Make an animation to visualize millions of points in 3 dimensions.

rotating-3d-mp4.R

library(data.table)
library(glue)
library(rgl)

# https://github.com/google/palette.js/blob/master/palette.js
mpn65 <- c(
  '#ff0029', '#377eb8', '#66a61e', '#984ea3', '#00d2d5', '#ff7f00', '#af8d00',
  '#7f80cd', '#b3e900', '#c42e60', '#a65628', '#f781bf', '#8dd3c7', '#bebada',
  '#fb8072', '#80b1d3', '#fdb462', '#fccde5', '#bc80bd', '#ffed6f', '#c4eaff',
  '#cf8c00', '#1b9e77', '#d95f02', '#e7298a', '#e6ab02', '#a6761d', '#0097ff',
  '#00d067', '#000000', '#252525', '#525252', '#737373', '#969696', '#bdbdbd',
  '#f43600', '#4ba93b', '#5779bb', '#927acc', '#97ee3f', '#bf3947', '#9f5b00',
  '#f48758', '#8caed6', '#f2b94f', '#eff26e', '#e43872', '#d9b100', '#9d7a00',
  '#698cff', '#d9d9d9', '#00d27e', '#d06800', '#009f82', '#c49200', '#cbe8ff',
  '#fecddf', '#c27eb6', '#8cd2ce', '#c4b8d9', '#f883b0', '#a49100', '#f48800',
  '#27d0df', '#a04a9b'
)

# 4 columns: X, Y, Z, color
coords <- fread("coords.tsv.gz")

# Thanks to Bryan Hanson for this post:
# https://stackoverflow.com/a/14479967/330558

rgl.open()
# background color 
rgl.bg(color = "white")
rgl.points(
  x = coords[,1],
  y = coords[,2],
  z = coords[,3],
  col = mpn65[coords$color]
)
my_height <- 900
my_width <- my_height * 1.618
par3d(windowRect = c(0, 0, my_width, my_height)) # make the window large
par3d(zoom = 0.6) # larger values make the image smaller
# you can test your settings interactively at this point
my_params <- par3d("userMatrix") # save your settings to pass to the movie

dir.create("frames", showWarnings = FALSE)
movie3d(
  par3dinterp(
    time = (0:2)*5,
    userMatrix = list(
      my_params,
      # rotate3d(my_params, pi / 4, 0, 1, 0), 
      rotate3d(my_params, pi, 0, 1, 0),
      rotate3d(my_params, -2 * pi, 0, 1, 0)
    ),
    method = "linear",
    extrapolate = "constant"
 ), 
 duration = 10,
 fps      = 30,
 movie    = "frame",
 convert  = FALSE,
 clean    = FALSE,
 dir      = "frames"
)
rgl.close()

cmd <- glue(
  "ffmpeg -y -framerate 30 -i frames/frame%03d.png -pix_fmt yuv420p movie.mp4"
)
system(cmd) # convert the .png files to a .mp4 file
system("rm -rf frames") # we don't need the .png files anymore

Below is an example of the output produced by this R script.

800k_cells.mp4