visualize_chrom: Triangle visualization of Hi-C data with tracks for chipseq,...

In AnnikaGable/chromium: Analyze and visualize high throughput chromatin interaction data, such as Hi-C or ChIA-PET

Description

An interaction matrix is plotted, rotated, and if required, smoothed. Using Gviz, tracks can be added as required.

Usage

visualize_chrom(Iset, chr, from = NULL, to = NULL, geneModels = NULL,
  printTranscripts = TRUE, outDir = getwd(),
  name = "triangle_visualization.pdf", scaleCol = 0.02, chipseqs = NULL,
  chipScale = NULL, colmapChipseqs = NULL, customAnno = NULL,
  smooth = "none", smoothing = NULL, filterSize = NULL, sigma = NULL)

Arguments

Iset	An interactionSet object, with the bin size stored as metadata under the name "binSize"
chr	The chromosome name to be plotted with or without "chr", depending on your interactionSet object.
from	Start of the region you want to plot.
to	End of the region you want to plot.
geneModels	This can either be a character identifying a genome or an a gene model object compatible with the range argument GeneRegionTrack. If it is a character and is one of "mm9", "mm10", "hg19", or "hg38" a pre-build gene model table is loaded. If it is a valid ENSEMBL organism identifier (mmusculus, hsapiens ...), the respective gene model is obtained from ensembl biomart directly.
printTranscripts	Boolean. Produce gene model track? Defaults to TRUE.
outDir	Give the directory where the PDF plot will be saved. Defaults to the working directory.
name	A string. Filename of the output PDF.
scaleCol	The color scale threshold. All values above the threshold will ne shown in the highest intensity color.
chipseqs	A named list of GRanges objects with ChIP-seq scores in the metadata column "score". Optional.
chipScale	A named list corresponding to chipseqs with a vector containing the highest and lowest score for each list element. Defaults to taking the non-zero 99% quantile (rounded to the nearest ten) as the maximum and -0.5 as the minimum value.
colmapChipseqs	A named character vector corresponding to chipseqs with a color name for each chipseq. Defaults to a vector of twelve colors. For a larger number of chipseq tracks, please define colmapChipseqs.
customAnno	A custom annotation, given as a list of BED dataframes. Optional.
smooth	Which smoothing type should be applied? Options are: "none", "box", and "gaussian".
smoothing	Smoothing parameter. The percentage of signal to be taken from the surrounding pixels. Smoothing is optional.
filterSize	Smoothing parameter. The dimension of filter mask, e.g. filterSize = 3 means 3x3 filter. Smoothing is optional.
sigma	In the case of Gaussian smoothing, how large should the sigma of the distribution be?

Value

Output will be in PDF format.

Examples

# visualize_chrom(Iset, chr = "11", from = 30000000, to = 30100000,
          gen = "mm9", customAnno = cpgIslands, smoothing = 80, filterSize = 3)

AnnikaGable/chromium documentation built on May 5, 2019, 6:04 a.m.