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

Description Usage Arguments Examples

View source: R/visualization.R

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

1
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

1
# myTriangle <- rotated_image(img, scaleCol = 0.02, smoothing = 80, filterSize = 3, binSize = 10000)

AnnikaGable/chromium documentation built on July 12, 2018, 4 p.m.