Rather then having a new window with a single scatterplot packed into it, you can also specify a parent widget for the Loon plot widget and place it using any layout manager you wish. To create the scatterplot widget use the parent argument

tt <- tktoplevel()
p1 <- l_plot(parent=tt, x=c(1,2,3), y=c(3,2,1))
p2 <- l_plot(parent=tt, x=c(4,3,1), y=c(6,8,4))

You will only see an empty window and the scatterplots showing up in the worldview of the inspector but the loon scatterplot widget will not show up. The p1 and p2 Loon plot widgets need to be placed on the window using a geometry manager such as pack or grid. This is how layouts of multiple Loon plot widgets in one window can be achieved. For example, a 1 row 2 columns layout may be achieved with the grid geometry manager as follows

tkgrid(p1, row=0, column=0, sticky="nesw")
tkgrid(p2, row=0, column=1, sticky="nesw")
tkgrid.columnconfigure(tt, 0, weight=1)
tkgrid.columnconfigure(tt, 1, weight=1)
tkgrid.rowconfigure(tt, 0, weight=1)

And if desired, you can specify a title for the window

tktitle(tt) <- "Loon plots with custom layout"