Visualizing a table in weave report?

[LasseKatten]

Hi

Is there a proper way to render tables in weave reports?

Following #125, I've tried to display a dataframe following the example provided at this page, but the output is not as visually appealing as I'd hoped.

The problem is that a line showing the number of rows and columns shows up on top of the data frame, as can be observed in the attached image. Furthermore, under the headline, I get a row showing the type of data in their respective columns. I haven't been able to remove these.

I'm not bound to using dataframes, so I don't mind switching to any other way of visualizing tables using Weave.jl

Thanks in advance

[kescobo]

Came with a similar issue - large tables generate giant output. I was hoping PrettyTables.jl would help, but no joy. Here's a gist with an example markdown and html output.

Long text doesn't take up the full screen:

Large tables are rendered in their entirety, and PrettyTables seems to think it can print the whole thing, but gets weirdly wrapped:

[kescobo]

Note: I figured out how to do this with PrettyTables.jl, you just have to provide a bit of extra info to weave and to pretty tables. Example:

pretty_table.jmd:

## Formatter test

```julia; line_width=120
using PrettyTables

mat = rand(100,100);
pretty_table(mat, screen_size=(10,120)) # use -1 for the first dim if you don't want to cut off the bottom
```

results in:

Unfortunately, the Highlighters don't work (#238), but you can use formatters and a bunch of the other functionality of PrettyTables.jl. It works great with DataFrames too - just use nosubheader=true to remove the type annotations for the Columns.

[korsbo]

You can also use Latexify.jl for this. This should work with both dataframes and matrices. It can output markdown tables which work well with Weave.jl.

[LasseKatten]

You can also use Latexify.jl for this. This should work with both dataframes and matrices. It can output markdown tables which work well with Weave.jl.

This works! The data type row doesn't show up.

Are there any cosmetic capabilities of this package? For example adding borderlines, changing strings to \text{string} (i.e. "green" => $\text{green}$ instead of $green$) and so on.

[korsbo]

There are some configurations that you can make along those lines but it may not be perfect yet.

The kwargs latex = false stops everything from turning into latex maths. A potential problem with this is that it applies to everything even if you might actually want your numbers or expressions to be latexified. Although this is not part of the public API, you could instead hack it to work by overloading latexraw.

M = [23.23 "hello there"; :(x/y) 3//4]

using LaTeXStrings
Latexify.latexraw(s::String; kwargs...) = LaTeXString("\\text{$s}")

latexify(M; env=:mdtable)

That way, you can still get the built-in number formatting, etc to work.

There is currently no way of adding lines to a markdown table from latexify but feel free to file issues/PRs about missing functionality.

Also, have a look at the package documentation.

[NicholasWMRitchie]

I've found that writing custom display(...) methods can really help. This allows you to add custom chuck options and other special formating. Here are a couple of examples for DataFrames and inserting HTML directly into the report.

# Customized output for DataFrame to HTML
function Base.display(report::Weave.Report, m::MIME"text/html", data::DataFrame)
	function wrap(ss)
		fig_w, fig_h = get(report.cur_chunk.options, :tab_width, 8), get(report.cur_chunk.options, :tab_height, 6)
		return "<div style=\"width:$(fig_w)in;height:$(fig_h)in;line-height:2em;overflow:auto;padding:0.1in;\">"*ss*"</div>"
	end
	io = IOBuffer()
        show(IOContext(io, :limit => false), m, data, summary=false, eltypes=false)
	report.rich_output *= string('\n', wrap(String(take!(io))))
end

Base.display(report::Weave.Report, m::MIME"text/html", data::HTML) =
	report.rich_output *= string('\n', data.content)

[bradcarman]

In general I think the show() function should work. However even though I include the semicolon ";" at the end, the result (14) is still displayed along with the table. Therefore a simple function can be used to display without the show() function result. Below is my code and result.

[nathanrboyer]

I fought for a while trying to weave this table, but I eventually got something working.

julia> df
7×7 DataFrame
 Row │ Material                           Maximum Temperature  m₂                 m₃                       m₄                     m₅       ϵₚ      
     │ String                             String               Expr               Expr                     Expr                   Float64  Float64
─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   1 │ Ferritic steel                     900°F (480°C)        0.6 * (1.0 - R)    2 * log(1 + El / 100)    log(100 / (100 - RA))      2.2   2.0e-5
   2 │ Austenitic stainless steel and n…  900°F (480°C)        0.75 * (1.0 - R)   3 * log(1 + El / 100)    log(100 / (100 - RA))      0.6   2.0e-5
   3 │ Duplex stainless steel             900°F (480°C)        0.7 * (0.95 - R)   2 * log(1 + El / 100)    log(100 / (100 - RA))      2.2   2.0e-5
   4 │ Precipitation hardening, nickel …  1000°F (540°C)       1.09 * (0.93 - R)  1 * log(1 + El / 100)    log(100 / (100 - RA))      2.2   2.0e-5
   5 │ Aluminum                           250°F (120°C)        0.52 * (0.98 - R)  1.3 * log(1 + El / 100)  log(100 / (100 - RA))      2.2   5.0e-6
   6 │ Copper                             150°F (65°C)         0.5 * (1.0 - R)    2 * log(1 + El / 100)    log(100 / (100 - RA))      2.2   5.0e-6
   7 │ Titanium and zirconium             500°F (260°C)        0.5 * (0.98 - R)   1.3 * log(1 + El / 100)  log(100 / (100 - RA))      2.2   2.0e-5

latexify did not work directly because the table contains strings. I couldn't get the latexraw workaround above to work.

julia> latexify(df)
ERROR: in Latexify.jl:
You are trying to create latex-maths from a `String` that cannot be parsed as
an expression: `Ferritic steel`.

I tried extending show as shown above, but my Unicode header characters did not appear.

using DataFrames, Latexify, LaTeXStrings

#+ results="hidden"
function beautify(df::DataFrame)
    bdf = copy(df)
    for col in names(bdf) # latexify all expressions
        if eltype(bdf[!, col]) === Expr
            transform!(bdf, col => ByRow(latexify), renamecols=false)
        end
    end
    io = IOBuffer();
    show(io, MIME("text/latex"), bdf; eltypes = false);
    return print(String(take!(io)));
end

#' # Table KM-620
#+ results="tex"
beautify(df)

PrettyTables initially gave similar results where the Unicode characters would not appear.

using DataFrames, Latexify, LaTeXStrings, PrettyTables

#+ results="hidden"
function beautify(df::DataFrame)
    bdf = copy(df)
    for col in names(bdf) # latexify all expressions
        if eltype(bdf[!, col]) === Expr
            transform!(bdf, col => ByRow(latexify), renamecols=false)
        end
    end
    return pretty_table(bdf, backend=Val(:latex), show_subheader = false)
end

#' # Table KM-620
#+ results="tex"
beautify(df)

However, I was able to pass LaTeXStrings to replace the header and get PrettyTables to work nicely!
(The documentation says all LaTeXString must be wrapped in PrettyTables.LatexCell, but it worked without that for me.)

using DataFrames, Latexify, LaTeXStrings, PrettyTables

#+ results="hidden"
function beautify(df::DataFrame)
    bdf = copy(df)
    for col in names(bdf) # latexify all expressions
        if eltype(bdf[!, col]) === Expr
            transform!(bdf, col => ByRow(latexify), renamecols=false)
        end
    end
    header = [L"Material", L"Max.\ Temp.", L"m_2", L"m_3", L"m_4", L"m_5", L"\epsilon_p"]
    return pretty_table(bdf, backend=Val(:latex), header = header)
end

#' # Table KM-620
#+ results="tex"
beautify(df)

My only remaining issue is that the table is too wide to fit on letter paper. One option I found helpful is the ability to adjust the -papersize to accommodate the table. However, this does not affect how the title and markdown chunks are rendered, so the elements don't really line up anymore. (The title is still broken because of #418.)

 weave(normpath(@__DIR__, "..", "test", "latexify_tables.jl");
    doctype = "md2pdf",
    out_path = normpath(@__DIR__, "..", "KM620_tables.pdf"),
    latex_cmd = ["xelatex", "-shell-escape", "-halt-on-error", "-papersize=11in,8.5in"] # landscape orientation
)

It would be better to decrease the font size instead of increasing the paper size to avoid that issue, but I cannot find a weave or xelatex option to change font size.

None of these worked:

• weave(..., latex_cmd = ["xelatex", "-font-max=8"]
• weave(..., latex_cmd = ["xelatex", "-font-max=8pt"]
• weave(..., args = Dict(:line_width =>100)
• weave(..., args = Dict(:dpi=>50)

[AhmedSalih3d]

#' # Table KM-620
#+ results="tex"

Hi!

Were you able to get this to render as a table in the pdf output of Weave.jl? Whenever I try to do it, it just outputs the text and does not display any formatted table.. do you happen to have a simpler code example or the full code example so I can learn from it?

Thanks!