R help - Jan 2013 - Very slow in processing the equation in the scatter plot ggplot

Hello All,

I have plotted a scatter plot in ggplot2 and added a regression line and a
regression equation. But the processing is very very slow. One reason might
be because I have so many data pairs. Is there any way to speed up this
code ? I need to create a multiple layout as well.

The code I have used is as follows:

setwd("C:/Users/jzd0009/Documents/R software")
mydata <- read.table("dataset.csv",header=TRUE,sep=",")
library(ggplot2)
p <-
ggplot(mydata,aes(date))+geom_line(aes(y=modeled,colour="modeled"))+geom_line(aes(y=observed,colour="observed"))
p


p1 <- ggplot(mydata, aes(modeled,observed))+geom_point(aes(y=observed))
#p1 <- p1+stat_smooth()

lm_eqn = function(mydata){
  m = lm(modeled ~ observed, mydata);
  eq <- substitute(italic(y) == a + b %.%
italic(x)*","~~italic(r)^2~"="~r2,
                   list(a = format(coef(m)[1], digits = 2),
                        b = format(coef(m)[2], digits = 2),
                        r2 = format(summary(m)$r.squared, digits = 3)))
  as.character(as.expression(eq));
}
p1 <- p1 + geom_text(aes(x = -0.1, y = 0.5, label = lm_eqn(mydata)), parse
= TRUE)
p1 <-
p1+geom_smooth(method="lm",se=FALSE,color="green",formula=y~x,lwd=2)
p1

#For multiple layout

library(grid)
grid.newpage()
pushViewport(viewport(layout=grid.layout(2,2)))
vplayout <- function(x,y)
viewport(layout.pos.row=x,layout.pos.col=y)
print(p,vp=vplayout(1,1))
print(p1,vp=vplayout(1,2))
print(p,vp=vplayout(2,1))
print(p1,vp=vplayout(2,2))


The data for the above code can be found on
https://www.dropbox.com/s/1xrgvnge0prf0a6/dataset.csv

Thank you so much.

Best Regards,
Janesh Devkota

	[[alternative HTML version deleted]]

Hi,

One problem is that you are printing the regression equation multiple
times. Compare:
> system.time({
+   p2 <- p1 + annotate(x = -0.1, y = 0.5, geom="text", label
lm_eqn(mydata), parse = TRUE)
+   print(p2)
+   })
   user  system elapsed
  0.930   0.006   0.976
> system.time({
+   p3 <- p1 + geom_text(aes(x = -0.1, y = 0.5, label lm_eqn(mydata)), parse
= TRUE)
+   print(p3)
+   })
   user  system elapsed
 38.667   0.046  38.956


So, use annotate instead of geom_text (as a bonus the equation will
look better). Further speedups are possible, but this is probably the
biggest problem.

Best,
Ista
On Mon, Jan 21, 2013 at 4:21 PM, Janesh Devkota
<janesh.devkota at gmail.com> wrote:
> Hello All,
>
> I have plotted a scatter plot in ggplot2 and added a regression line and a
> regression equation. But the processing is very very slow. One reason might
> be because I have so many data pairs. Is there any way to speed up this
> code ? I need to create a multiple layout as well.
>
> The code I have used is as follows:
>
> setwd("C:/Users/jzd0009/Documents/R software")
> mydata <-
read.table("dataset.csv",header=TRUE,sep=",")
> library(ggplot2)
> p <-
>
ggplot(mydata,aes(date))+geom_line(aes(y=modeled,colour="modeled"))+geom_line(aes(y=observed,colour="observed"))
> p
>
>
> p1 <- ggplot(mydata, aes(modeled,observed))+geom_point(aes(y=observed))
> #p1 <- p1+stat_smooth()
>
> lm_eqn = function(mydata){
>   m = lm(modeled ~ observed, mydata);
>   eq <- substitute(italic(y) == a + b %.%
> italic(x)*","~~italic(r)^2~"="~r2,
>                    list(a = format(coef(m)[1], digits = 2),
>                         b = format(coef(m)[2], digits = 2),
>                         r2 = format(summary(m)$r.squared, digits = 3)))
>   as.character(as.expression(eq));
> }
> p1 <- p1 + geom_text(aes(x = -0.1, y = 0.5, label = lm_eqn(mydata)),
parse
> = TRUE)
> p1 <-
p1+geom_smooth(method="lm",se=FALSE,color="green",formula=y~x,lwd=2)
> p1
>
> #For multiple layout
>
> library(grid)
> grid.newpage()
> pushViewport(viewport(layout=grid.layout(2,2)))
> vplayout <- function(x,y)
> viewport(layout.pos.row=x,layout.pos.col=y)
> print(p,vp=vplayout(1,1))
> print(p1,vp=vplayout(1,2))
> print(p,vp=vplayout(2,1))
> print(p1,vp=vplayout(2,2))
>
>
> The data for the above code can be found on
> https://www.dropbox.com/s/1xrgvnge0prf0a6/dataset.csv
>
> Thank you so much.
>
> Best Regards,
> Janesh Devkota
>
>         [[alternative HTML version deleted]]
>
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