first of all, please show what packages are you using in your code (dplyr, scales).

there's a boost module for highcharts. sadly rcharts dont include that module by default so you need to add manually.

by other hand. there is a new wrapper for highcharts called highcharter which have an implementation of this module. using it dont take more than 1 second to chart the 3900 columns.

highchart2() %>% 
  hc_title(text = "not so slow chart ;)") %>% 
  hc_subtitle(text = "thanks boost module") %>% 
  hc_chart(zoomtype = "x", animation = false, type = "column") %>% 
  hc_plotoptions(series = list(turbothreshold = 4000)) %>% 
  hc_add_serie(data = input)

check the speed/here:

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