R help - Nov 2011 - tip: large plots

Hi all,

I'm working with a bunch of large graphs, and stumbled across
something useful. Probably many of you know this, but I didn't and so
others might benefit.

Using pch="." speeds up plotting considerably over using symbols.
> x <- runif(1000000)
> y <- runif(1000000)
> system.time(plot(x, y, pch="."))
   user  system elapsed
  1.042   0.030   1.077
> system.time(plot(x, y))
   user  system elapsed
 37.865   0.033  38.122

If you have enough points, the result is also more legible.

Choice of which pch symbol makes a difference too, the default pch=1 being
the slowest of what I tried, but "." is by far the speediest.
> system.time(plot(x, y, pch=0))
   user  system elapsed
 11.191   0.011  11.270
> system.time(plot(x, y, pch=1))
   user  system elapsed
 38.024   0.008  38.245
> system.time(plot(x, y, pch=2))
   user  system elapsed
 14.140   0.027  14.270
> system.time(plot(x, y, pch=3))
   user  system elapsed
 15.696   0.011  15.799
> system.time(plot(x, y, pch=4))
   user  system elapsed
 18.770   0.007  18.888

This is a vanilla R session, 2.13.1 for x86_64-redhat-linux-gnu. I
haven't tried it on any other OS, but it's making my life a lot
smoother right now.

Sarah

-- 
Sarah Goslee
http://www.functionaldiversity.org

Very cool.  Sadly, as far as I can tell, it doesn't work with ggplot though
:(

> x<-runif(1e6)
> y<-runif(1e6)
> system.time(plot(x,y,pch='.'))
   user  system elapsed
  0.824   0.012   0.845
> system.time(plot(x,y))
   user  system elapsed
 33.422   0.016  33.545
> system.time(print(qplot(x,y)))
   user  system elapsed
 45.142   0.228  45.687
> system.time(print(qplot(x,y,pch='.')))
   user  system elapsed
 47.483   1.060  49.040
> system.time(print(qplot(x,y,shape='.')))
   user  system elapsed
 44.807   0.689  45.710


On Fri, Nov 18, 2011 at 11:03 AM, Sarah Goslee
<sarah.goslee@gmail.com>wrote:
> Hi all,
>
> I'm working with a bunch of large graphs, and stumbled across
> something useful. Probably many of you know this, but I didn't and so
> others might benefit.
>
> Using pch="." speeds up plotting considerably over using symbols.
>
> > x <- runif(1000000)
> > y <- runif(1000000)
> > system.time(plot(x, y, pch="."))
>   user  system elapsed
>  1.042   0.030   1.077
> > system.time(plot(x, y))
>   user  system elapsed
>  37.865   0.033  38.122
>
> If you have enough points, the result is also more legible.
>
> Choice of which pch symbol makes a difference too, the default pch=1 being
> the slowest of what I tried, but "." is by far the speediest.
>
> > system.time(plot(x, y, pch=0))
>   user  system elapsed
>  11.191   0.011  11.270
> > system.time(plot(x, y, pch=1))
>   user  system elapsed
>  38.024   0.008  38.245
> > system.time(plot(x, y, pch=2))
>   user  system elapsed
>  14.140   0.027  14.270
> > system.time(plot(x, y, pch=3))
>   user  system elapsed
>  15.696   0.011  15.799
> > system.time(plot(x, y, pch=4))
>   user  system elapsed
>  18.770   0.007  18.888
>
> This is a vanilla R session, 2.13.1 for x86_64-redhat-linux-gnu. I
> haven't tried it on any other OS, but it's making my life a lot
> smoother right now.
>
> Sarah
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

Dear Sarah,

RE:
> Hi all,
> 
> I'm working with a bunch of large graphs, and stumbled across
> something useful. Probably many of you know this, but I didn't and so
> others might benefit.
> 
> Using pch="." speeds up plotting considerably over using symbols.
> 
>> x <- runif(1000000)
>> y <- runif(1000000)
>> system.time(plot(x, y, pch="."))
>   user  system elapsed
>  1.042   0.030   1.077
>> system.time(plot(x, y))
>   user  system elapsed
> 37.865   0.033  38.122
> 
> If you have enough points, the result is also more legible.
> 
> Choice of which pch symbol makes a difference too, the default pch=1 being
> the slowest of what I tried, but "." is by far the speediest.
> 
>> system.time(plot(x, y, pch=0))
>   user  system elapsed
> 11.191   0.011  11.270
>> system.time(plot(x, y, pch=1))
>   user  system elapsed
> 38.024   0.008  38.245
>> system.time(plot(x, y, pch=2))
>   user  system elapsed
> 14.140   0.027  14.270
>> system.time(plot(x, y, pch=3))
>   user  system elapsed
> 15.696   0.011  15.799
>> system.time(plot(x, y, pch=4))
>   user  system elapsed
> 18.770   0.007  18.888
> 
> This is a vanilla R session, 2.13.1 for x86_64-redhat-linux-gnu. I
> haven't tried it on any other OS, but it's making my life a lot
> smoother right now.
> 
> Sarah



With Mac OS10 (Snow Leopard, MacBookPro, R version 2.14.0), it 's a bit
different:
2.14)
source("/var/folders/t6/t6uCNQmsHsSw6tS6HuHp4U+++TI/-Tmp-//Rtmp4ZzIWp/file6b861d06")
[1] "plot symbol . (dot)"
   user  system elapsed 
 16.620   0.087  16.731 
[1] "plot symbol default (circle)"
   user  system elapsed 
 53.132   0.134  52.959 
[1] "symbol#  0"
   user  system elapsed 
 18.828   0.090  18.803 
[1] "symbol#  1"
   user  system elapsed 
 53.046   0.134  52.877 
[1] "symbol#  2"
   user  system elapsed 
 22.000   0.154  22.401 
[1] "symbol#  3"
   user  system elapsed 
 20.794   0.096  20.763 
[1] "symbol#  4"
   user  system elapsed 
 23.534   0.098  23.542 

It seems that even-numbered symbols are plotted faster than the odd ones

By the way, I learn a lot about R programming by just following r-help!

Best regards,


Franklin Bretschneider
--
Dept Biologie
Kruytgebouw W711
Padualaan 8
3584 CH Utrecht
The Netherlands
--
f.bretschneider at uu.nl

Another few data points, just for the heck of it.  This is on a 2.66GHz 
Intel Core Duo iMac.


Rgames> system.time(plot(runif(1e6),runif(1e6)))
    user  system elapsed
  34.405   0.079  34.432
Rgames> system.time(plot(runif(1e6),runif(1e6),pch='.'))
    user  system elapsed
  12.602   0.032  12.596

Rgames> system.time(print(xyplot(runif(1e6)~runif(1e6))))
    user  system elapsed
  36.651   0.837  37.371

Rgames> system.time(print(xyplot(runif(1e6)~runif(1e6),pch='.')))
    user  system elapsed
  16.866   0.777  17.578

Rgames> system.time(scatterplot3d(runif(1e6),runif(1e6),rep(1,1e6)))
    user  system elapsed
  36.081   0.959  36.932
Rgames> 
system.time(scatterplot3d(runif(1e6),runif(1e6),rep(1,1e6),cex.symbols='.'))
    user  system elapsed
  18.834   0.864  19.629
-- 

Sent from my Cray XK6
"Pendeo-navem mei anguillae plena est."