plotMatrix: Plotting a contact matrix

In js2264/cooleR: Analysing cool files in R with HiContacts

Plotting a contact matrix

Description

Plotting a contact matrix

Usage

plotMatrix(x, ...)

montage(x, ...)

## S4 method for signature 'HiCExperiment'
plotMatrix(
  x,
  compare.to = NULL,
  use.scores = "balanced",
  scale = "log10",
  maxDistance = NULL,
  loops = NULL,
  borders = NULL,
  tracks = NULL,
  limits = NULL,
  dpi = 500,
  rasterize = TRUE,
  symmetrical = TRUE,
  chrom_lines = TRUE,
  show_grid = FALSE,
  cmap = NULL,
  caption = TRUE
)

## S4 method for signature 'GInteractions'
plotMatrix(
  x,
  use.scores = NULL,
  scale = "log10",
  maxDistance = NULL,
  loops = NULL,
  borders = NULL,
  tracks = NULL,
  limits = NULL,
  dpi = 500,
  rasterize = TRUE,
  symmetrical = TRUE,
  chrom_lines = TRUE,
  show_grid = FALSE,
  cmap = NULL
)

## S4 method for signature 'matrix'
plotMatrix(
  x,
  scale = "log10",
  limits = NULL,
  dpi = 500,
  rasterize = TRUE,
  cmap = NULL
)

## S4 method for signature 'AggrHiCExperiment'
plotMatrix(
  x,
  use.scores = "balanced",
  scale = "log10",
  maxDistance = NULL,
  loops = NULL,
  borders = NULL,
  limits = NULL,
  dpi = 500,
  rasterize = TRUE,
  chrom_lines = TRUE,
  show_grid = FALSE,
  cmap = NULL,
  caption = TRUE
)

## S4 method for signature 'AggrHiCExperiment'
montage(
  x,
  use.scores = "balanced",
  scale = "log10",
  limits = NULL,
  dpi = 500,
  rasterize = TRUE,
  cmap = NULL
)

Arguments

x	A HiCExperiment object
...	Extra arguments passed to the corresponding method.
compare.to	Compare to a second HiC matrix in the lower left corner
use.scores	Which scores to use in the heatmap
scale	Any of 'log10', 'log2', 'linear', 'exp0.2' (Default: 'log10')
maxDistance	maximum distance. If provided, the heatmap is plotted horizontally
loops	Loops to plot on top of the heatmap, provided as GInteractions
borders	Borders to plot on top of the heatmap, provided as GRanges
tracks	Named list of bigwig tracks imported as Rle
limits	color map limits
dpi	DPI to create the plot (Default: 500)
rasterize	Whether the generated heatmap is rasterized or vectorized (Default: TRUE)
symmetrical	Whether to enforce a symetrical heatmap (Default: TRUE)
chrom_lines	Whether to display separating lines between chromosomes, should any be necessary (Default: TRUE)
show_grid	Whether to display an underlying grid (Default: FALSE)
cmap	Color scale to use. (Default: bgrColors() if limits are c(-1, 1) and coolerColors() otherwise)
caption	Whether to display a caption (Default: TRUE)

Value

ggplot object

Examples

contacts_yeast <- contacts_yeast()
plotMatrix(
    contacts_yeast, 
    use.scores = 'balanced', 
    scale = 'log10', 
    limits = c(-4, -1)
)

js2264/cooleR documentation built on Jan. 29, 2024, 10:47 p.m.