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Tuesday, 19 January 2016

ggplot2 2.0.0 geom_smooth() requires different arguments...

A new version of ggplot (2.0.0) was released on December 21st 2015. The new version has changed the requirements of the arguments in the geom_smooth() function in ggplot2 which I have used to generate non-linear curves for enzyme kinetics curves and an LD50 plot.

The old code (pre ggplot 2.0.0) has the formula as an argument in the geom_smooth() function. I've changed one of the scripts - the one for the LD50 plot. I'll change the enzymology scripts over the next few days.

Old code:
# Add the line to graph
p <- p +  geom_smooth(method = "nls", 
              formula = y ~ bot+(top-bot)/(1+( x / LD50)^slope), 
              start=list(bot=20, top=95, LD50=3, slope=-12),
              se = F, size = 0.5)


The new code makes the arguments for the method used for smoothing more obvious. I can see the value but it's made work for me in the short term.

New ggplot 2.0.0 code:

# Add the line to graph using methods.args (New: Jan 2016)
p <- p +  geom_smooth(method = "nls",
                      method.args = list(formula = y ~ bot+(top-bot)/(1+( x / LD50)^slope), 
                                         start=list(bot=20, top=95, LD50=3, slope=-12)),
                      se = FALSE)


 Thanks to 오세진 and Ali for commenting on my scripts and bringing this to my attention.

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