Specifying lower limits of a facetted plot with scale="free" in ggplot2

[Kendra Millard]

    df <- data.frame(Taxa=c(rep("A", 4), rep("B", 4)),
                     Day=as.factor(c(1,1,2,2,1,1,2,2)),
                     Treatment=c(rep(c("t1","t2"),4)),
                     Values=c(100,110,120,130, 120, 130,150, 1800),
                     SD = c(10,11,12,13,12,13,14,200)) # i have one big outlier in the data
   
    library(ggplot2)
    p1 <- ggplot(df, aes(x=Day, ymax=Values+SD, ymin=Values-SD, y=Values, fill=Treatment))+
      geom_bar(stat="identity", position=position_dodge(width=0.7), col="black", width=0.7) +
      facet_wrap(~Taxa, scale="free_y", nrow=2) +
      scale_y_continuous(labels = scales::scientific) +
      geom_errorbar(position=position_dodge(width=0.7), col="black", lty="solid", width=0.3)
    p1

i tried:

    p1 + expand_limits(ylim = c(100, NA)) # is ignored
    p1 + scale_y_continuous(labels = scales::scientific, limits = c(100, NA)) # removes geom_bar
    p1 + coord_cartesian(ylim=100,NA)  # error


I have been asked to start a similar, but more complex plot at a fixed y-value, but let ggplot calculate the x-max individually for each facet. But with `scale="free_y"` is seems to be impossible. Since i have this one big outlier, i do not want to control the ymax globally. Is there a way to achieve this, without plotting all Taxa individually?

At SO, it was suggested to tinker around with y-values to shift the the bar baseline:
https://stackoverflow.com/questions/35324892/ggplot2-setting-geom-bar-baseline-to-1-instead-of-zero

But this does not work with scales::scientific in the scale_y_continous call.

[Brandon Hurr]

p1 + scale_y_continuous(labels = scales::scientific, limits=c(100, NA), oob = scales::rescale_none)

From: https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim

I'm not sure why this works, but it seems to fix it.

Brandon

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