[R] my first R program

[kannaiah at bsd.uchicago.edu]

I have attached a graph image of what i am trying to plot.
The x-axis in the image(rs*), would correspond to the position column in my
first file. The ticks are not equidistant but are placed based on their
proportionate distance from the eachother.
So, the horizontal line i need to draw would be for example:
from file 2:
col1 =1 corresponds to position 120(in file1)
col2 = 2 (position 134)
p-value = 0.45 (p-val on y-axis, actually i will be plotting the -log10 of p-val)

so i am trying to draw a line from positions 120 to 134 on x-axis at their
corresponding p-value(0.45) on y-axis

What i have done so far:
1) read the files into a data frame object:
   mpos = read.table("file 1", header=TRUE)
   snpem = read.table("file 2", header=TRUE)
2) snpem[4] = -log10(snpem[3])
3) i tried some of the suggestions that i got from people here...
   so trying to map the position col(first file) to the col1 and col2 didnt work

   position = mpos[2]
   col1 = snpem[1]
   so, now when i did position[col1], it was giving an error

Thanks for the help..

-kiran


 
 



Quoting Albyn Jones <jones at reed.edu>:

> I'm not sure I understand what you are trying to do exactly, but
> "to associate the col1 and col2 with their corresponding position values"
> looks like
> 
>      (position[col1], position[col2])
> 
> so you _might_ want something like
> 
>    
> plot(position[col1],pval,xlim=c(110,175),ylim=c(0,1),type="n",xlab="Position")
>     segments(position[col1],pval, position[col2],pval)
>     abline(h=.5)
> 
> regards
> 
> albyn
> 
> 
> Quoting kannaiah at bsd.uchicago.edu:
> 
> > Hello,
> >
> > This is my first attempt at using R. Still trying to figure out and 
> > understand
> > how to work with data frames.
> > I am trying to plot the following data(example). Some experimental data i
> am
> > trying to plot here.
> >
> > 1) i have 2 files
> > 2) First File:
> > 	Number	Position
> > 	  1	120
> > 	  2	134
> > 	  3	156
> > 	  4	169
> >          5	203
> > 3) Second File:
> > 	Col1 	Col2	p-val
> > 	1	2 	0.45
> > 	1	2	0.56
> > 	2	3	0.56
> > 	2	3	0.68
> > 	2	3	0.88
> > 	3	4	0.76
> > 	3	5	0.79
> > 	3	5	0.92
> >
> > I am trying to plot this with "position" as x-axis and "p-val" as the
> y-axis.
> > The col1 and col2 in the second file correspond to the number column in
> first
> > file.
> >
> > I am having trouble to figure out how to associate the col1 and col2 with
> > their corresponding position values
> >
> > The x-axis should start with 120 as that is the min value and next values
> > should be spaced proportionally away from the
> > first. I tried using the percentage method to place them...but couldnt
> > completely get it correct.
> >
> > so it would look like :
> > 	|   |        |    |          |
> > 	120 134      156  169        203
> >
> > Hopefully i explained it correctly.
> >
> > i would like to plot the p-value as horizontal lines drawn between the
> col1
> > and col2 values (ie: positions)
> > So, the plot will have as many horizontal lines as the rows in the 
> > second file.
> > And ONE reference horizontal line passing thru the plot at p-val=0.5, to
> see
> > what values lie below that and what above it.
> >
> >
> > I have made some progress in plotting the horizontal axis, but having
> trouble
> > bringing all the data together.Not sure yet how to
> > manipulate them using the data frames:(
> >
> > Any suggestions and tips will be greatly appreciated.
> >
> > Thank you
> > -Kiran
> >
> >
> >
> >
> > -------------------------------------------------
> > This email is intended only for the use of the individual
> or...{{dropped}}
> >
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> http://www.R-project.org/posting-guide.html
> >
> 
> 
> 
> 
> 
> 
> 





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