gene_tracks: Gene Tracks

In zentnerlab/TSRexploreR: TSS and TSR Analysis

Gene Tracks

Description

Generate gene tracks with GViz.

Usage

gene_tracks(
  experiment,
  feature_name,
  genome_annotation = NULL,
  feature_type = "gene",
  samples = "all",
  threshold = NULL,
  upstream = 250,
  downstream = 250,
  promoter_only = FALSE,
  use_normalized = FALSE,
  tss_colors = "black",
  tsr_colors = "black",
  axis_scale = 0.25,
  ymax = NA,
  anno_pos = "top"
)

Arguments

experiment	TSRexploreR object.
feature_name	Name of gene or transcript to visualize
genome_annotation	Genome annotation in GTF, GFF3, or TxDb format.
feature_type	Either 'gene' or 'transcript'
samples	Names of samples to plot. Append sample names with 'TSS:' or 'TSR:' for TSS and TSR tracks, respectively.
threshold	TSSs or TSRs with a score below this value will not be considered.
upstream	Bases upstream to extend gene or promoter track.
downstream	Bases downstream to extend gene or promoter track.
promoter_only	Instead of plotting the entire gene, plot only the promoter region.
use_normalized	Whether to use the normalized (TRUE) or raw (FALSE) counts.
tss_colors	Either a single color value for all TSS tracks, or a vector of colors.
tsr_colors	Either a single color value for all TSR tracks, or a vector of colors.
axis_scale	Relative size scale for axis text and title.
ymax	Maximum value on y-axis for all TSS tracks.
anno_pos	Genome annotation and axis track position. Either 'top' or 'bottom'.

Details

This function generates a GViz gene track of either the promoter region, or the specified gene or transcript and surrounding region. The gene or transcript name should be supplied to 'feature_name'. 'promoter_only' controls whether the plot is of the feature promoter or the entire gene. 'upstream' and 'downstream' is relative to either the the TSS (if promoter only) or the feature boundaries (if gene/transcript).

Value

GViz gene track plot.

Examples

data(TSSs_reduced)
annotation <- system.file("extdata", "S288C_Annotation.gtf", package="TSRexploreR")

exp <- TSSs_reduced %>%
  tsr_explorer(genome_annotation=annotation) %>%
  format_counts(data_type="tss") %>%
  tss_clustering(threshold=3)

## Not run: 
gene_tracks(exp, "YDR418W", samples=c(TSS="S288C_D_1", TSR="S288C_D_1"))

## End(Not run)

zentnerlab/TSRexploreR documentation built on Dec. 30, 2022, 10:27 p.m.