track.gencode: Constructor a 'gTrack' from GENCODE transcripts

In mskilab/gTrack: Plotting multiple tracks of complex genomic data across multiple genomic windows

Constructor a gTrack from GENCODE transcripts

Description

Returns gTrack object representing GENCODE transcripts and their components (utr, cds etc) with assigned colors. Usually built from cached data objects but can also be built from provided GRangesList

Usage

track.gencode(
  gencode = NULL,
  gene.collapse = TRUE,
  genes = NULL,
  grep = NULL,
  grepe = NULL,
  build = "hg19",
  bg.col = alpha("blue", 0.1),
  cds.col = alpha("blue", 0.6),
  utr.col = alpha("purple", 0.4),
  st.col = "green",
  en.col = "red",
  grl.labelfield,
  gr.labelfield,
  col,
  cached = T,
  cached.dir = Sys.getenv("GENCODE_DIR"),
  cached.path = paste(cached.dir, "gencode.composite.rds", sep = "/"),
  cached.path.collapsed = paste(cached.dir, "gencode.composite.collapsed.rds", sep = "/"),
  gr.srt.label = 0,
  gr.cex.label = 0.3,
  cex.label = 0.5,
  labels.suppress.gr = T,
  drop.rp11 = TRUE,
  stack.gap = 1e+06,
  gencode.cols = "gene_label",
  use.gene.ids = FALSE,
  ...
)

Arguments

gencode	(optional) path to GENCODE gtf or a GRanges object from which to generate and cache new gTrack GENCODE object (into path specified by GENCODE_DIR or provided as cached.dir argument to this function object). Only necessary to run if gTrack GENCODDE .rds has not already been cacned, (note: cached = FALSE in order for new GENCODE gTrack to be generated )
gene.collapse	scalar logical specifying whether to collapse genes by transcript (or used stored version of transcripts)
genes	(optional) character vector specifying genes to limit gTrack object to
grep	character vector for which to grep genes to positively select
grepe	character vector for which to grep genes which to exclude
build	character can be 'hg19', 'hg38', if GENCODE_DIR and gencode not specified will download this build from mskilab.com
bg.col	scalar character representing background color for genespan
cds.col	scalar character representing background color for CDS
st.col	scalar character representing color of CDS start
en.col	scalar character representing color of CDS end
cached	logical scalar whether to use "cached" version provided with package
gr.srt.label	scalar numeric specifying angle on exon label
gr.cex.label	scalar numeric > 0 specifying character expansion on exon label
labels.suppress.gr	scalar logical specifying whether to suppress exon label plotting
stack.gap	stack.gap argument to gTrack
gencode.cols	character vector specifying additional columns to include in the gencode data used to generate the gTrack. By default if gencode includes a metadata column "gene_label" then this column is included. "gene_label" is regarded as a special case in which the value for each gene is assumes to be unique and the "gene_label" value is also used to annotate the GRangesList associated with the output gTrack. This allows the users to supply alternative values for annotations of the genes. In this case gngt$grl.labelfield = 'gene_label' could be used in order for the "gene_label" values to be show up when plotting the gencode gTrack.
use.gene.ids	(logical) use the gene_id column to name items in the GRangesList. By default set to FALSE to maintain backwards compatibility, which means "gene_name" is used to name items in the output. The problem with this is that gene_name is not unique. For example, 5S_rRNA is a gene_name that is associated with multiple different gene_id's, each representing a different copy of 5S_rRNA on various chromossomes.
...	additional arguments passed down to gTrack
rg	(optional) GRangesList representing transcript models imported from GENCODE gff3 file using rtracklayer import
cds.utr	scalar character representing background color for UTR

Author(s)

Marcin Imielinski

mskilab/gTrack documentation built on Aug. 17, 2024, 6:10 a.m.