Plot nucleic acid secondary structures with Julia. The Julia implementation currently only provides very basic functionality.

There is also an interface to the VARNA package which offers a lot of advanced features, and an interface to R2R for plotting multiple sequence alignments with consensus structures. If you use the VARNA or R2R interface in this package, please make sure to cite the corresponding VARNA or R2R publication.

Enter the package mode from the Julia REPL by pressing ] and then install with

add PlotRNA

Please excuse the rather long compile times on installation (around 5 minutes on julia-1.9).

using PlotRNA

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

# color bases according to their probability of being basepaired or
# unpaired
using ViennaRNA: prob_of_basepairs
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 (on julia-1.9: about 10 seconds for using CairoMakie, PlotRNA and 10 seconds for PlotRNA.plot_structure_makie("(((...)))")). Subsequent plots are very fast though. To use this function, you must load CairoMakie before PlotRNA. Code using CairoMakie is only loaded optionally with Requires.jl, as otherwise PlotRNA's package load time is a lot higher.

using CairoMakie, PlotRNA
PlotRNA.plot_structure_makie("(((...)))")

This uses the very 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")

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.

• savepath="": output file path where the image should be written to, or a temporary file if not set. The file ending determines the output file type.

• fileformat="svg": output file format, only used if savepath is not set.

• verbose=false: print stdout and stderr captured from VARNA.

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

This uses the R2R program via its command-line interface.

using PlotRNA, BioStockholm
msa = parse(MSA, """
    # STOCKHOLM 1.0
    human        ACACGCGAAA.GCGCAA.CAAACGUGCACGG
    chimp        GAAUGUGAAAAACACCA.CUCUUGAGGACCU
    bigfoot      UUGAG.UUCG..CUCGUUUUCUCGAGUACAC
    #=GC SS_cons ...<<<.....>>>....<<....>>.....
    //
    """)

# or alternatively
msa = MSA{Char}(;
    seq = Dict("human"   => "ACACGCGAAA.GCGCAA.CAAACGUGCACGG",
               "chimp"   => "GAAUGUGAAAAACACCA.CUCUUGAGGACCU",
               "bigfoot" => "UUGAG.UUCG..CUCGUUUUCUCGAGUACAC"),
     GC = Dict("SS_cons" => "...<<<.....>>>....<<....>>.....")
)

# this should show a svg image in Pluto or Jupyter
plot = R2R.plot(msa)

# save the svg image to a file
write("out.svg", plot.svg)

All code in this repository is licensed under the MIT license, a copy of which can be found in the LICENSE file. VARNA is licensed under the GNU GPL as mentioned on the VARNA homepage. R2R is licensed under the GNU GPL.

• ViennaRNA.jl
• RNAstructure.jl
• LinearFold.jl
• FoldRNA.jl