dl_nexus_col[2], cic_nexus_col[2], cic_nexus_col[2]))
genometrack <- GenomeAxisTrack(range =region.gr )
tlist <- c(list(genometrack), nexus_track_list, list(gtrack))
if(!is.null(motif_list)){
motif_track_list <- mapply(build_motif_track,
motif_list,
list(r_chr), list(r_start),list(r_end),
c("dl motif", "cic motif no mm", "cic motif 1 mm"),
motif_colors)
tlist <- c(list(genometrack), nexus_track_list, motif_track_list, list(gtrack))
}
tlist
}
plot_tracks <- function(tlist, region.gr, name, zoomed =F){
r_chr <- as.character(seqnames(region.gr))
r_start <- start(region.gr)
r_end <- end(region.gr)
if(zoomed){
tsizes <- c(0.2,rep(0.4, 3), rep(0.1, 3), 0.2)
x <- plotTracks(tlist, chromosome=r_chr, from=r_start,to=r_end, sizes = tsizes,
cex.title=0.8, cex.axis=0.8, col.title="black", col.axis="black",
fontcolor.legend="black", cex.legend=0.8, main = name, rotation.title = 0)
}else{
tsizes <- c(0.2, rep(0.4, 3), 0.2)
x <- plotTracks(tlist, chromosome=r_chr, from=r_start,to=r_end, sizes = tsizes,
cex.title=0.8, cex.axis=0.8, col.title="black", col.axis="black",
fontcolor.legend="black", cex.legend=0.8, main = name, rotation.title = 0)
}
}
zoomed_view_tlist <- cache("zoomed_view", function(){
lapply(enhancer_zoomed, function(x)build_track_plot(x, samples, motif_gr_list))
})
names(zoomed_view_tlist) <- enhancer_zoomed$region_name
nothing <- lapply(names(zoomed_view_tlist), function(x)plot_tracks(zoomed_view_tlist[[x]], enhancer_zoomed[enhancer_zoomed$region_name == x], paste(x, "zoomed"), T))
```
```{r single_gene_whole, fig.height=6}
whole_view_tlist <- cache("whole_view", function(){
lapply(enhancer_whole, function(x)build_track_plot(x, samples))
})
names(whole_view_tlist) <- enhancer_whole$region_name
nothing <- lapply(names(whole_view_tlist), function(x)plot_tracks(whole_view_tlist[[x]], enhancer_whole[enhancer_whole$region_name == x], x))
```
```{r echo= F}
sessionInfo()
```