track_plot: Generate IGV style locus tracks with ease
In scfurl/seqGlue: Makes sequencing data come together like glue

track_plot

R Documentation

Generate IGV style locus tracks with ease

Description

Generate IGV style locus tracks with ease

Usage

track_plot(
  summary_list = NULL,
  draw_gene_track = TRUE,
  query_ucsc = TRUE,
  show_ideogram = FALSE,
  build = "hg19",
  col = "gray70",
  groupAutoScale = TRUE,
  txname = NULL,
  genename = NULL,
  gene_track_height = 2,
  scale_track_height = 1,
  show_axis = TRUE,
  gene_fsize = 0.6,
  track_names = NULL,
  track_names_pos = 0,
  regions = NULL,
  region_width = 1,
  collapse_txs = FALSE,
  boxcol = "#192A561A",
  boxcolalpha = 0.2,
  gene_model = NULL,
  isGTF = FALSE
)

Arguments

`summary_list`	Output from track_extract
`draw_gene_track`	Default FALSE. If TRUE plots gene models overlapping with the queried region
`query_ucsc`	Default FALSE. But switches to TRUE when 'gene_model' is not given. Requires 'mysql' installation.
`show_ideogram`	Default TRUE. If TRUE plots ideogram of the target chromosome with query loci highlighted. Works only when 'query_ucsc' is TRUE.
`build`	Genome build. Default 'hg19'
`col`	Color for tracks. Default '#2f3640'. Multiple colors can be provided for each track
`groupAutoScale`	Default TRUE
`txname`	transcript name to draw. Default NULL. Plots all transcripts overlapping with the queried region
`genename`	gene name to draw. Default NULL. Plots all genes overlapping with the queried region
`gene_track_height`	Default 2
`scale_track_height`	Default 1
`show_axis`	Default FALSE
`gene_fsize`	Font size. Default 1
`track_names`	Default NULL
`track_names_pos`	Default 0 (corresponds to left corner)
`regions`	genomic regions to highlight. A data.frame with at-least three columns containing chr, start and end positions.
`collapse_txs`	Default FALSE. Whether to collapse all transcripts belonging to same gene into a unified gene model
`boxcol`	color for highlighted region. Default "#192A561A"
`boxcolalpha`	Default 0.5
`gene_model`	File with gene models. Can be a gtf file or UCSC file format. If you have read them into R as a data.frame, that works as well. Default NULL, automatically fetches gene models from UCSC server
`isGTF`	Default FALSE. Set to TRUE if the 'gene_model' is a gtf file.