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chrisamiller / fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors
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Evaluation nested too deeply: infinite recursion #13

Closed ghost closed 6 years ago

ghost commented 6 years ago

Dear chrisamiller, I am trying to run fishplot but everytime I get this error of infinite recursion error. Also, could you please explain that should we consider VAF's in the matrix and what about the parents. I donot understand the parent column? What does this refer to? My code is: library(fishplot) timepoints=c(0,300,500,700,1200) frac.table = matrix( c(100,90,02,30,45, 9,6,02,02,02, 38,19,02,22,22, 44,39,02,31,50, 02,02,02,59,90), ncol=length(timepoints)) parents = c(1,1,1,1) fish = createFishObject(frac.table,parents,timepoints=timepoints, clone.labels=c("Subclone 1","Subclone 2","Subclone 3", "Subclone 4", "Subclone 5" )) fish = layoutClones(fish) sample.times = c(0,1200) pdf("clonal.out.pdf",width=8,height=4) fishPlot(fish,shape="spline",title.btm="Clonal", vlines=sample.times, vlab=sample.times, cex.title=0.5, bg.type="solid") drawLegend(fish) dev <- dev.off()

Error: evaluation nested too deeply: infinite recursion / options(expressions=)? Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)?

chrisamiller commented 6 years ago

The parent vector describes the relationship of nested subclones. For example, in this image (second plot on the README page): https://camo.githubusercontent.com/8bf7791c59bf2669c9e39a7d00ea18454f871617/687474703a2f2f692e696d6775722e636f6d2f67594f323373692e706e67

The parental relationship looks like c(0,1,1,3). That is, the founding clone (grey) has no parent clone, the purple subclone is derived from the grey clone, as is the orange subclone. The yellow subclone is derived from the third (orange) subclone.

Fix that parental vector and I imagine things will work.

ghost commented 6 years ago

Thank you for your suggestions. I did it finally. Here is the plot" Final Fish.pdf