plotHiC: Plot HiC samples
In aryeelab/sparseHiC: Efficient compression and analysis of Hi-C Data

plotHiC prints a base R image of the region specified for the sparseHiCdata supplied.

plotHiC(x, y, res, libraryNorm = FALSE, log2trans = TRUE, quantiles = c(5,
  95), color = getHiCcolor(16), missingco = "min", showLegend = TRUE,
  organism = "h", showGenes = FALSE)

## S4 method for signature 'ANY'
plotHiC(x, y, res, libraryNorm = TRUE, log2trans = TRUE,
  quantiles = c(5, 95), color = getHiCcolor(16), missingco = "min",
  showLegend = TRUE, organism = "h", showGenes = FALSE)

`x`	A sparseHiCdata object with samples to be visualized
`y`	A GRanges object containing region of interest
`res`	The resolution to be plotted
`libraryNorm`	= FALSE When plotting multiple samples, normalize for library complexity?
`log2trans`	= TRUE log2transform the HiC data?
`quantiles`	= c(5, 95). A vector of length 2 OR the boolean FALSE. Every value below the first element of the vector (e.g. less than the 5th percentile) will be plotted as the minimum and everything bigger than the second element of the vector (e.g. greater than the 95th percentile) will be plotted as the maximum.
`color`	A colorRamp defined by the getHiCcolor function. Default is 13 from the getHiCcolor function
`missingco`	= "min" By default, missing pixels are plotted with the minimum color, but users can specify other color options so long as they exist in base R (e.g. 'red', 'black', etc.)
`showLegend`	= TRUE display legend on plots?
`organism`	= 'h'; 'h' for human or 'm' for mouse supported for viewing the gene annotation. Only matters if showGenes is TRUE
`showGenes`	= FALSE; show gene annotation at bottom panel.

library(GenomicRanges)
region <- GRanges(seqnames=c("22"),ranges=IRanges(start=c(0),end=c(9000000)))
rdsA<-paste(system.file('rds',package='sparseHiC'),'hESCdata.rds',sep='/')
hESCdata <- readRDS(rdsA)
region <- GRanges(seqnames=c("chr21"),ranges=IRanges(start=c(23000000),end=c(40000000)))
res <- "1000000"
a <- plotHiC(hESCdata, region, res, showGenes = FALSE)