track_epilogos {rGenomeTracks}R Documentation

Generate epilogos track

Description

Generate epilogos genome_track from qcat file.

Usage

track_epilogos(
  file,
  title = NULL,
  height = 2,
  overlay_previous = "no",
  categories_file = NULL,
  orientation = NULL
)

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".

categories_file

Optionally pass a string of JSON custom colors configuration file directory. Default is NULL.

orientation

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

Details

Epilogos is used widely to represent multiple "states" across genome, like ChromHMM states. More details here qcat file is needed which can be generated using epilogos track_epiolog can optionally take categories_file parameter which specify the color scheme for the states present in qcat file. Check the example section for demonestration.

Value

None

Note

fontsize argument can be overriden by the same argument in plot_gtracks()

Author(s)

Omar Elashkar

Examples

epilog_dir <- system.file("extdata", "epilog.qcat.bgz", package = "rGenomeTracks")
epi_cat <- data.frame(
  category = 1:15,
  label = c(
    "Active TSS",
    "Flanking Active TSS",
    "Transcr at gene 5 and 3",
    "Strong transcription",
    "Weak transcription",
    "Genic enhancers",
    "Enhancers",
    "ZNF genes & repeats",
    "Heterochromatin",
    "Bivalent/Poised TSS",
    "Flanking Bivalent TSS/Enh",
    "Bivalent Enhancer",
    "Repressed PolyComb",
    "Weak Repressed PolyComb",
    "Quiescent/Low"
  ),
  color = c(
    "#ff0000", "#ff4500", "#32cd32", "#008000",
    "#006400", "#c2e105", "#ffff00", "#66cdaa",
    "#8a91d0", "#cd5c5c", "#e9967a", "#bdb76b",
    "#808080", "#c0c0c0", "#ffffff"
  )
)
epilog <- track_epilogos(file = epilog_dir, categories_file = epilogos_json(epi_cat))
## Not run: 
plot_gtracks(epilog, chr = "X", start = 3100000, 3150000)

## End(Not run)

[Package rGenomeTracks version 0.99.8 Index]