genometracks: Plot Genome Tracks for NGS Data
In liuyujie0136/tinyfuncr: tiny R functions

genometracks

R Documentation

Plot Genome Tracks for NGS Data

Description

Plot genome tracks for NGS data, resembling GBrowse/JBrowse style. Supporting coverage data in bigWig format from RNA-seq, sRNA-seq, BS-seq, ChIP-seq, RIP-seq, GRO-seq, NET-seq, DNase-seq, MNase-seq, ATAC-seq, SHAPE-seq etc. Annotation should be provided in GTF format. Some codes refers to https://github.com/PoisonAlien/trackplot and genomemodel package with some major modifications. Requires bedtools and bwtool on Linux.

Usage

genometracks(
  bed_file,
  track_conf,
  gene_model,
  ann_region = NULL,
  ann_color = "goldenrod1",
  out_format = "png",
  out_dir = "out"
)

Arguments

`bed_file`	BED file containing locus to plot. For each line, TAB-delimited information should containing: <chr>, <start>, <end>, <locus_name>.
`track_conf`	configuration file containing track info. For each line, TAB-delimited information should containing: <track_name>, <path_to_track_file>, <y_min>, <y_max>, <color>, <group>, without header.
`gene_model`	BED file containing all elements of gene and TE model, generated by `⁠[tinyfuncr::extractPos]⁠`
`ann_region`	BED file of annotation regions. If not provided, no annotation will be added. For each line, TAB-delimited information should containing: <chr>, <start>, <end>, <annotation_name>. <annotation_name> could be empty but the last TAB should be kept.
`ann_color`	color of annotated regions
`out_format`	format of output figures, one of "png" and "pdf"
`out_dir`	path to output directory, create it if not exist