rotated_image: Plot a rotated and, if required, smoothed interaction matrix.

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

Description

A matrix with the interactions is rotated and cut along the diagonal to form a triangle plot of the interactome. Smoothing is performed utilizing the filter2 convolution filter from the EBImage package.

Usage

rotated_image(img, scaleCol, smooth, smoothing, filterSize, sigma, binSize)

Arguments

img	The symmetric, non-sparse interaction matrix (for feasibility, choose only a limited chromosomal region).
scaleCol	The color scale threshold. All values above the threshold will ne shown in the highest intensity color.
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 number of pixels surrounding the central pixel. (Size of filter mask.) Smoothing is optional.
sigma	In the case of Gaussian smoothing, how large should the sigma of the distribution be?
binSize	Size of bins into which the interaction matrix is binned.

Examples

# myTriangle <- rotated_image(img, scaleCol = 0.02, smoothing = 80, filterSize = 3, binSize = 10000)

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