circleplot: Generate circos plots from overlap data output

In mworkman13/HiCAGE: Hi-C Annotation and Graphics Ensemble

Description

Generate circos plots from overlap data output

Usage

circleplot(datatable, plot.subset = FALSE, display.legend = TRUE,
  hic.legend = "Avg. Hi-C Score", hic.range = c(0, 130),
  rna.legend = "Avg. log(FPKM)", rna.range = c(0, 3.2),
  circos.color = NULL, ...)

Arguments

datatable	The GRanges datatable generated by overlap function
plot.subset	Allows for plotting interactions with Hi-C scores only. Set to TRUE if no RNAseq or gene expression file was used to generate the overlap output.
display.legend	Adds legend to circos plot
hic.legend	Title for Hi-C legend
hic.range	A vector representing the low and high values for the legend of Hi-C values
rna.legend	Title for RNA legend
rna.range	A vector representing the low and high values for the legend of RNA values
circos.color	Passes colors to chord diagram for each group
...	Addtional arguments passed to chordDiagram function

Value

Generates a chord diagram containing circluar tracks with an inner track displaying average Hi-C interaction score and an inner track with displaying average RNA-seq log(FPKM) values for each segment in the plot

Examples

hic_chr20 <- system.file("extdata", "hic_chr20.txt", package = "HiCAGE")
segment_chr20 <- system.file("extdata", "segment_chr20.bed",
    package = "HiCAGE")
rna_chr20 <- system.file("extdata", "rna_chr20.tsv", package = "HiCAGE")
example <- overlap(hicfile = hic_chr20,
         segmentfile = segment_chr20,
         rnafile = rna_chr20,
         rna.columns = c(1, 7))
circleplot(example)

mworkman13/HiCAGE documentation built on May 23, 2019, 11:58 a.m.