PlotRNA.jl

Plot nucleic acid secondary structures with Julia. Currently only the most basic structure visualisation is implemented.

This package is quite new and there might be some sharp edges.

Installation

As PlotRNA is not yet registered you have to add it like this:

] add https://github.com/marcom/PlotRNA.jl

Usage

using PlotRNA, ViennaRNA

Built-in plotting functionality (basic at the moment)

# plot_structure: draw an image of a secondary structure
dbn = "(((...)))"
seq = "GGGAAACCC"
plot_structure(dbn)
plot_structure(dbn; savepath="rna.png")
plot_structure(dbn; sequence=seq, base_colors=prob_of_basepairs(seq, dbn))

There is also an experimental PlotRNA.plot_structure_makie which looks a bit nicer but currently has a rather large time to first plot (40 seconds). Subsequent plots are very fast though.

Plotting structures with VARNA

This uses the quite featureful VARNA program via its command-line interface.

using PlotRNA
VARNA.plot("(((...)))")
VARNA.plot("(((...)))"; seq="GCGAAACGC", savepath="rna.png")
VARNA.plot_compare(dbn1="(((.....)))", seq1="GCGAAAAACGC",
                   dbn2="((-...---))", seq2="GG-AAA---CC")

Note: Java must be installed for VARNA plotting to work

You will need a working Java installation (can be headless i think). You can test this by running:

run(`java -version`)

If you don't get an error, plotting with VARNA should work.

The VARNA jar file will get downloaded automatically the first time you plot something with VARNA. It gets stored in a scratch space that gets cleaned up by the Julia package manager when you uninstall PlotRNA.

Plot options

More details about these parameters can be found in the VARNA documentation.

• algorithm=:radiate: RNA graph layout algorithm to use. Options are: :line, :circular, :naview, :radiate..

• additional_basepairs="": the option is called -auxBPs in VARNA. String of the form "(i1,j1);(i2,j2):opt1=val1,opt2=val2;...".

  • edge5, edge3=[wc|h|s]: classification of noncanonical basepair as defined by Leontis & Westhof. Values are "wc" (Watson-Crick edge), "h" (Hoogsteen edge), "s" (sugar edge)
  • stericity=[cis|trans]: strand orientation
  • color: base pair color as string
  • thickness: basepair thickness as integer

  Example: additional_basepairs="(1,10);(2,9):edge5=h,edge3=s,stericity=cis,color=#ff0000,thickness=5"

• annotations="": annotation string of the form "text1:opt1=val1,...;type=T2,opt2=val2;...".

  • type=[P|B|H|L]: can be P (static), B (anchored on base), H (anchored on helix), or L (anchored on loop)
  • x, y: x and y coordinates for a static annotation (P)
  • anchor: which base should annotation be anchored to (not applicable for static annotations)
  • size font size as an integer
  • color as a string e.g. "#FF0000"

  Example: annotations="Static annotation:type=P,x=100,y=50,size=12,color=#ff0000;Base annotation:type=B,anchor=42"

• auto_helices=false: annotate helix n with "Hn"

• auto_interior_loops=false: annotate interior loop n with "In"

• auto_terminal_loops=false: annotate terminal loop n with "Tn"

• backbone_color=""

• background_color=""

• base_inner_color=""

• base_name_color=""

• base_num_color=""

• base_outline_color=""

• base_style_define=String[]: corresponds to the -basesStyleX options in VARNA.

• base_style_apply_on=String[]: corresponds to the -applyBasesStyleXon options in VARNA.

• basepair_color=""

• basepair_style="": can be "none" (no basepairs drawn), "line", "rnaviz" (draw square equidistant from both bases), or "lw" (Leontis/Westhof rendering).

• border_dist="0x0": x and y distance of drawing area from border, e.g. 10x20

• chemical_probing="": markers on the RNA backbone, for example from chemical probing. String of the form "a1-b1:opt1=v1,...;a2-b2:opt1=v2,...". Here a1 and b1 are adjacent bases, the marker is placed on the backbone between them.

  • glyph=[arrow|dot|pin|triangle]: shape of annotation
  • dir=[in|out]: direction of annotation
  • intensity=float: annotation thickness
  • color=color

  Example: chemical_probing="2-3:glyph=triangle,dir=in,intensity=1.0,color=#ff0000;4-5:glyph=dot"

• color_map=Float64[]: color map for coloring bases

• color_map_caption=""

• color_map_min=0.0: color map range minimum

• color_map_max=1.0: color map range maximum

• color_map_style="heat": color map style. Predefined styles are: "red", "blue", "green", "heat", "energy", and "bw". A custom palette can be passed in the form "0:#ff0000;1:#ffffff".

• draw_backbone=true

• draw_bases=true

• draw_noncanonical_bp=true

• draw_tertiary_bp=true

• fill_bases=true

• flat_radiate_mode=true: align exterior loop horizontally in the :radiate layout algorithm.

• highlight_region="": string for highlighting consecutive regions of bases of the format "i1-j1:opt1=val1,...;i2-j2:opt1=val2,...". Options are:

  • radius: thickness of highlight
  • fill=color: highlight fill color
  • outline=color: highlight outline color

  Example: highlight_region="2-5:radius=10,fill=#00ff00;7-12:radius=10,fill=#00ff00,outline=#000000"

• line_mode_bp_vertical_scale=1.0: vertical scaling of basepair lines in the :line layout algorithm

• nonstandard_bases_color=""

• numbering_period=10: numbering interval for bases

• resolution=1.0

• rotation=0.0: rotate RNA structure by an angle in degrees

• show_errors=true

• show_warnings=true

• space_between_bases=1.0

• title="": plot title

• title_color=""

• title_size=18: title font size

• zoom=1.0

Other Julia packages for RNA secondary structure prediction

• ViennaRNA.jl
• LinearFold.jl