Coloring labels using scatterplot3d in R
For the colors  argument you need to assign a vector with the same length as your data points. 

You don't explain how colors must be assigned to values of your output columms . In any regard, this would assign 4 different colors randomly: 

cols = sample(1:4, nrow(output), replace=TRUE) 


plot it with 

scatterplot3d(output$X2,output$X6 , output$X7 , color=cols, pch=19, cex=1)


You could create a new column in your dataframe, e.g. rgbcolor and assign that:

scatterplot3d(output$X2,output$X6 , output$X7 , color=output$rgbcolor, pch=19, cex=1)


pch is the plotting character id, usually 1, 19 or 20 (circle or larger dot or smaller dot. (see for yourself: plot(1:25, 1:25, pch=1:25))

Tune the cex param to make it larger or smaller (1 means size = 100%)