Styling Guide • RNAPeaks

Overview

This article documents all visual styling parameters across the RNAPeaks function suite. Parameters are grouped by function family.

library(RNAPeaks)
data(gtf_human)

PlotGene and PlotRegion

PlotGene() and PlotRegion() share a common set of styling arguments.

Gene structure

Parameter	Default	Description
`exon_fill`	`"navy"`	Exon / CDS fill color
`utr_fill`	`"lightgray"`	UTR fill color
`utr_col`	`"darkgray"`	UTR border color
`intron_color`	`"gray60"`	Intron line color
`intron_linewidth`	`0.9`	Intron line width

Peaks

Parameter	Default	Description
`peak_col`	`"purple"`	Peak rectangle fill color
`peak_alpha`	`0.95`	Peak opacity (0–1)
`peak_border_color`	`NA`	Peak border color (`NA` = none)
`peaks_width`	`0.3`	Vertical height of each peak row

Labels

Parameter	Default	Description
`label_size`	`5`	Protein track label font size
`label_color`	`"black"`	Protein track label color
`title_size`	`25`	Plot title font size
`bam_label_size`	`8`	BAM coverage track label size

Layout

Parameter	Default	Description
`axis_pad_bp`	`500`	Padding (bp) added to each side of the x-axis
`axis_breaks_n`	`5`	Number of x-axis tick marks
`max_proteins`	`40`	Maximum number of protein tracks shown
`x_lims`	`NULL`	Custom x-axis limits as `c(min, max)`

Background bands

Parameter	Default	Description
`band_even_fill`	`"#F7F8FA"`	Even-row band fill
`band_odd_fill`	`"#FFFFFF"`	Odd-row band fill
`band_sep_color`	`"#E5E7EB"`	Band separator line color

Example

PlotGene(
    bed             = sample_bed,
    geneID          = "GAPDH",
    gtf             = gtf_human,
    exon_fill       = "steelblue",
    utr_fill        = "lightblue",
    peak_col        = "firebrick",
    peak_alpha      = 0.8,
    label_size      = 4,
    band_even_fill  = "#F0F4FF",
    band_odd_fill   = "#FFFFFF"
)

createSplicingMap, createRetainedIntronSplicingMap, createSequenceMap, createRetainedIntronSequenceMap

All four analysis functions share the same visual parameters.

Line colors

Parameter	Default	Description
`retained_col`	`"blue"`	Retained group line color
`excluded_col`	`"red"`	Excluded group line color
`control_col`	`"black"`	Control group line color

Lines and ribbon

Parameter	Default	Description
`line_width`	`0.8`	Frequency line width
`line_alpha`	`0.7`	Frequency line opacity
`ribbon_alpha`	`0.3`	Opacity of the control SD ribbon

Schematic

Parameter	Default	Description
`boundary_col`	`"gray70"`	Region boundary dashed line color
`exon_col`	`"navy"`	Skipped / flanking exon fill in the schematic

Title and axes

Parameter	Default	Description
`title`	`""`	Plot title
`title_size`	`20`	Plot title font size
`title_color`	`"black"`	Plot title color
`axis_text_size`	`11`	Y-axis tick label font size
`ylab`	`"Frequency"`	Y-axis label

Legend

Parameter	Default	Description
`legend_position`	`"bottom"`	Legend position: `"bottom"`, `"top"`, `"left"`, `"right"`, or `"none"`

Example

createSplicingMap(
    bed_file        = sample_bed,
    SEMATS          = sample_se.mats,
    retained_col    = "#1f77b4",
    excluded_col    = "#d62728",
    control_col     = "#7f7f7f",
    ribbon_alpha    = 0.2,
    exon_col        = "steelblue",
    boundary_col    = "gray50",
    title           = "RBP Binding Around SE Junctions",
    title_size      = 18,
    ylab            = "Binding Frequency",
    legend_position = "right"
)