From: <kannaiah_at_bsd.uchicago.edu>

Date: Wed 24 May 2006 - 03:58:41 EST

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R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed May 24 04:02:42 2006

Date: Wed 24 May 2006 - 03:58:41 EST

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@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@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}}
**> >
**> > ______________________________________________
**> > R-help@stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide!
**> http://www.R-project.org/posting-guide.html
**> >
**>
**>
**>
**>
**>
**>
**>
*

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R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed May 24 04:02:42 2006

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