plot.BchronologyRun not recognizing normal plot arguments

[cmbarton]

Hi Andy. Beginning in some recent version plot.BchronologyRun stopped recognizing standard plot arguments xlab, ylab, main, and cex.

It also does not seem to be producing a plot object that is recognized by subsequent plot commands like abline or axis. When these are run immediately after plot.BchronologyRun, it generates the error: "plot.new has not been called yet". So there is no way to modify the plot.

I updated to bchron 4.7.5 and R 4.0.5 and have the newest Mac OS.

[andrewcparnell]

Hi Michael,

Apologies this changed a few versions ago but I don't think I documented it well. You can customise the plots by adding on standard ggplot2 commands. Here's a reproducible example:

library(Bchron)
library(ggplot2)
data(Glendalough)
GlenOut = with(Glendalough, 
               Bchronology(ages=ages,
                           ageSds=ageSds, 
                           calCurves=calCurves,
                           positions=position, 
                           positionThicknesses=thickness,
                           ids=id, 
                           predictPositions=seq(0,1500,by=10)))
plot(GlenOut) +
  labs(title = "Glendalough",
       x = "Age (cal years BP)",
       y = "Depth (cm)")

I've updated the documentation and the manual to make this clearer.

[cmbarton]

Thanks. ggplot2 commands will be very nice. Is this the case for all bchron plots now?

[andrewcparnell]

It is for the functions which use ggplot2, which I think is all of them apart from plot.BchronDensityRun. One day I'll get round to improving that function too.

[blongworth]

Plot labels are not working in the current github version. Running the example in the comment above with version 4.7.6 does add a plot title, but leaves x and y axis labels as the default "Age" and "Position".

[andrewcparnell]

Thanks for spotting this - there was a typo in the above code snippet (should have been x and y instead of xlab and ylab). I've edited it and it should work now.

Andrew

[blongworth]

Can't believe I missed this! I had used the correct parameters earlier in the same document. Would be nice if ggplot returned a warning if unknown parameters are passed to labs(). I noticed the BChron vignette has the same typo. I'll submit a PR to fix. Thanks!

[andrewcparnell]

Doubly well spotted!