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Dustin Fife

2014-May-07 18:37 UTC

[R] plotting lines on old graph after par(new=TRUE)

Hi,

In my work, I often investigate relationships between highly skewed data.
Example:

set.seed(111)
require(MASS)
d = data.frame(mvrnorm(1000, mu=c(0,0), Sigma=matrix(c(1,.6,.6,1), nrow=2)))
names(d) = c("x","y")
## Skew Y
d$y = d$y^4
plot(d$x, d$y)
lines(lowess(d$x, d$y), lwd=2, col="blue")

Unfortunately, with such skewed data, it's hard to see the line unless we
"zoom in," by either ignoring the outliers, or "breaking"
the scale of the
y axis, such that the first 2/3 of the graph correspond to a "normal"
scale, and the remaining 1/3 correspond to a "compressed" scale. (I
know
this is generally not recommended, see
http://r.789695.n4.nabble.com/split-a-y-axis-to-show-data-on-different-scales-td805816.html).
I created a function to do this:

scaleBreak = function(x,y,axis=2, breakpos=1,...){

    #### figure out which Y values are above the breakpos
    y_above = y[y>breakpos]; x_above = x[y>breakpos]
    y_below = y[y<=breakpos]; x_below = x[y<=breakpos]

    #### pick ranges
    range_1 = range(y_below)
    range_2 = range(y_above)

    #### find limits of y axis (so it spans 2/3rds)
    mx = max(y_below); mn = min(y_below)
    ylims1 = c(mn, mx + (mx-mn)/2)

    #### plot bottom graph
    plot(range(x), ylims1, type="n", yaxt="n",...)
    points(x_below, y_below, yaxt="n",...)
    axis(2, pretty(y_below))

    min2 = (breakpos + .45*breakpos - max(y))/.45

    #### add second graph
    par(new=TRUE)
    plot(range(x), c(min2, max(y)), type="n", yaxt="n",
xaxt="n", ylab="",
axes=F)
    points(x_above, y_above, yaxt="n",...)
    axis(2, pretty(y_above)[-1])
    require(plotrix)
    axis.break(axis=axis, breakpos)

}

The problem I'm having is that the fitted line is not printed on the scale
of the bottom 2/3 plot:

scaleBreak(d$x, d$y, breakpos=20)
lines(lowess(d$x, d$y), lwd=2, col="blue")

Can anyone think of a solution where the line is on the scale of the bottom
2/3 of the plot, in the right location? (Again, let me preempt the
objections others might raise about how this should not be done. I know it
generally should not be done, but let's pretend I have an excellent reason
:) )

Thanks in advance!

	[[alternative HTML version deleted]]

Boris Steipe

2014-May-07 18:50 UTC

head link

[R] plotting lines on old graph after par(new=TRUE)

Since points() and lines() plot on the scale of the last plot, you could plot
your "first" graph after the "second" one, or if there is a
particular reason why you plot them in the order you do, add a third, empty
graph with the scale of the first one as the last plot.

B.




On 2014-05-07, at 2:37 PM, Dustin Fife wrote:
> Hi,
> 
> In my work, I often investigate relationships between highly skewed data.
> Example:
> 
> set.seed(111)
> require(MASS)
> d = data.frame(mvrnorm(1000, mu=c(0,0), Sigma=matrix(c(1,.6,.6,1),
nrow=2)))
> names(d) = c("x","y")
> ## Skew Y
> d$y = d$y^4
> plot(d$x, d$y)
> lines(lowess(d$x, d$y), lwd=2, col="blue")
> 
> Unfortunately, with such skewed data, it's hard to see the line unless
we
> "zoom in," by either ignoring the outliers, or
"breaking" the scale of the
> y axis, such that the first 2/3 of the graph correspond to a
"normal"
> scale, and the remaining 1/3 correspond to a "compressed" scale.
(I know
> this is generally not recommended, see
>
http://r.789695.n4.nabble.com/split-a-y-axis-to-show-data-on-different-scales-td805816.html).
> I created a function to do this:
> 
> scaleBreak = function(x,y,axis=2, breakpos=1,...){
> 
>    #### figure out which Y values are above the breakpos
>    y_above = y[y>breakpos]; x_above = x[y>breakpos]
>    y_below = y[y<=breakpos]; x_below = x[y<=breakpos]
> 
>    #### pick ranges
>    range_1 = range(y_below)
>    range_2 = range(y_above)
> 
>    #### find limits of y axis (so it spans 2/3rds)
>    mx = max(y_below); mn = min(y_below)
>    ylims1 = c(mn, mx + (mx-mn)/2)
> 
>    #### plot bottom graph
>    plot(range(x), ylims1, type="n", yaxt="n",...)
>    points(x_below, y_below, yaxt="n",...)
>    axis(2, pretty(y_below))
> 
>    min2 = (breakpos + .45*breakpos - max(y))/.45
> 
>    #### add second graph
>    par(new=TRUE)
>    plot(range(x), c(min2, max(y)), type="n", yaxt="n",
xaxt="n", ylab="",
> axes=F)
>    points(x_above, y_above, yaxt="n",...)
>    axis(2, pretty(y_above)[-1])
>    require(plotrix)
>    axis.break(axis=axis, breakpos)
> 
> }
> 
> The problem I'm having is that the fitted line is not printed on the
scale
> of the bottom 2/3 plot:
> 
> scaleBreak(d$x, d$y, breakpos=20)
> lines(lowess(d$x, d$y), lwd=2, col="blue")
> 
> Can anyone think of a solution where the line is on the scale of the bottom
> 2/3 of the plot, in the right location? (Again, let me preempt the
> objections others might raise about how this should not be done. I know it
> generally should not be done, but let's pretend I have an excellent
reason
> :) )
> 
> Thanks in advance!
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at 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.

Jim Lemon

2014-May-07 23:57 UTC

head link

[R] plotting lines on old graph after par(new=TRUE)

Hi Dustin,
Similar to what Boris suggested, try scaling the values and not 
resetting the plot limits:

scaleBreak = function(x,y,axis=2,breakpos=1,ymult=0.45,...){

    #### figure out which Y values are above the breakpos
    y_above<-y[y>breakpos]
    x_above<-x[y>breakpos]
    y_below<-y[y<=breakpos]
    x_below<-x[y<=breakpos]

    # scale the y limit according to the compression of high y values
    ylim<-c(min(y),(max(y_above)-breakpos)*1.1*ymult+breakpos)
    
    #### plot bottom graph
    plot(0,xlim=range(x),ylim=ylim,type="n", yaxt="n",...)
    points(x_below, y_below, yaxt="n",...)
    axis(2, pretty(y_below))

    #### add second graph
    newy<-(y_above-breakpos)*ymult+breakpos
    points(x_above,newy,...)
    ylabels<-pretty(y_above)
    cat(ylabels,(ylabels-breakpos)*ymult+breakpos,"\n")
    axis(2, at=(ylabels-breakpos)*ymult+breakpos,labels=ylabels)
    require(plotrix)
    axis.break(axis=axis, breakpos,style="gap")
}

I would also suggest using the gap style axis break.

Jim

On Wed, 7 May 2014 01:37:17 PM Dustin Fife wrote:> Hi,
> 
> In my work, I often investigate relationships between highly skewed 
data.> Example:
> 
> set.seed(111)
> require(MASS)
> d = data.frame(mvrnorm(1000, mu=c(0,0), 
Sigma=matrix(c(1,.6,.6,1), nrow=2)))> names(d) = c("x","y")
> ## Skew Y
> d$y = d$y^4
> plot(d$x, d$y)
> lines(lowess(d$x, d$y), lwd=2, col="blue")
> 
> Unfortunately, with such skewed data, it's hard to see the line 
unless we> "zoom in," by either ignoring the outliers, or
"breaking" the scale of
the> y axis, such that the first 2/3 of the graph correspond to a
"normal"
> scale, and the remaining 1/3 correspond to a "compressed" scale.
(I
know> this is generally not recommended, see
>
http://r.789695.n4.nabble.com/split-a-y-axis-to-show-data-on-different-scale
> s-td805816.html). I created a function to do this:
> 
> scaleBreak = function(x,y,axis=2, breakpos=1,...){
> 
>     #### figure out which Y values are above the breakpos
>     y_above = y[y>breakpos]; x_above = x[y>breakpos]
>     y_below = y[y<=breakpos]; x_below = x[y<=breakpos]
> 
>     #### pick ranges
>     range_1 = range(y_below)
>     range_2 = range(y_above)
> 
>     #### find limits of y axis (so it spans 2/3rds)
>     mx = max(y_below); mn = min(y_below)
>     ylims1 = c(mn, mx + (mx-mn)/2)
> 
>     #### plot bottom graph
>     plot(range(x), ylims1, type="n", yaxt="n",...)
>     points(x_below, y_below, yaxt="n",...)
>     axis(2, pretty(y_below))
> 
>     min2 = (breakpos + .45*breakpos - max(y))/.45
> 
>     #### add second graph
>     par(new=TRUE)
>     plot(range(x), c(min2, max(y)), type="n", yaxt="n",
xaxt="n",
ylab="",> axes=F)
>     points(x_above, y_above, yaxt="n",...)
>     axis(2, pretty(y_above)[-1])
>     require(plotrix)
>     axis.break(axis=axis, breakpos)
> 
> }
> 
> The problem I'm having is that the fitted line is not printed on the 
scale> of the bottom 2/3 plot:
> 
> scaleBreak(d$x, d$y, breakpos=20)
> lines(lowess(d$x, d$y), lwd=2, col="blue")
> 
> Can anyone think of a solution where the line is on the scale of the 
bottom> 2/3 of the plot, in the right location? (Again, let me preempt the
> objections others might raise about how this should not be done. I 
know it> generally should not be done, but let's pretend I have an excellent 
reason> 
> :) )
> 
> Thanks in advance!
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at 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.

R help - May 2014 - plotting lines on old graph after par(new=TRUE)

[R] plotting lines on old graph after par(new=TRUE)

[R] plotting lines on old graph after par(new=TRUE)

[R] plotting lines on old graph after par(new=TRUE)