OncoPrint figures

[jaclyn-taroni]

⚠️ Stacked on #1193

Addressing #1177 and #1178, but made slightly different choices than what is detailed in those issues. Importantly, I've only removed cancer groups with less than 10 samples for the other CNS plot. In the current version of #1193, cancer groups with n < 10 in the other 3 broad histologies are randomly assigned a hex code from the Greys color brewer palette. There are over 20 cancer groups with n < 10 that'd be included in the Other CNS plot (fewer than that when you consider which groups actually show up in the plots using the other CNS genes of interest list), so it's not feasible to randomly assign greys to them in the same way. Instead, the Other CNS cancer groups with n < 10 are in a supplemental PDF where they are assigned colors based on the Paired color brewer palette.

Similar to #1194, I've created an Rscript (figures/scripts/fig2-oncoprint-landscape.R) that creates individual panels & legends as PDFs (figures/pdfs/fig2/panels) and then I've assembled a draft figure in Illustrator. You can see that draft as figures/pngs/figure2.png. I've removed the old script that used multipanelfigure to assemble the figure from the PNGs in the module (figures/scripts/oncoprint-landscape.R).

I needed to rerun the oncoprint-landscape module because we had been manually updating the OncoPrint palette, rather than updating the script that has all the palettes, so some colors got dropped in #1161 when the tumor descriptor palette was created and those colors were missing when things were run as part of #1189. I've also deprecated the former figure 2 script to hopefully avoid confusion.

[jharenza]

Instead, the Other CNS cancer groups with n < 10 are in a supplemental PDF where they are assigned colors based on the Paired color brewer palette.

I like this! I will modify Supplemental Figure 3 in the manuscript repo to add this panel.

For the oncoprint_alteration_legend.pdf, it looks like we have a few alterations/colors which we do not use due to the renaming of CNV alterations, so I updated the code to remove those. I also made a few suggestions for swapping some colors.

The only other minor thing I saw was that the oncoprint panel pdfs do not contain goi in the filename while the analysis module does, so maybe you can add this to be consistent (I double checked you are using goi here and you are 😄 ).

[jharenza]

Suggested change

	Hom_Deletion #313695
	Hem_Deletion #abd9e9

We are not actually using these

[jaclyn-taroni]

We need to edit the script that generates them (figures/scripts/color_palettes.R), not this file directly. Editing this file directly caused problems (see the mentions of #1161 and #1189 in the original PR comment).

[jharenza]

gotcha!

[jharenza]

Suggested change

	Del #0072B2
	Amp #D55E00
	Del #386db0
	Amp #c51b7d

new color suggestions

[jharenza]

Suggested change

	5'Flank #386db0
	3'Flank #c51b7d
	5'Flank #7CCBAC
	3'Flank #FD8344

new color suggestions - moving these two to Amp/Del, where I had meant them to be previously, but it looks like things got shuffled. Let's see what these look like 😬

[jharenza]

Suggested change

High_Level_Gain #FF0000

We are not using this one either

[jaclyn-taroni]

@jharenza I've updated the color palette and rerun the figures. Can you take a look before I invest any more effort, i.e., attempt to put together the multipanel version?

[jharenza]

@jharenza I've updated the color palette and rerun the figures. Can you take a look before I invest any more effort, i.e., attempt to put together the multipanel version?

The colors I mentioned look fine, but what is "Complex_event"? I hadn't seen that before and it is black, along with nonsense mutations, so that would need a new color if we use it. I would think it would fit into other categories, unless it is an SV of some sort?

[jaclyn-taroni]

but what is "Complex_event"? I hadn't seen that before and it is black, along with nonsense mutations, so that would need a new color if we use it. I would think it would fit into other categories, unless it is an SV of some sort?

A couple notes:

• Complex event is not new as of my most recent update - we can see it here in f6bcf25: https://github.com/jaclyn-taroni/OpenPBTA-analysis/blob/f6bcf253ac3ceb242e2557e82ad259ea3eb0f729/analyses/oncoprint-landscape/plots/primary-plus_embryonal_oncoprint.png
• Complex event isn't documented as far as I can tell outside of: https://github.com/PoisonAlien/maftools/blob/db66c013049e04999eca8e6aaa440cfe1eb08703/R/oncoplot.R#L644 which I take to mean that we expect to see it when a gene is impacted by both by a mutation and a copy number alteration of some kind
• It's the same navy (or at least close enough) as Translation Start Site. I'll add it to the palette with another color. I'll probably start with a darker green.

[jaclyn-taroni]

@jharenza ready for another look

[jharenza]

Complex event isn't documented as far as I can tell outside of: https://github.com/PoisonAlien/maftools/blob/db66c013049e04999eca8e6aaa440cfe1eb08703/R/oncoplot.R#L644 which I take to mean that we expect to see it when a gene is impacted by both by a mutation and a copy number alteration of some kind

Interesting, I had not noticed that before and I wonder if that was earlier code before the CNVs were added as smaller rectangles in which we are able to see a mutation/fusion + a CNV with two different colors. That begs the question why is it showing as complex rather than the two colors for mut/cnv, unless perhaps a multi-hit SNV + CNV? I can't look into that right now, but probably can later tonight. If you get to it before me, let me know.

[jaclyn-taroni]

From a cursory look at the code, I think it might arise when there are multiple CNVs. If we set writeMatrix = TRUE when we call oncoplot(), that might help confirm/reject that idea.

[jharenza]

From a cursory look at the code, I think it might arise when there are multiple CNVs. If we set writeMatrix = TRUE when we call oncoplot(), that might help confirm/reject that idea.

Just noting that we should explain this in the figure legend.

I can't distinguish between the green for complex event and missense, but otherwise, the flank/amp colors are ok for me.

[jaclyn-taroni]

Going to request a review from @cbethell! The main file to take a look at is: figures/scripts/fig2-oncoprint-landscape.R. We can add the compiled figures later.

[cbethell]

This LGTM! Just left a comment re: fixing the file path to the figure script in generate-figures.sh (tested it to make sure it works successfully and it does) 👍