The pdf format works well for large numbers of plots on a single page. You can use a viewer like Acrobat Reader to zoom in to the areas of interest. Ideally you can arrange the plots in a meaningful order, maybe where both their horizontal and vertical position convey information.

If you want something you can actually print or read without zooming in and if you can live with a slightly more abstract view of your data you might try putting multiple box plots in a single graph. Something like:

n = 1000
m = 49

data = data.frame(x = rnorm(n), y = trunc(runif(n, min = 1, max = m + 1)))

splits = split(data$x, data$y)

o = order(sapply(splits, median), decreasing = TRUE)

boxplot(splits[o], horizontal = TRUE)

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