View source: R/shaman_plot_map.R
shaman_plot_tracks_and_annotations | R Documentation |
shaman_gplot_tracks_and_annotations
shaman_plot_tracks_and_annotations( genome, interval_range, misha_tracks = list(), mt_colors = getOption("shaman.track_colors"), mt_ylims = NULL, annotations = list(), a_colors = getOption("shaman.annotation_colors"), add_genes = T, add_ideogram = T, add_axis = T, gene_stacking = "squish", gene_size = 0.7, track_size = 0.8, annotation_size = 0.7 )
genome |
Name of reference genome (e.g. "hg19", "mm10") |
interval_range |
1D interval (chrom, start, end) specifying the region to plot |
misha_tracks |
List of 1D track expressions (virtual tracks also supported) which can be extracted from. |
mt_colors |
Array of colors, one for each misha_track, which will be used to plot each 1d track. |
annotations |
List of gintervals highlighting annotated regions. |
a_colors |
Array of colors, one for each annotation set. |
add_genes |
Boolean flag indicating whether to show gene annotations. |
add_ideogram |
Boolean flag indicating whether to add an chromosomal ideogram. |
add_axis |
Boolean flag indicating whether to show chromosmal axis. |
gene_stacking |
Describes the viewing option of the genes track. Can be either "squish", or "dense" |
gene_size |
Size of gene annotation view |
track_size |
Size of track view |
my_ylims |
Y-axis limits for each misha track. If not provided, generated automatically based on the data to be displayed in the region. |
annot_size |
Size of annotation view |
Plots 1D tracks in UCSC format. Along with gene annotations and chromosomal axis, this function plots one dimensional misha tracks (e.g. rna-seq, chip-seq data) and marks annotated intervals in the plotting region.
gsetroot(shaman_get_test_track_db()) shaman_plot_tracks_and_annotations("hg19", gintervals(2, 175.5e06, 177.5e06))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.