a question about fishplot

Question

[meizi2015]

Hello All,

I want to use fishplot in R to draw a model picture like this: https://ibb.co/h7WtX0

Here is my code:

library(fishplot)

timepoints=c(0,1,5,10)

frac.table=matrix(c(2,0,0,3,1,0,50,40,2,90,75,30),ncol = length(timepoints))
parents = c(0,1,2)

fish = createFishObject(frac.table,parents,timepoints=timepoints)
fish = layoutClones(fish)
fish = setCol(fish,col=c("grey","lightpink","lightblue"))`

fishPlot(fish,shape="spline",title.btm="Sample1",
         cex.title=0.5,bg.type = 'solid',bg.col = c('white'))

But finally i get a picture :https://ibb.co/eoHgkL

I tried several times changing the matrix and the picture is still sunk in the middle and looks ugly. Can anyone tell me how to fix it?

Thanks!

[Santosh Anand]

Are you able to reproduce their USAGE example ?

https://github.com/chrisamiller/fishplot

[meizi2015]

Yes, I think i understand the example and i set my own timepoint, matrix and parents. The problem is that i can't get a roundish cruve in my picture. In timepoint 3 there is alaways a sunken and i don't know why.

Answer 1

[Chris Miller]

That has to do with the way that the splining function is generating curves to fit your points. Unfortunately, the goals of having perfectly smooth curves and conforming precisely to the values you enter are mutually exclusive (or at least quite difficult!) If you want a perfectly smooth one, you can omit your middle timepoints and things should look smoother. Alternately, you can try adding additional, intermediate timepoints to smooth things out. As a final option, you can pull that plot into Illustrator (or Inkscape, etc) to try to tweak things manually.

[Chris Miller]

I should mention that you can also dig into the drawing code if you really want to tweak things. If you come up with useful options, pull requests are welcome!