Add uniplot for plotting to terminal with UnicodePlots

Author: marcom

Project.toml

@@ -13,6 +13,7 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Scratch = "6c6a2e73-6563-6170-7368-637461726353"
 SnoopPrecompile = "66db9d55-30c0-4569-8b51-7e840670fc0c"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 ViennaRNA = "05a721ad-238d-4945-8c85-8b5c1fff3465"
 
 [compat]

README.md

@@ -61,6 +61,15 @@ using CairoMakie, PlotRNA
 PlotRNA.plot_structure_makie("(((...)))")
 ```
 
+### Terminal plotting with UnicodePlots
+
+Plotting in the terminal is supported via UnicodePlots.
+
+```julia
+using UnicodePlots, PlotRNA
+PlotRNA.uniplot("(((...)))")
+```
+
 
 ### Plot structures with VARNA
 

src/PlotRNA.jl

@@ -7,6 +7,7 @@ export VARNA, R2R, plot_structure
 
 function __init__()
     @require CairoMakie="13f3f980-e62b-5c42-98c6-ff1f3baf88f0" include("plot_structure_makie.jl")
+    @require UnicodePlots="b8865327-cd53-5732-bb35-84acbb429228" include("uniplot.jl")
 end
 
 include("plot_structure.jl")
@@ -18,13 +19,14 @@ include("r2r.jl")
     plot_structure("(((...)))"; sequence="GGGAAACCC")
     # TODO: how to precompile but using @require from Requires.jl?
     #       measure: are these precompile statements improving TTFP?
+    #uniplot("(((...)))")
     #plot_structure_makie("(((...)))")
     #plot_structure_makie("(((...)))"; sequence="GGGAAACCC")
 end
 
-# We define the docstring of plot_structure_makie here so it's always
-# available, even if the plot_structure_makie implementation wasn't
-# included because CairoMakie was not loaded.
+# We define the docstrings of plot_structure_makie and uniplot here so they're always
+# available, even if they weren't loaded via @require in __init__().
+
 """
     plot_structure_makie(structure; [sequence, savepath, layout_type, colorscheme])
 
@@ -35,4 +37,16 @@ PlotRNA with `using CairoMakie, PlotRNA`.
 """
 function plot_structure_makie end
 
+"""
+    uniplot(dbn; title, width, height)
+
+Plot secondary structure using UnicodePlots, usually to show inside a
+terminal.
+
+Using this function requires UnicodePlots to have been loaded before
+PlotRNA with `using UnicodePlots, PlotRNA`.
+"""
+function uniplot end
+
+
 end # module PlotRNA

src/uniplot.jl

@@ -0,0 +1,29 @@
+# Secondary structure plotting to terminal with UnicodePlots
+
+# TODO
+# - smaller plots for smaller structures, e.g. (((...))), (((((....)))))
+# - bad aspect ratio for some structure, e.g. "Gladio" from Eterna100
+#   "((....))..(...(...(..(.(..(...(((.(((...((((....)))).((((((.((((((.((((((.((((((.((((((((((.((((((.(((((.((((.((((..((((...)))).))).)))))).))))).)))))).)))))))).)))))).)))))).)))))).))))))).)))...(((.(((((.(..((((.(..((((.(..((((.(..(((((((.((((((.(((((.((((((.(((.((((((....))))))..)))).)))).))))).)))))).)))))))).)..)))).)..)))).)..)))).)..))))).((((....))))...))).)))...)..).)..)...)...)..((....))"
+
+# Note: we have to use the dot before UnicodePlots as we are using
+# Requires.jl to only compile this code if UnicodePlots is available
+import ViennaRNA
+import .UnicodePlots
+
+# the docstring is in PlotRNA.jl so it's always available, even if
+# this file wasn't loaded because of @require
+function uniplot(dbn; title="", width=:auto, height=:auto)
+    n = length(dbn)
+    n > 0 || throw(ArgumentError("secondary structure dbn has length 0"))
+    x, y = ViennaRNA.plot_coords(ViennaRNA.Pairtable(dbn))
+    plot = UnicodePlots.lineplot(x, y; border=:none, labels=false, title, width, height)
+    pt = Pairtable(dbn)
+    for i = 1:n
+        j = pt[i]
+        if i < j
+            # i,j form a base pair
+            UnicodePlots.lines!(plot, x[i], y[i], x[j], y[j])
+        end
+    end
+    return plot
+end

test/runtests.jl

@@ -9,5 +9,6 @@ showtestset() = println(" "^(2 * Test.get_testset_depth()), "testing ",
     include("plot_structure.jl")
     include("varna.jl")
     include("r2r.jl")
+    include("uniplot.jl")
     include("plot_structure_makie.jl")
 end

test/uniplot.jl

@@ -0,0 +1,7 @@
+using Test
+import UnicodePlots
+
+@testset "uniplot" begin
+    showtestset()
+    @test PlotRNA.uniplot("(((...)))") isa UnicodePlots.Plot
+end