track_hic_matrix {rGenomeTracks}R Documentation

Generate HiC track

Description

Create a genome_track for matrix files. Currently, only cool format and h5 format.

Usage

track_hic_matrix(
  file,
  title = NULL,
  height = NULL,
  overlay_previous = "no",
  orientation = NULL,
  max_value = NULL,
  min_value = NULL,
  transform = "no",
  rasterize = TRUE,
  colormap = "RdYlBu_r",
  depth = 100000,
  show_masked_bins = FALSE,
  scale_factor = 1
)

Arguments

file

String. The location of the track file

title

String. If specificed, the title of the track to be displayed.

height

Numeric. The height of the plotted track in cm. Default is 2. See notes.

overlay_previous

String. Options are "no" (default) or "yes" or "share-y".

orientation

String. Set to "inverted" to make the track upside down. Default is NULL.

max_value

Numeric. Default is NULL. The max value cut-off for the numeric column.

min_value

Numeric. Default is NULL. The max value cut-off for the numeric column.

transform

String to indicate type of transformation applied. Default is "no".

rasterize

Boolean. Default is FALSE.

colormap

String with matplotlib-compatible colormap. Default is set to "viridis".

depth

Numeric value above 1 to indicate the maximum distance that should be plotted. Default is 100000.

show_masked_bins

Boolean. If TRUE, showing masked bins as white lines. Default is FALSE.

scale_factor

Numeric factor by which matrix is to be scaled.

Details

This function expect cool or h5 format. Format converter like hicConvertFormat can help converting to supported formats. depth is the maximum distance that should be plotted. If it is more than 125% of the plotted region, it will be adjsted to this maximum value. colormap argument should be compatible with matplotlib. show_masked_bins plots bins not used during the corrections as white lines. Setting this argument to FALSE (default) extends neighboring bins to obtain an aesthetically pleasant output. scale argument scales the matrix by specific factor. This is useful if plotting multiple hic-matrices to be on the same scale.

Value

genom_track

Author(s)

Omar Elashkar

Examples

## Not run: 
# Get example data directories
# Download h5 example
ah <- AnnotationHub()
query(ah, "rGenomeTracksData")
h5_dir <- ah[["AH95901"]]
tads_dir <- system.file("extdata", "tad_classification.bed",
  package = "rGenomeTracks"
)
arcs_dir <- system.file("extdata", "links2.links", package = "rGenomeTracks")
bw_dir <- system.file("extdata", "bigwig2_X_2.5e6_3.5e6.bw", package = "rGenomeTracks")
#
# Create HiC track from HiC matrix
h5 <- track_hic_matrix(
  file = h5_dir, depth = 250000, min_value = 5, max_value = 200,
  transform = "log1p", show_masked_bins = FALSE
)

# Create TADS track
tads <- track_domains(
  file = tads_dir, border_color = "black",
  color = "none", height = 5,
  line_width = 5,
  show_data_range = FALSE,
  overlay_previous = "share-y"
)

# Create arcs track
arcs <- track_links(
  file = arcs_dir, links_type = "triangles", line_style = "dashed",
  overlay_previous = "share-y",
  color = "darkred",
  line_width = 3,
  show_data_range = FALSE
)

# Create bigwig track
bw <- track_bigwig(
  file = bw_dir, color = "red",
  max_value = 50,
  min_value = 0,
  height = 4,
  overlay_previous = "yes",
  show_data_range = FALSE
)

# Create one object from HiC, arcs and bigwid
tracks <- h5 + arcs + bw

# Plot the tracks
plot_gtracks(tracks, chr = "X", start = 25 * 10^5, end = 31 * 10^5)
# Plot HiC, TADS and bigwig tracks
plot_gtracks(h5 + tads + bw, chr = "X", start = 25 * 10^5, end = 31 * 10^5)

## End(Not run)

[Package rGenomeTracks version 0.99.8 Index]