2017.12.16

Since yesterday, I have been looking into how to visualise our data and results. It has proven to be quite challenging. In my previous post, I showed a histogram of log10 of the adjusted p-values. But that plot was, for the lack of a better word, ugly. So now I'm crawling over different papers, looking for inspiration~

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Hours spent to try to learn how to plot in R have been fruitful. Et voilà, a volcano plot! This is for the progression between NASH and HCC.
I'm still trying to figure out how to modify the legends manually, but the dots are in 5 different colours:

• Red: q-val < 0.05, log2FoldChange over 2 fold (either direction), present in liver tissue;
• Light blue: q-val < 0.05, log2FoldChange less than 2 fold (either direction), present in liver tissue;
• Violet: q-val < 0.05, log2FoldChange over 2 fold (either direction);
• Gold: q-val < 0.05; and
• Dark grey: everything else.

I have also added a bit more to the code to plot for HS and SN progressions:


Legend:

• Red: q-val < 0.05, log2FoldChange over 2 fold (either direction);
• Light blue: q-val < 0.05; and
• Dark grey: everything else.

Edit 14.01.2018: I managed to do the legends on 13.01.