genomic.tracks: Genomic tracks plotter

In sebastian-gregoricchio/Rseb: An R-package for NGS data managing and visualization

Genomic tracks plotter

Description

The functions allows to plot different types of genomic data (bigWig, bed, bedpe) at a specific genomic region. It is possible to highlight specific regions and the gene annotations are plotted automatically at the bottom of all the tracks.

Usage

genomic.tracks(
  tracks,
  genomic.region,
  genome,
  track.labels = NULL,
  track.labels.fontzise = 5,
  track.labels.position = c(-0.1, 0),
  track.colors = "#000000",
  grouping = NULL,
  gene.annotation.color = "darkblue",
  expand.bed = TRUE,
  arcs.direction = "down",
  fraction.arc.base = 0.025,
  highlight.bed = NULL,
  highlight.color = "yellow",
  highlight.transparency = 0.15,
  missing.data.as.zero.bw = FALSE,
  smooth.bigWig.signal = TRUE,
  smooth.bigWig.loess.span = 0.05,
  plot.bigWig.area = TRUE,
  bigWig.range.label.size = 2.5,
  score.bed.shadow = FALSE,
  height.ratios = NULL,
  width.ratios = c(1, 5)
)

Arguments

tracks	A vector indicating the list of full paths of the files/tracks/signals to plot. Supported formats: bed/bd/narrowPeak/broadPeak, bw/bigWig/bigwig, bedpe.
genomic.region	An atomic string indicating the genomic region into which restrict the final plot in the format 'chr1:1234-5678'.
genome	An atomic string indicating the genome to use for the annotations. Allowed values are: hg19: loads an 'EnsDb' object from the library EnsDb.Hsapiens.v75; hg38: loads an 'EnsDb' object from the library EnsDb.Hsapiens.v86; mm10: loads an 'EnsDb' object from the library EnsDb.Mmusculus.v79; custom 'EnsDb' object: provide an 'EnsDb' object manually generated; visit the page https://bioconductor.org/packages/release/bioc/vignettes/ensembldb/inst/doc/ensembldb.html#102_building_annotation_packages for more information.
track.labels	A vector indicating the labels to use for each track (genome annotation track excluded). By default NULL: the file base-name will be used.
track.labels.fontzise	A numerical value to indicate the font size of the track labels. Default value 5.
track.labels.position	A two-element numeric vector passed to xlim function for the the definition of the frame size of the track labels. Default value c(-0.1, 0).
track.colors	A string vector indicating the color to use for each track (genome annotation track excluded). If only one value is provided it will be used for all the tracks. Default value "#000000" ("black").
grouping	A single numerical vector or a list of numeric vectors. Each list's element indicates the indexes corresponding to the tracks (1 = first track, 2 = second track, etc) for which the y-axes should be normalized. Each element will be taken into account in the order. Default value NULL.
gene.annotation.color	A string indicating the color to use for the genome annotation track.
expand.bed	A logical value to define whether overlapping regions in a bed should be plotted on different levels. Default TRUE.
arcs.direction	A string indicating the direction on which arcs should be plotted for bedpe files. Available options "up" or "down". Default value "down".
fraction.arc.base	A numerical value indicating the fraction of total plot height to be used as arc base thickness. By default 0.025 (2.5% of the track height).
highlight.bed	Either a string indicating the full path to a bed file or a data.frame in BED3 format (chr, start, end) containing regions that should be highlighted in the plot. Regions included in the genomic range will be automatically selected. By default NULL.
highlight.color	A string indicating the color to use for the regions to highlight in the plot. By default 'yellow'.
highlight.transparency	A numerical value indicating the transparency (alpha) to use for the highlighted regions. Default value 0.15.
missing.data.as.zero.bw	A logical value to define wthere missing data in the bigWigs should be converted to zeros. Default FALSE.
smooth.bigWig.signal	Logical value to indicate whether the bigWig signals should be smoothed (by loess x ~ y function). By default TRUE.
smooth.bigWig.loess.span	Numerical value to indicate the span value for the loess function used to smooth bigWig signals. By default 0.05.
plot.bigWig.area	Logical value to indicate whether the bigWig profile should be filled or not. If FALSE only the signal outline will be plotted. By default TRUE.
bigWig.range.label.size	A numerical value to indicate the font size of the bigWig signal range. Default value 2.5.
score.bed.shadow	Logical value to define whether the filling intensity of the bed segments should reflect the score of each signal. By default FALSE.
height.ratios	Numerical vector of relative track heights, passed to 'rel_heights' parameter of cowplot::plot_grid(). For example, in a two-row grid, rel_heights = c(2, 1) would make the first column twice as wide as the second column. Value 1 indicates that all the tracks should have the same size. By default NULL, automatic ratios will be computed by this function.
width.ratios	Numerical vector of relative labels vs tracks widths, passed to 'rel_widths' parameter of cowplot::plot_grid(). For example, in a two-column grid, rel_widths = c(2, 1) would make the first column twice as wide as the second column. Value 1 indicates that all the tracks should have the same size. By default c(1,5) (1 label : 5 tracks).

Value

The function returns a named list containing:

• configuration: data.frame with the parameters used to build the plot(s);

• highlighted.region: data.frame with the regions used for the highlighting;

• single.track.list: a named list containing each single track plot used for the creation of the multi.track.plot;

• single.label.plot.list: a named list containing each single track label plot used for the creation of the multi.track.plot;

• multi.track.plot: the assembled multi.track labelled plot.

sebastian-gregoricchio/Rseb documentation built on May 15, 2024, 5:45 a.m.