Compile Figure 1 in illustrator

[allyhawkins]

Closes #42 Closes #15

Here I combined the panels for Figure 1 into a full figure on illustrator. I took a look at the Author guidelines for figures for Cell Genomics as some guidance here.

• I updated the scripts to save the files as pdfs in addition to pngs. Do we want to keep both or should we just convert everything to pdf and remove the pngs?
• I put all of the panels into the figure and then adjusted all the fonts so that they are Arial size 6 or size 8. Axis labels and the numbers for each bar in the sample plot are all size 6. The titles of the facets, axis titles, and legends are size 8.
• I adjusted the linewidth for the facet boxes since they were closer to 2 to be 1.
• Here I also added in the project card example. We made a simplified version of one of the existing project cards that has almost all additional items so that we can mention them in the text. I did not adjust the font size or style here since it comes from the Portal. Do we like this? We chose this project because it had both publications and external accessions.
• I included both the ai file and the pdf.

[jaclyn-taroni]

General comment – tagging @sjspielman too – I'd remove saving the panels as PNGs unless we also need PNGs (I vaguely recall some conversation about too many points). But I'd add saving the assembled figures as PNGs. That's likely the format that's going to get used for writing using Manubot – the PDFs are what we'll use for submission – to say nothing of making it easier to review the figures via the GitHub interface.

It's probably too late for this conversation, but I'd put the AI files somewhere centralized on Google Drive instead. I'd expect them to be big, and the version control probably doesn't help us over and above the ability to roll things back up to 30 days in Google Drive. (We could also keep certain versions forever as I understand it: https://support.google.com/drive/answer/2409045?hl=en&co=GENIE.Platform%3DDesktop#zippy=%2Cdownload-recent-versions)

[allyhawkins]

General comment – tagging @sjspielman too – I'd remove saving the panels as PNGs unless we also need PNGs (I vaguely recall some conversation about too many points). But I'd add saving the assembled figures as PNGs. That's likely the format that's going to get used for writing using Manubot – the PDFs are what we'll use for submission – to say nothing of making it easier to review the figures via the GitHub interface.

This is fine with me. I wasn't sure if we would want both the pdfs and the pngs, but there are a small handful of panels where there are a lot of points so we used the pngs that we can keep as pngs.

We can also update to save the AI files as pngs.

It's probably too late for this conversation, but I'd put the AI files somewhere centralized on Google Drive instead. I'd expect them to be big, and the version control probably doesn't help us over and above the ability to roll things back up to 30 days in Google Drive. (We could also keep certain versions forever as I understand it: https://support.google.com/drive/answer/2409045?hl=en&co=GENIE.Platform%3DDesktop#zippy=%2Cdownload-recent-versions)

I'm also fine with moving the AI files to google drive. I can go ahead and make these changes for all the figures that I compiled.

[allyhawkins]

I made the following organizational changes that once approved we can apply to other figures. I'll work on the aesthetic updates next, but just wanted to get this part figured out.

• Removed the png files for individual panels where we don't need them.
• Moved the AI files to a folder on our drive, ScPCA/Manuscript figures.
• Saved the pdf and png versions of the compiled panels to compiled_figures/pngs and compiled_figures/pdfs.

[allyhawkins]

Something's wrong with the warning symbol in panel C. I also find the drop shadow for the panel to be too light to be effective.

I removed the box around the panel with the drop shadow and fixed the warning symbol.

This might be an edit at the panel generation step. I can't tell what the 1(?) adrenocortical carcinoma sample is that's not an initial diagnosis. Progressive? Making the lines in the pattern itself thinner might help with this, and I think it might also benefit the Brain and CNS panel.

I made all the linewidths to be 0.5. When you zoom in you can see the ACC tumor that is Unknown, but I think it's still not going to be the easiest to distinguish a pattern there with just one sample. What do we think of the updated linewidth though? @jaclyn-taroni

[jaclyn-taroni]

@allyhawkins

• The updated linewidth is much better, thanks. Naively, I might expect that to be a code change, too, but maybe that's too difficult.
• I think you do need something to indicate that the last panel is a card of some kind – try adding back the drop shadow and darkening it

[allyhawkins]

The updated linewidth is much better, thanks. Naively, I might expect that to be a code change, too, but maybe that's too difficult.

The only way to adjust the actual pattern linewidth is to adjust spacing and density. We are already using almost the smallest version of those and they don't just adjust linewidth so I thought it would be easier to just do it in illustrator.

I think you do need something to indicate that the last panel is a card of some kind – try adding back the drop shadow and darkening it

I added it back and darkened it, how does it look now @jaclyn-taroni?