track_epilogos {rGenomeTracks} | R Documentation |
Generate epilogos genome_track from qcat file.
track_epilogos( file, title = NULL, height = 2, overlay_previous = "no", categories_file = NULL, orientation = NULL )
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. |
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.
None
fontsize
argument can be overriden by the same argument in plot_gtracks()
Omar Elashkar
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)