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Currently there seems to only be the option to manually control the subfigure widths, which resize the figures per line as in the documentation. For plot output from knitr or jupyter, that can be resized (unlike images that are embedded without distortion), it should be possible to set heights for the subfigures as well.
Currently if you set layout-nrow: 3 as below, you just get three full-size plots (as if they would be plotted by themselves), one after the other.
```{r}
#| layout-ncol: 3
plot(cars)
plot(pressure)
plot(mtcars)
```I have also noticed when looking into this that currently the subplots are just scaled-down versions of the full-size plots, resulting in smaller font sizes and the like, rather than rendering the plot itself in a smaller area first, and then inserting it into the subfigure.