Common Figure Setting

[othomantegazza]

This isn't urgent.

We might have to decide a common set of colors, species orders, plotting characters etc... for the figures.

Shall I note down the ones that I am currently using in the README? then we can see how to improve them.

[othomantegazza]

How do we do it, shall we store those parameters in some kind of config file?

[TomHarrop]

Yep, I'll look after that once we decide where we're submitting. For now, I suggest sizing all plots to a maximum of 180 × 240 mm, and using something like 8 pt sans serif for any text on the plots.

[TomHarrop]

Since we're aiming for PNAS, here's their figure guide.

How about 114 or 178 mm wide with max height 225 mm?

For font Helvetica 8pt would be easiest from R in Ubuntu although Arial is possible too.

I can make a ggplot2 theme if that helps.

High-resolution figure files are not required for initial submissions. Resolution of at least 300 dpi for all figures is required. EPS, high-resolution PDF, and PowerPoint are preferred formats for figures that will be used in the main text. Authors may submit PRC or U3D files for 3D images; these must be accompanied by 2D representations in TIFF, EPS, or high-resolution PDF format. (See SI below for supplementary material.) Color images must be in RGB (red, green, blue) mode. Include the font files for any text.

Images must be final size, preferably one column width (8.7 cm). Figures wider than one column should be sized to 11.4 cm or 17.8 cm wide. Numbers, letters, and symbols should be no smaller than 6 points (2 mm) and no larger than 12 points (6 mm) after reduction and must be consistent. Composite figures must be preassembled. Figures must be submitted as separate files, not embedded in manuscript text. See the PNAS Digital Art Guidelines. Figures and tables may be enlarged to improve legibility of text.

[TomHarrop]

2. Start by making the height of your canvas less than the height of the page to accomodate the figure legend. Recommended max height: 54 picas / 9” / 22.5 cm. Use one of the following widths: 1 column wide (20.5 picas / 3.42” / 8.7 cm) 1.5 columns wide (27 picas / 4.5” / 11.4 cm) 2 columns wide (42.125 picas / 7” / 17.8 cm)

[TomHarrop]

Labeling and font usage: Please use the same font for all figures in your manuscript. Use standard fonts such as Arial, Helvetica, Times, Symbol, Mathematical Pi, and European Pi. Embed all fonts used in vector files. In Illustrator, check the box that reads Embed Fonts when saving the file. See page 3 for more detailed instructions on embedding fonts.

[TomHarrop]

@othomantegazza it would also be good to use consistent colours. You suggested viridis, which is fine, but there is no diverging scale (e.g. when you have positive and negative values and you want 0 to be the "middle" of the scale).

[TomHarrop]

@othomantegazza I've been using this for consistent naming of phenotypes. Let me know if we need any changes.

mtp_name	cali_name	full_name	short_name	text_name
Rachis_length (RL)	RL	rachis_length	RL	Rachis length
Pb_nb (PbN)	PbN	primary_branch_number	PBN	Primary branch number
Pb_Length_average (PbL in cm)	PbL	primary_branch_length	PBL	Primary branch length
primary branch internode average length (PBintL in cm)	PbIntL	primary_branch_internode_length	PBIL	Primary branch internode length
Sb_nb (SbN)	SbN	secondary_branch_number	SBN	Secondary branch number
secondary branch average length (SbL in cm)	SbL	secondary_branch_length	SBL	Secondary branch length
secondary branch internode average length (SbintL in cm)	SbIntL	secondary_branch_internode_length	SBIL	Secondary branch internode length
Tb_nb (TbN)	TbN	tertiary_branch_number	TBN	Tertiary branch number
Sp_nb (SpN)	SpN	spikelet_number	SpN	Spikelet number
	PanL	panicle_length	PL	Panicle length

[othomantegazza]

I missed some of your messages on this thread. Sorry, thank you for your input.

I'm not sure how should we organize all these standards, in a folder called lib?

Regarding the journal, we should discuss it in the next meeting. Could it be Plant Phys? We could also discuss if we want to use Biorxiv.

When we decide the journal, it would be great if you can do a ggplot theme. I'm also curious to learn how to make one.

Regarding the standard names for the phenotypes, do you have a csv of that table? In case can you put it on github?

I think that the standard short name is the cali_name, then maybe we can keep the full_name and the text_name column also. Maybe we could also add the measurement unit to the text_name column.

We might have to conform the raw data to cali_name standard. But let's wait for this, because the real raw data here should be the XML files.

Best :)

Otho

[TomHarrop]

Yes, sorry, it's in data-raw.

The capitalisation in cali_name is strange, SpN looks like it should be Secondary panch number ;) short_name was an attempt to standardise them.