Editorial Revision: Artwork Guidelines

[tylerjereddy]

Attachment from Nature Methods Editorial team wrt formatting of images:

NMETH-P39410A_Figure_Guidelines_1569514283_1.pdf

[ilayn]

@mdhaber Should we assign ourselves to this ?

[mdhaber]

I'll take a more detailed look and let you know.

[tylerjereddy]

@mdhaber it looks like Figure 4 might already be in "vector" format (they accept PDF); I suppose it may need a slight resizing to match their guidelines for two-column width & height limits & possibly a font check to match their requirements

[tylerjereddy]

I imagine for Figure 3, it shouldn't be too hard to split that tikz code out of the manuscript & produce a standalone vector PDF as per their requirements.

[ilayn]

Figure 3 is already in vector format but sure we can separate the file out to a PDF. I think For fig 2 and 4, Matt has the inkscape files (and also TikZ version in #179).

I think we need to change the caption of Fig. 1 to maybe a quote. Feels strange to have it as a figure.

[tylerjereddy]

I think we need to change the caption of Fig. 1 to maybe a quote. Feels strange to have it as a figure.

Yeah, I think the specific request was to change it to a "Box" that wouldn't count against the word count total.

[mdhaber]

@ilayn I just created #263 for figures 2 and 4. If you could take care of 3 (please use Arial instead of Helvetica), I'd appreciate it. For consistency, could you use two of the colors from Figure 4?

It sounds like 1 needs to be changed in MS word?

[mdhaber]

I'd suggest that we don't change these in the LaTeX document; I would prefer the existing font for arXiv version 2.0.

[mdhaber]

@ilayn will you be able to convert the code coverage figure?

[ilayn]

@mdhaber I am a bit lost in the requirement between the Arxiv and the journal submission. Which one should I convert ?

The fonts are taken from the surrounding TeX document hence I am not selecting any fonts.

[mdhaber]

For Nature Methods, we have to submit a Word document. The figure is supposed to be a separate PDF: 180mm wide, and the text inside it should be Arial 7 pt. Can you produce the code coverage figure with that formatting? Full specifications are in the guidelines document at the top of this issue.

(We don't want the arXiv v2 submission to reflect these changes, so I'd only ask that you generate the figure as a PDF - not change the source in the LaTeX document here.)

[tylerjereddy]

@ilayn If you are swamped I can try to make the standalone PDF. We'll want to avoid long delays in resubmitting if possible. I suspect Matt & I still need to look over the paper carefully a little more given the conversion to Word, though I do hope we're converging on pretty decent quality soon.

[ilayn]

Just came home finally. Doing it now asap.

[ilayn]

This is the code coverage figure codecov.pdf

created via :

\documentclass{standalone}
\usepackage{fontspec}
\usepackage{pgfplotstable}
\setmainfont[SizeFeatures={Size=7}]{Arial}
\begin{document}

\begin{tikzpicture}[]
\pgfplotstableread[column/ver/.style=string type]{
ver totpyline covpyline uncovpyline totcompline covcompline uncovcompline
v0.12.1 33844 25721 8123 273634  142290 131344
v0.13.3 36638 28944 7694 338926  172852 166074
v0.14.1 37301 30587 6714 277643  147151 130492
v0.15.1 38339 30288 8051 304898  158547 146351
v0.16.1 40094 32075 8019 322398  167647 154751
v0.17.1 42566 34478 8088 340903  170452 170451
v0.18.1 44711 36216 8495 353417  173174 180243
v0.19.1 43823 36373 7450 436900  200974 235926
v1.0.0 106878 92984 13894 462574 208158 254416
}\covtable
    \begin{axis}[
    width=181.65mm,
    height=7cm,
    enlargelimits=false,
    ymin=0,
    ymax=6e5,
    stack plots=y,%   
    area style,
    xtick=data,
    ytick={2e5,4e5,6e5},
    xticklabels from table={\covtable}{ver},
    scaled y ticks=false,
    yticklabel={\pgfmathparse{\tick}\pgfmathprintnumber[precision=1,fixed zerofill=false,assume math mode]{\pgfmathresult}},
    y tick label style={/pgf/number format/.cd, fixed, 1000 sep={}},
    legend entries={Compiled (covered),Compiled (uncovered),Python (covered),Python (uncovered)},
    legend style={draw=none,fill=none, cells={align=left},/tikz/every even column/.append style={column sep=3mm}},
    legend columns=-1,
    legend image code/.code={\fill[#1] (0cm,-0.1cm) rectangle (0.2cm,0.1cm);},
    ]
  \addplot+[fill=blue!50] table[x expr=\coordindex, y=covcompline] {\covtable} \closedcycle;
  \addplot+[fill=blue!10] table[x expr=\coordindex, y=uncovcompline] {\covtable} \closedcycle;
  \addplot+[fill=red!70] table[x expr=\coordindex, y=covpyline] {\covtable} \closedcycle;
  \addplot+[fill=red!30] table[x expr=\coordindex, y=uncovpyline] {\covtable} \closedcycle;
\end{axis}
\end{tikzpicture}

\end{document}

[mdhaber]

@ilayn thanks for fixing the font. What is the 23.3584 number at the bottom left?

[ilayn]

Ah my bad. I was testing something. Editing comment now. ... Done. Thanks for catching that.