R help - Aug 2015 - plotting over a raster image with control over location and orientation

Hi,I would like to get some help in plotting over an image. I have a png image
over which I would like to have a plot. I would like to be able to control the
location, area and orientation of the plot on the image.
I have taken help from the following references
:http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Murrell.pdfhttp://stackoverflow.com/questions/12918367/in-r-how-to-plot-with-a-png-as-background
In order to give a reproducible example, I set up my image with the help of some
code from the the first reference above.

#Setting up the initial example raster image
x <- y <- seq(-4*pi, 4*pi, len=27)
r <- sqrt(outer(x^2, y^2, "+"))
z <- cos(r^2)*exp(-r/6)
image <- (z - min(z))/diff(range(z))
step <- diff(x)[1]
xrange <- range(x) + c(-step/2, step/2)
yrange <- range(y) + c(-step/2, step/2)
plot(x, y, ann=FALSE,xlim=xrange, ylim=yrange,xaxs="i",
yaxs="i")
rasterImage(image,xrange[1], yrange[1],xrange[2], yrange[2],interpolate=FALSE)

# the explanation of my problem starts here
# First, I want to mark out a particular line
lines(c(10,10.5),c(-10.5,10),col="red",lwd=2)
#In my problem, I have to locate these points graphically from the image
calpoints <- locator(n=2,type='p',pch=4,col='blue',lwd=2)
# this gives the line corresponding to the x-axis for my overlay plot
# I don't want the red line on my plot
#the red line plotted earlier is just to show the example location
newOrigin<-calpoints[1]
xLimit<-calpoints[2]#xlimit marks the limit of the x-axis on the image# on
this new line as the x-axis, I want to make a new plot# the y-axis should be
perpendicular to the x-axis. I would like to be able to specify the width of
coverage over the image#example
xx<-1:10
yy<-xx^2
plot(xx,yy,xlim=range(xx),ylim=range(yy),col="blue",type="b",xlab="x",ylab="square
of x")
# I would prefer to have the image more transparent just under the x and y
labels and axis labelsThanks, Ravi


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Hi,I havetried to find a simple way for my overlay plot. A simple summary of
myapproach would to first plot the raster image and then overlay the second pot
with :
par(new=TRUE,plt=c(x1,x2,y1,y2)) # not sure if the plt or usr argument should be
used# have some difficulty in knowing the units for x1,x2,y1 and y2
plot(1:10,1:10)#justan example plot
But my problem is that I do not understand the unit conversions for graphics.
What exactly are "npc" and "native"?Let me explain by
starting with the code again:#Setting up the initial example raster image
library(grid)
x <- y <- c(-15,seq(-4*pi, 4*pi, len=27),15)
r <- sqrt(outer(x^2, y^2, "+"))
z <- cos(r^2)*exp(-r/6)
image <- (z - min(z))/diff(range(z))
plot(x, y, ann=FALSE,xaxs="i", yaxs="i")
rasterImage(image,xrange[1], yrange[1],xrange[2], yrange[2],interpolate=FALSE)#
let's say that I want to draw an overlay plot with the follwing line as
x-axis
lines(c(-10,10),c(-12,-12),col="red",lwd=2)

lim<-par("usr")
lim
limplt<-par("plt")
limplt

#convertX(unit(0:1,"npc"),"native")
convertX(unit(-10,"native"),"npc")
convertX(unit(10,"native"),"npc")
convertY(unit(-12,"native"),"npc")
> lim<-par("usr")
> lim
[1] -15  15 -15  15
> limplt<-par("plt")
> limplt
[1] 0.09132251 0.95322506 0.18000000 0.85529412
> 
> #convertX(unit(0:1,"npc"),"native")
> convertX(unit(-10,"native"),"npc")
[1] -0.0116009280742459npc
> convertX(unit(10,"native"),"npc")
[1] 0.0116009280742459npc
> convertY(unit(-12,"native"),"npc")
[1] 1.02205882352941npc


These converted values and the values for the limplt variable do not seem to be
in agreement. How do I convert, for example, the point (10,-12) to
"npc" units?

I hope that I have explained my problem sufficiently well. If I can get help
with an approach involving viewports also, I would be grateful for any help that
I can get.
Thanks,
Ravi

      From: ravi <rv15i at yahoo.se>
 To: R-help <r-help at r-project.org> 
 Sent: Friday, 21 August 2015, 16:30
 Subject: plotting over a raster image with control over location and
orientation
   
Hi,I would like to get some help in plotting over an image. I have a png image
over which I would like to have a plot. I would like to be able to control the
location, area and orientation of the plot on the image.
I have taken help from the following references
:http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Murrell.pdfhttp://stackoverflow.com/questions/12918367/in-r-how-to-plot-with-a-png-as-background
In order to give a reproducible example, I set up my image with the help of some
code from the the first reference above.

#Setting up the initial example raster image
x <- y <- seq(-4*pi, 4*pi, len=27)
r <- sqrt(outer(x^2, y^2, "+"))
z <- cos(r^2)*exp(-r/6)
image <- (z - min(z))/diff(range(z))
step <- diff(x)[1]
xrange <- range(x) + c(-step/2, step/2)
yrange <- range(y) + c(-step/2, step/2)
plot(x, y, ann=FALSE,xlim=xrange, ylim=yrange,xaxs="i",
yaxs="i")
rasterImage(image,xrange[1], yrange[1],xrange[2], yrange[2],interpolate=FALSE)

# the explanation of my problem starts here
# First, I want to mark out a particular line
lines(c(10,10.5),c(-10.5,10),col="red",lwd=2)
#In my problem, I have to locate these points graphically from the image
calpoints <- locator(n=2,type='p',pch=4,col='blue',lwd=2)
# this gives the line corresponding to the x-axis for my overlay plot
# I don't want the red line on my plot
#the red line plotted earlier is just to show the example location
newOrigin<-calpoints[1]
xLimit<-calpoints[2]#xlimit marks the limit of the x-axis on the image# on
this new line as the x-axis, I want to make a new plot# the y-axis should be
perpendicular to the x-axis. I would like to be able to specify the width of
coverage over the image#example
xx<-1:10
yy<-xx^2
plot(xx,yy,xlim=range(xx),ylim=range(yy),col="blue",type="b",xlab="x",ylab="square
of x")
# I would prefer to have the image more transparent just under the x and y
labels and axis labelsThanks, Ravi



   
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Hi,I am sorry for not having control checked the code before posting (in my
earlier mail). I have done this now.
I just have a simple question now. Why is the overlay plot (the final plot ) not
falling into the intended position (as defined by the viewport vp2)?#Setting up
the initial example raster image
library(grid)
x <- y <- c(-15,seq(-4*pi, 4*pi, len=27),15)
r <- sqrt(outer(x^2, y^2, "+"))
z <- cos(r^2)*exp(-r/6)
image <- (z - min(z))/diff(range(z))
xrange <- range(x)
yrange <- range(y)

vp1<-viewport(x = unit(0.5, "npc"), y = unit(0.5, "npc"),
???????? width = unit(1, "npc"), height = unit(1, "npc"),
???????? default.units = "npc", just =
c("left","bottom"),name="vp1")
pushViewport(vp1)
plot(x, y, ann=FALSE,xlim=xrange, ylim=yrange,xaxs="i",
yaxs="i")
rasterImage(image,xrange[1], yrange[1],xrange[2], yrange[2],interpolate=FALSE)
lines(c(-10,4),c(-12,-12),col="red",lwd=2)

lim<-par("usr")
lim
limplt<-par("plt")
limplt
#par(new=TRUE,plt=c(limplt[1],limplt[2],limplt[3]))

#convertX(unit(0:1,"npc"),"native")
x1<-convertX(unit(-10,"native"),"npc")
x2<-convertX(unit(5,"native"),"npc")
y1<-convertY(unit(-12,"native"),"npc")
y2<-convertY(unit(3,"native"),"npc")

wx<-(5-(-10))/(15-(-15))
wy<-(3-(-12))/(15-(-15))

xw<-convertWidth(unit(wx,"native"),"npc")
yw<-convertHeight(unit(wy,"native"),"npc")


vp2<-viewport(x = unit(x1, "npc"), y = unit(y1, "npc"),
????????????? width = unit(xw, "npc"), height = unit(yw,
"npc"),
????????????? default.units = "npc", name="vp2")
pushViewport(vp2)
#data with a different scale
xs<-seq(0.01,0.1,0.01)ys<-xs^2
#points(xs,ys,type='b',col='red',newpage=FALSE)

plot(xs,ys,type='b',col='red') #fills the whole screen instead
of just the intended viewport


Thanks,Ravi


   

  
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For base plotting functions (not grid) then you may be interested in
the updateusr function in the TeachingDemos package.  If you can find
the current coordinates of 2 points on the 1st plot (the background
image) that are not in the same horizontal or vertical line (use the
locator function if nothing else) and you know what you would like the
coordinates of the 2 points to be, then you just call updateusr with
the current coordinates and the desired coordinates and it resets them
for you so that you can add to the current plot with lines or other
low level functions.

On Fri, Aug 21, 2015 at 8:30 AM, ravi <rv15i at yahoo.se>
wrote:
> Hi,I would like to get some help in plotting over an image. I have a png
image over which I would like to have a plot. I would like to be able to control
the location, area and orientation of the plot on the image.
> I have taken help from the following references
:http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Murrell.pdfhttp://stackoverflow.com/questions/12918367/in-r-how-to-plot-with-a-png-as-background
> In order to give a reproducible example, I set up my image with the help of
some code from the the first reference above.
>
> #Setting up the initial example raster image
> x <- y <- seq(-4*pi, 4*pi, len=27)
> r <- sqrt(outer(x^2, y^2, "+"))
> z <- cos(r^2)*exp(-r/6)
> image <- (z - min(z))/diff(range(z))
> step <- diff(x)[1]
> xrange <- range(x) + c(-step/2, step/2)
> yrange <- range(y) + c(-step/2, step/2)
> plot(x, y, ann=FALSE,xlim=xrange, ylim=yrange,xaxs="i",
yaxs="i")
> rasterImage(image,xrange[1], yrange[1],xrange[2],
yrange[2],interpolate=FALSE)
>
> # the explanation of my problem starts here
> # First, I want to mark out a particular line
> lines(c(10,10.5),c(-10.5,10),col="red",lwd=2)
> #In my problem, I have to locate these points graphically from the image
> calpoints <-
locator(n=2,type='p',pch=4,col='blue',lwd=2)
> # this gives the line corresponding to the x-axis for my overlay plot
> # I don't want the red line on my plot
> #the red line plotted earlier is just to show the example location
> newOrigin<-calpoints[1]
> xLimit<-calpoints[2]#xlimit marks the limit of the x-axis on the image#
on this new line as the x-axis, I want to make a new plot# the y-axis should be
perpendicular to the x-axis. I would like to be able to specify the width of
coverage over the image#example
> xx<-1:10
> yy<-xx^2
>
plot(xx,yy,xlim=range(xx),ylim=range(yy),col="blue",type="b",xlab="x",ylab="square
of x")
> # I would prefer to have the image more transparent just under the x and y
labels and axis labelsThanks, Ravi
>
>
>         [[alternative HTML version deleted]]
>
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-- 
Gregory (Greg) L. Snow Ph.D.
538280 at gmail.com