plot_matrix: Plot HiC contact matrix

In qenvio/dryhic: Some Functions to Handle HiC Data

Description

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

Usage

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

plot(0)

qenvio/dryhic documentation built on March 17, 2020, 8:37 p.m.