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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