ggepitracks2: Plot Epigenetics Tracks for NGS Data using ggplot2 (version...
In liuyujie0136/tinyfuncr: tiny R functions

ggepitracks2

R Documentation

Plot Epigenetics Tracks for NGS Data using ggplot2 (version 2)

Description

Plot genome tracks for NGS data using ggplot2, resembling GBrowse/JBrowse/IGV style (ver.2 for enhanced performance). Supporting coverage data in bigWig or bedGraph 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. Especially optimized for BS-seq data in single-base resolution. Requires bigWigToBedGraph and bedtools on Linux.

Usage

ggepitracks2(
  locus_file,
  track_conf,
  bsseq_conf = NULL,
  gene_model,
  ann_region = NULL,
  ann_color = "goldenrod1",
  out_dir = "out",
  height = NULL,
  width = 80
)

Arguments

`locus_file`	BED file containing locus to plot. For each line, TAB-delimited information should contain: <chr>, <start>, <end>, <locus_name>, without header.
`track_conf`	Configuration file containing track info. For each line, TAB-delimited information should contain: <track_name>, <track_type>, <track_bw/bg>, <y_min>, <y_max>, <color>, <group>, without header. NOTE: If you write "BS-seq" in "<track_type>", provide mC type (one of CG, CHG, CHH, All) to plot in "<track_bw/bg>" and provide detailed info in `bsseq_conf`, "<color>" is ignored in multi-mC mode of BS-seq. "<group>" is currently unused.
`bsseq_conf`	Configuration file of BS-seq track. If there is no BS-seq track to plot, keep `NULL`. For each line, TAB-delimited information should contain: <track_name>, <CG_bw/bg>, <CHG_bw/bg>, <CHH_bw/bg>, <C_context_file>, without header. "<track_name>" here should be the same as in `track_conf`. If you choose only one mC type to plot, you can keep the column of other files as "NA", but provide all the bigWig files may be safe. "<C_context_file>" can be "NA" to ignore drawing C context track (currently unused).
`gene_model`	BED file containing all elements of gene and/or 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 contain: <chr>, <start>, <end>, <annotation_name>, without header. <annotation_name> could be empty but the last TAB should be kept.
`ann_color`	Color of annotated regions, defalut "goldenrod1" (alpha 30)
`out_dir`	Path to output directory, will be created if not exist, default "out/". Output plots in PDF format will be saved as <out_dir>/<locus_name>.pdf
`height`	Plot height, in "mm", defalut 6*ntracks+10
`width`	Plot width, in "mm", defalut 80