Genomic_tracks_plot: Genomic tracks plotter

In RubD/GeTrackViz2:

Description

Main function which is a wrapper for individual plotters and combinations of tracks

Usage

Genomic_tracks_plot(format_vec, figure_list, uniq_name_vec, color_vec,
  mychr = "chr14", start_loc = 61100000, end_loc = 61195000,
  coord_axis_line_size = 0.5, marginvec_mm = c(0, 0, 0, 0),
  reverse_strand = FALSE, model_show_partial_overlap = T, transcript,
  exon, five_UTR, three_UTR, breaks_wanted = 4, label_size = 10,
  exon_size = 0.5, UTR_size = 0.5, y_coord_gene_dist = 0.5,
  y_top_space = 2, y_genename_space = 1, genename_size = 4,
  rna_bdg_binsize = 100, rna_bdg_y_title = "RPM/bp",
  rna_bdg_forced_y_min_vec = NULL, rna_bdg_forced_y_max_vec = NULL,
  rna_bdg_axis_line_size = 0.2, rna_bdg_chrom_col = "chr",
  rna_bdg_start_col = "start", rna_bdg_end_col = "end",
  rna_bdg_counts_col = "RPKM", rna_bdg_strand_col = NA,
  rna_min_strand_sign = "-", rna_plus_strand_sign = "+",
  rna_make_minus_strand_negative = F, rna_use_barplot = F,
  rna_alpha_fill = 0.7, bdg_binsize = 100, bdg_y_title = "RPM/bp",
  bdg_forced_y_min_vec = NULL, bdg_forced_y_max_vec = NULL,
  bdg_axis_line_size = 0.2, bdg_chrom_col = "chr",
  bdg_start_col = "start", bdg_end_col = "end",
  bdg_counts_col = "RPKM", loop_y_title = "prob",
  loop_show_partial_overlap = T, loops_axis_line_size = 0.2,
  loops_color_column = NULL, loops_color_bedpe = "black",
  bed_y_title = "SE", bed_size_bed = 4, bed_show_partial_overlap = T,
  bed_same_y_level = T, bed_axis_line_size = 1, show_labels = F,
  print_plot = T, ...)

Arguments

format_vec	transcript in bed format
figure_list	exon coordinates in bed format
uniq_name_vec	five_UTR coordinates in bed format
color_vec	three_UTR coordinates in bed format
mychr	chromosome
start_loc	start location on chromomse
end_loc	end location on chromosome
coord_axis_line_size	line size for coordinate axis
marginvec_mm	margin around plot, default = c(0,0,0,0)
model_show_partial_overlap	include loops that do not entirely overlap the coordinates
transcript	transcript in bed format
exon	exon in bed format
five_UTR	five_UTR in bed format
three_UTR	three_UTR in bed format
breaks_wanted	number of breaks on x-axis
label_size	size of labels
rna_bdg_binsize	= 100,
rna_bdg_y_title	= 'RPM/bp',
rna_bdg_forced_y_min_vec	= NULL
rna_bdg_forced_y_max_vec	= NULL,
rna_bdg_axis_line_size	= 0.2,
rna_bdg_chrom_col	= 'chr',
rna_bdg_start_col	= 'start',
rna_bdg_end_col	= 'end',
rna_bdg_counts_col	= 'RPKM',
rna_bdg_strand_col	= NA,
rna_min_strand_sign	= '-',
rna_plus_strand_sign	= '+',
rna_make_minus_strand_negative	= F,
bdg_binsize	= 100,
bdg_y_title	= 'RPM/bp',
bdg_forced_y_min_vec	= NULL,
bdg_forced_y_max_vec	= NULL,
bdg_axis_line_size	= 0.2,
bdg_chrom_col	= 'chr',
bdg_start_col	= 'start',
bdg_end_col	= 'end',
bdg_counts_col	= 'RPKM',
loop_y_title	= 'prob',
loop_show_partial_overlap	= T,
loops_axis_line_size	= 0.2,
loops_color_column	= NULL,
loops_color_bedpe	= 'black',
bed_y_title	= 'SE',
bed_size_bed	= 4,
bed_show_partial_overlap	= T,
bed_same_y_level	= T,
bed_axis_line_size	= 1,
show_labels	boolean: show x-axis lables
print_plot	boolean: print individual plot

Value

ggplot object

Examples

    Genomic_tracks_plot(format_vec, ...)

RubD/GeTrackViz2 documentation built on May 31, 2019, 2:45 p.m.