R help - May 2011 - Reordering inputs

Hello All,

I have 2 matrices consisting of the same inputs, but having different
outputs. I created a heatmap for both of them; the point is to compare them
side by side. The best way to organize the inputs is to make sure that the
order of the inputs are the same for both heatmaps. How would I go about
making sure that the order of inputs of both heatmaps are the same?

As it is right now, I can only control the the order of the inputs by using
the decreasing=TRUE/FALSE function, but that only serves to reorder the
matrix by the output values.

-- 
Best,
Dat Mai
PhD Rotation Student
Albert Einstein College of Medicine

	[[alternative HTML version deleted]]

Matrices just *are* . They don't have inputs or outputs.  Can you 
provide an example of what you are trying to do?


<Quote>
From: Dat Mai <dat.d.mai_at_gmail.com>
Date: Wed, 11 May 2011 19:43:23 +0000


Hello All,

I have 2 matrices consisting of the same inputs, but having different 
outputs. I created a heatmap for both of them; the point is to compare 
them side by side. The best way to organize the inputs is to make sure 
that the order of the inputs are the same for both heatmaps. How would I 
go about making sure that the order of inputs of both heatmaps are the same?

As it is right now, I can only control the the order of the inputs by 
using the decreasing=TRUE/FALSE function, but that only serves to 
reorder the matrix by the output values.


</quote>

You can order each matrix by any column you choose like:

a<-matrix(rnorm(20),ncol=2)
> a[order(a[,1]),] #orders by column 1
             [,1]       [,2]
 [1,] -1.86523489 -1.6920270
 [2,] -0.94488744  0.2815087
 [3,]  0.02380494  0.2491136
 [4,]  0.37295795  0.8156993
 [5,]  0.55533366 -0.7053233
 [6,]  0.79799294 -0.8224082
 [7,]  0.80497452  0.4260842
 [8,]  1.12438976 -0.1567863
 [9,]  1.29213037 -1.6783762
[10,]  1.33496542  0.7807943

On Fri, May 13, 2011 at 1:31 AM, Dat Mai <dat.d.mai at gmail.com>
wrote:
> Yes, but I want to make it so that 2 different square matrices to both have
> the same order for the x and y axis while, at the same time, the x and y
> axis having variables in the same order as well:
>
> ????????? a?????? b?????? c???? d?????? e???? ...
> a??????? Outputs here------------>
> b??????????????? |
> c??????????????? |
> d??????????????? |
> e?????????????? V
> .
> .
> .
>
> Both matrices 1 and 2 should look like this. That way, comparing them via a
> heatmap would be much easier.
>
> That command would only serve or order each matrix individually by the
> values in column 1. The problem with this is that both matrices in question
> do not have the same or similar values for each output. Therefore, both
> matrices would be ordered by some column I choose, but will not be in the
> same order.


Sorry - I didn't know that you were trying to order by the dimnames of
the matrix. In that case, you should be able to do something like the
following:
> #row and column names
> dnames<-c('a','b','c','d','e')
> #matrix with rows and columns in correct order
> mat1<-matrix(rnorm(25),ncol=5,dimnames=list(dnames,dnames))
>
> #random order for row and column names
> rnames1<-sample(dnames,5)
> rnames2<-sample(dnames,5)
> #matrix with rows and columns in incorrect order
> mat2<-matrix(rnorm(25),ncol=5,dimnames=list(rnames1,rnames2))
> mat2
            d          c           b          a          e
c -0.04923684  0.4765760  0.43840872 -0.5524667 -0.2905828
d -0.32432997  0.4206066  0.47332957 -0.4519173 -0.4126728
e  0.61084905 -0.6585749  0.06420868  1.7143967 -1.4071063
a  1.58412898 -1.4497131 -1.03201925  1.5232362  1.9599125
b  0.85896345 -1.4203311 -0.12717927  0.2900827
-1.0357730
>
> #mat2 with rows and columns in correct order
> mat3<-mat2[order(dimnames(mat2)[[1]]),order(dimnames(mat2)[[2]])]
> mat3
           a           b          c           d          e
a  1.5232362 -1.03201925 -1.4497131  1.58412898  1.9599125
b  0.2900827 -0.12717927 -1.4203311  0.85896345 -1.0357730
c -0.5524667  0.43840872  0.4765760 -0.04923684 -0.2905828
d -0.4519173  0.47332957  0.4206066 -0.32432997 -0.4126728
e  1.7143967  0.06420868 -0.6585749  0.61084905
-1.4071063
>