

Dear all,
I am having this trouble and posted this query before.Can you please help me.
I have two matrices- x1 and y1 with same row names and column names(actually the names of the patients).

x1

          a         b                    c             d            e
a 1.0000000 0.4730679 0.6226994 0.6036036 0.6433333
b 0.4730679 1.0000000 0.6227273 0.6303855 0.5730858
c 0.6226994 0.6227273 1.0000000 0.7290503 0.6900585
d 0.6036036 0.6303855 0.7290503 1.0000000 0.7096774
e 0.6433333 0.5730858 0.6900585 0.7096774 1.0000000


y1
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          a          b         c           d         e
a 1.0000000 0.00 0.5000000 0.00 0.3333333
b 0.0000000 1.00 0.0000000 0.25 0.0000000
c 0.5000000 0.00 1.0000000 0.00 0.1666667
d 0.0000000 0.25 0.0000000 1.00 0.0000000
e 0.3333333 0.00 0.1666667 0.00 1.0000000



basically these two matrices are the similarity matrices between the patients. x1 is genotypically and y1 is phenotypically.
Now I want to generate a plot to see which patients have high similarity genotypically as well as phenotypically. So I am using

plot(x1[upper.tri(x1)],y1[upper.tri(y1)])                  #taking only the upper triangle of matrices as other half is same.

The plot is coming fine.But I am loosing the row names,therefore I have no idea which patients are on the top right corner of the plot.

Can you please help me.I will be very thankful to you.


Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London

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