plot_matrix: Plot HiC contact matrix

Description Usage Arguments Examples

View source: R/plot_matrix.R

Description

This function takes a HiC contact matrix and creates heatmap-like prepresentation of it

Usage

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plot_matrix(mat, coord, resolution, transformation = logfinite,
  color = colorRampPalette(c("white", "red"))(100), sym = FALSE,
  trim = 0.01, rotate = FALSE, unit_x_axis = 1e+06,
  label_x_axis = "Genomic Position / Mbp", na.col = "white", ...)

Arguments

mat

HiC contact matrix (it could be the output of get_contacts_matrix)

coord

A vector of size two with the start and end coordinates of the desired region to plot

resolution

Resolution (bin size) in bp

transformation

Transformation to apply to the contacts prior to the heatmap representation

color

Vector of colors

sym

Logical indicating if the color scale should be symmetrical (around 0)

trim

Numeric proportion of the data that should be 'flattened' on both extremes

rotate

Logical indicating if the matrix should be rotated

unit_x_axis

Numeric unit for the X axis

label_x_axis

Character X axis label

na.col

Color to depict NA values

...

Further arguments to be passed to plot

Examples

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plot(0)

qenvio/dryhic documentation built on May 26, 2019, 11:35 a.m.