Bansal, Vikas
2011-Oct-31 16:19 UTC
[R] Plot two matrices and keeping the record of row names
Dear all,
I have two data frames- 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
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
[[alternative HTML version deleted]]
Bansal, Vikas
2011-Oct-31 21:45 UTC
[R] Plot two matrices and keeping the record of row names
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
<UrlBlockedError.aspx>
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
[[alternative HTML version deleted]]
Peter Alspach
2011-Oct-31 22:08 UTC
[R] Plot two matrices and keeping the record of row names
Tena koe Vikas If I understand you correctly, you could generate a character matrix the elements of which are the row.names and col.names of x1 pasted together (perhaps with : as a separator). Then the upper.tri of this will give you the associations. HTH ... Peter Alspach> -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- > project.org] On Behalf Of Bansal, Vikas > Sent: Tuesday, 1 November 2011 10:46 a.m. > To: r-help at r-project.org > Subject: [R] Plot two matrices and keeping the record of row names > > > > 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 > <UrlBlockedError.aspx> > > 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 > > [[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.The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.
Bansal, Vikas
2011-Oct-31 22:16 UTC
[R] Plot two matrices and keeping the record of row names
Dear Peter, Thanks for your reply.I am familiar with this solution but I was trying to make the plot user friendly.I have seen some plots,in which if we keep a cursor on any point of plot,it will automatically shows you the row names.Is it possible? I did not find anything related to this. Thanking you, Warm Regards Vikas Bansal Msc Bioinformatics Kings College London ________________________________________ From: Peter Alspach [Peter.Alspach at plantandfood.co.nz] Sent: 31 October 2011 22:08 To: Bansal, Vikas; r-help at r-project.org Subject: RE: Plot two matrices and keeping the record of row names Tena koe Vikas If I understand you correctly, you could generate a character matrix the elements of which are the row.names and col.names of x1 pasted together (perhaps with : as a separator). Then the upper.tri of this will give you the associations. HTH ... Peter Alspach> -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- > project.org] On Behalf Of Bansal, Vikas > Sent: Tuesday, 1 November 2011 10:46 a.m. > To: r-help at r-project.org > Subject: [R] Plot two matrices and keeping the record of row names > > > > 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 > <UrlBlockedError.aspx> > > 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 > > [[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.The contents of this e-mail are confidential and may be ...{{dropped:15}}