Plotting a contact matrix

plotMatrix(x, ...)

montage(x, ...)

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

# S4 method for class '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 class '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()
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
plotMatrix(
    contacts_yeast, 
    use.scores = 'balanced', 
    scale = 'log10', 
    limits = c(-4, -1)
)