Plots in notebook

[truefalsename]

Hi,

I noticed that after the new update plots are shown on an external electron window. Is there a way to have them shown in a cell of a jupyter notebook instead?

Thanks

[sglyon]

Hi @truefalsename sorry about that. I will investigate and report back in the next couple days

[truefalsename]

Hello,

thanks. A bit more of puzzling info: not all the plots open in a separate window, most open correctly inline. The only one that is display in an electron window is based on the quiver function I made:

function plot_v_slice(res::DataFrame, n::Int, ax::String, min::Float64, max::Float64; scale = 1.0)
 """
Fuction to plot velocity maps for a slice between min and max along ax",

Inputs:
      - res:: Dataframe for cells properties
      - n:: minimum number of stars in cell
      - ax:: x, y or z
      - min, max:: edges of the desired slice

Kwargs:
      - scale:: magnification factor for the arrow lengths 
"""   

if ax == "z"

    # cells in slice
    
    res_slice = res[.&(res[:n_star] .> n-1, res[:z_cell] .>= min, res[:z_cell] .<= max) , :]

    xmin = floor(minimum(collect(res_slice[:x_cell])))
    xmax = ceil(maximum(collect(res_slice[:x_cell])))

    ymin = floor(minimum(collect(res_slice[:y_cell])))
    ymax = ceil(maximum(collect(res_slice[:y_cell])))


    # Galactic Centre

    t0 = scatter(; x = [0], y = [0], mode = "markers",
                 marker = attr(color = "#000000", size = 8, symbol = "o", opacity = 1))

    #Cells

     t1 = scatter(;  x = collect(res_slice[:x_cell]), 
                     y = collect(res_slice[:y_cell]), 
                     mode = "markers",
                     marker = attr(color = "#47d157", size = 8, symbol = "circle", opacity = 0.85),
                     text = ["n stars: $k <br>u: $(round(i, digits = 2)) km/s <br>v: $(round(j, digits=2)) km/s" for (i,j,k)
                            in zip(collect(res_slice[:u_mean]),collect(res_slice[:v_mean]),collect(res_slice[:n_star]))]
        )


    # velocities array
    vels = [attr(
            x = star[:x_cell] + scale * star[:u_mean], 
            y = star[:y_cell] + scale * star[:v_mean],
            showarrow = true,
            axref = "x",
            ayref = "y",
            arrowcolor = "#707070",
            arrowhead = 3,
            ax = star[:x_cell], 
            ay = star[:y_cell])
    for star in DataFrames.eachrow(res_slice)]


    layout = Layout(; 
                autosize = false, width = 800, height = 800, 
                margin = attr(l = 50, r = 50, b = 50, t = 50),
                showlegend = false,
                title = "velocity field section; $(min)<$(ax)<$(max)",
                annotations = vels,
                xaxis = attr(title = "xGC [pc]"),
                yaxis = attr(title = "yGC [pc]"),
                )

    plot([t0, t1], layout)
    
elseif ax == "y"
    
    # cells in slice
    
    res_slice = res[.&(res[:n_star] .> n-1, res[:y_cell] .>= min, res[:y_cell] .<= max) , :]

    xmin = floor(minimum(collect(res_slice[:x_cell])))
    xmax = ceil(maximum(collect(res_slice[:x_cell])))

    ymin = floor(minimum(collect(res_slice[:z_cell])))
    ymax = ceil(maximum(collect(res_slice[:z_cell])))


    # Galactic Centre

    t0 = scatter(; x = [0], y = [0], mode = "markers",
                 marker = attr(color = "#000000", size = 8, symbol = "o", opacity = 1))

    #Cells

     t1 = scatter(;  x = collect(res_slice[:x_cell]), 
                     y = collect(res_slice[:z_cell]), 
                     mode = "markers",
                     marker = attr(color = "#47d157", size = 8, symbol = "circle", opacity = 0.85),
                     text = ["n stars: $k <br>u: $(round(i, digits = 2)) km/s<br>w: $(round(j, digits=2)) km/s" for (i,j,k)
                            in zip(collect(res_slice[:u_mean]),collect(res_slice[:w_mean]),collect(res_slice[:n_star]))]

        )


    # velocities array
    vels = [attr(
            x = star[:x_cell] + scale * star[:u_mean], 
            y = star[:z_cell] + scale * star[:w_mean],
            showarrow = true,
            axref = "x",
            ayref = "y",
            arrowcolor = "#707070",
            arrowhead = 3,
            ax = star[:x_cell], 
            ay = star[:z_cell])
    for star in DataFrames.eachrow(res_slice)]


    layout = Layout(; 
                autosize = false, width = 800, height = 800, 
                margin = attr(l = 50, r = 50, b = 50, t = 50),
                showlegend = false,
                title = "velocity field section; $(min)<$(ax)<$(max)",
                annotations = vels,
                xaxis = attr(title = "xGC [pc]"),
                yaxis = attr(title = "zGC [pc]"),
                )

    plot([t0, t1], layout)
    
    
elseif ax == "x"
    
    # cells in slice
    
    res_slice = res[.&(res[:n_star] .> n-1, res[:x_cell] .>= min, res[:x_cell] .<= max) , :]

    xmin = floor(minimum(collect(res_slice[:z_cell])))
    xmax = ceil(maximum(collect(res_slice[:z_cell])))

    ymin = floor(minimum(collect(res_slice[:y_cell])))
    ymax = ceil(maximum(collect(res_slice[:y_cell])))


    # Galactic Centre

    t0 = scatter(; x = [0], y = [0], mode = "markers",
                 marker = attr(color = "#000000", size = 8, symbol = "o", opacity = 1))

    #Cells

     t1 = scatter(;  x = collect(res_slice[:z_cell]), 
                     y = collect(res_slice[:y_cell]), 
                     mode = "markers",
                     marker = attr(color = "#47d157", size = 8, symbol = "circle", opacity = 0.85),
                     text = ["n stars: $k <br>v: $(round(i, digits = 2)) km/s <br>w: $(round(j, digits=2)) km/s" for (i,j,k)
                            in zip(collect(res_slice[:v_mean]),collect(res_slice[:w_mean]),collect(res_slice[:n_star]))]
        )


    # velocities array
    vels = [attr(
            x = star[:z_cell] + scale * star[:w_mean], 
            y = star[:y_cell] + scale * star[:v_mean],
            showarrow = true,
            axref = "x",
            ayref = "y",
            arrowcolor = "#707070",
            arrowhead = 3,
            ax = star[:z_cell], 
            ay = star[:y_cell])
    for star in DataFrames.eachrow(res_slice)]


    layout = Layout(; 
                autosize = false, width = 800, height = 800, 
                margin = attr(l = 50, r = 50, b = 50, t = 50),
                showlegend = false,
                title = "velocity field section; $(min)<$(ax)<$(max)",
                annotations = vels,
                xaxis = attr(title = "zGC [pc]"),
                yaxis = attr(title = "yGC [pc]"),
                )

    plot([t0, t1], layout)
    
end

end

The test function I have provided however does not have this problem.

[sglyon]

Hi @truefalsename I just tried it out and didn't have any problems getting my plot to display in the notebook.

Is this still a problem for you?

If it is, would you please provide a minimal example that I could use to try to reproduce the issue?

Thank you

[YermolenkoIgor]

Hello! Have problem with simple plot:
julia> using Plots

julia> plotlyjs()
[ Info: Recompiling stale cache file C:\Users\Игорь.julia\compiled\v1.0\PlotlyJ
S\1r9Ld.ji for PlotlyJS [f0f68f2c-4968-5e81-91da-67840de0976a]
WARNING: could not import Base.quit into AtomShell
[ Info: Recompiling stale cache file C:\Users\Игорь.julia\compiled\v1.0\ORCA\jv
X7k.ji for ORCA [47be7bcc-f1a6-5447-8b36-7eeeff7534fd]
Plots.PlotlyJSBackend()
julia> plot([1; 2], [3; 4])
Error showing value of type Plots.Plot{Plots.PlotlyJSBackend}:
ERROR: Cannot find Electron. Try Blink.AtomShell.install().
Stacktrace:
[1] error(::String) at .\error.jl:33
[2] electron at C:\Users\Игорь.julia\packages\Blink\vKGzM\src\AtomShell\proces
s.jl:62 [inlined]
[3] #init#6(::Bool, ::Function) at C:\Users\Игорь.julia\packages\Blink\vKGzM\s
rc\AtomShell\process.jl:80
[4] #init at .\none:0 [inlined]
[5] #shell#9(::Bool, ::Function) at C:\Users\Игорь.julia\packages\Blink\vKGzM
src\AtomShell\process.jl:123
[6] shell at C:\Users\Игорь.julia\packages\Blink\vKGzM\src\AtomShell\process.j
l:121 [inlined]
.........................................
(v1.0) pkg> build Blink
Building MbedTLS → C:\Users\Игорь\.julia\packages\MbedTLS\eaAxb\deps\build.lo g
Building WebIO ──→ C:\Users\Игорь\.julia\packages\WebIO\myl19\deps\build.log
julia> using Blink

julia> Blink.AtomShell.install()
ERROR: IOError: could not spawn 7z x electron-v2.0.5-win32-x64.zip -oatom: no
such file or directory (ENOENT)
Stacktrace:
[1] _jl_spawn(::String, ::Array{String,1}, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) a
t .\process.jl:367
[2] (::getfield(Base, Symbol("##494#495")){Cmd})(::Tuple{RawFD,RawFD,RawFD}) at
.\process.jl:509
[3] setup_stdio(::getfield(Base, Symbol("##494#495")){Cmd}, ::Tuple{RawFD,RawFD
,RawFD}) at .\process.jl:490
[4] #_spawn#493(::Nothing, ::Function, ::Cmd, ::Tuple{RawFD,RawFD,RawFD}) at .
process.jl:508
[5] _spawn at .\process.jl:504 [inlined]
[6] #run#504(::Bool, ::Function, ::Cmd) at .\process.jl:662
[7] run at .\process.jl:661 [inlined]
[8] (::getfield(Blink.AtomShell, Symbol("##1#2")))() at C:\Users\Игорь.julia\p
ackages\Blink\vKGzM\src\AtomShell\install.jl:48
[9] cd(::getfield(Blink.AtomShell, Symbol("##1#2")), ::String) at .\file.jl:85
[10] install() at C:\Users\Игорь.julia\packages\Blink\vKGzM\src\AtomShell\inst
all.jl:27
[11] top-level scope at none:0
(v1.0) pkg> status
Status C:\Users\Игорь\.julia\environments\v1.0\Project.toml
[537997a7] AbstractPlotting v0.9.0
[ad839575] Blink v0.8.1
[159f3aea] Cairo v0.5.6
[5ae59095] Colors v0.9.5
[8f4d0f93] Conda v1.1.1
[0c46a032] DifferentialEquations v5.3.1
[a1bb12fb] Electron v0.2.0
[5789e2e9] FileIO v1.0.2
[5752ebe1] GMT v0.5.0
[28b8d3ca] GR v0.35.0
[c91e804a] Gadfly v1.0.0+ #master (https://github.com/GiovineItalia/Gadfly.jl.
git)
[4c0ca9eb] Gtk v0.16.4
[a1b4810d] Hexagons v0.2.0
[7073ff75] IJulia v1.13.0+ [C:\Users\Игорь\.julia\dev\IJulia]
[6218d12a] ImageMagick v0.7.1
[c601a237] Interact v0.9.0
[ee78f7c6] Makie v0.9.0+ #master (https://github.com/JuliaPlots/Makie.jl.git)
[7269a6da] MeshIO v0.3.1
[47be7bcc] ORCA v0.1.1
[58dd65bb] Plotly v0.2.0
[f0f68f2c] PlotlyJS v0.11.2+ #master (https://github.com/sglyon/PlotlyJS.jl.gi
t)
[91a5bcdd] Plots v0.21.0
[c4c386cf] Rsvg v0.2.2
[60ddc479] StatPlots v0.8.1
[b8865327] UnicodePlots v0.3.1
[0f1e0344] WebIO v0.4.0
[c2297ded] ZMQ v1.0.0

[YermolenkoIgor]

Problem for Jupyter notebook

using Plots

plotlyjs()
out Plots.PlotlyJSBackend()

x = 1:10; y = rand(10); # These are the plotting data
plot(x,y)

UndefVarError: _use_remote not defined

Stacktrace:
[1] _show(::Base.GenericIOBuffer{Array{UInt8,1}}, ::MIME{Symbol("text/html")}, ::Plots.Plot{Plots.PlotlyJSBackend}) at C:\Users\Игорь.julia\packages\Plots\rmogG\src\backends\plotlyjs.jl:54
[2] show(::Base.GenericIOBuffer{Array{UInt8,1}}, ::MIME{Symbol("text/html")}, ::Plots.Plot{Plots.PlotlyJSBackend}) at C:\Users\Игорь.julia\packages\Plots\rmogG\src\output.jl:201
[3] #sprint#325(::Nothing, ::Int64, ::Function, ::Function, ::MIME{Symbol("text/html")}, ::Vararg{Any,N} where N) at .\strings\io.jl:101
[4] sprint(::Function, ::MIME{Symbol("text/html")}, ::Vararg{Any,N} where N) at .\strings\io.jl:97
[5] display_dict(::Plots.Plot{Plots.PlotlyJSBackend}) at C:\Users\Игорь.julia\packages\Plots\rmogG\src\init.jl:76
[6] #invokelatest#1 at .\essentials.jl:697 [inlined]
[7] invokelatest at .\essentials.jl:696 [inlined]
[8] execute_request(::ZMQ.Socket, ::IJulia.Msg) at C:\Users\Игорь.julia\dev\IJulia\src\execute_request.jl:256
[9] #invokelatest#1 at .\essentials.jl:697 [inlined]
[10] invokelatest at .\essentials.jl:696 [inlined]
[11] eventloop(::ZMQ.Socket) at C:\Users\Игорь.julia\dev\IJulia\src\eventloop.jl:8
[12] (::getfield(IJulia, Symbol("##12#15")))() at .\task.jl:259

[sglyon]

Thanks for contributing @YermolenkoIgor

This is an issue with Plots.jl, not PlotlyJS.jl

We are hoping to address this soon and get Plots + PlotlyJS working again. I've looked into the issue and will need a little bit of help from WebIO experts like @shashi, but we'll get it sorted out soon!

[truefalsename]

Hey,

sorry for the late reply. The problem remains after updating everything to the newest release
. I am attaching a strip down version of the notebook I am using. The first plotting function (v_slice I believe) opens an external julia window. The remaining two functions are correctly visualised in the notebook.
Archive.zip

[sglyon]

Hi @truefalsename is this a problem still?

Thanks

[truefalsename]

Hello,

sorry for the late reply: i changed computer moving to windows.
Yes, it still happens

[truefalsename]

Btw, I noticed also another thing: I cannot interact with 3d plots anymore. I am using the same code as on my old mac, the plots display in notebook (not the arrows one, that is still in the atom window) but they are rather buggy: cannot rotate them with the mouse and annotations are stuck to the first object I hover on. Has this something to do with the WebIO issue? I tried to downgrade and pin WebIO but the same issue happens