I assume my matrix should look something like this?..
>round(distance, 4)
P00A P00B M02A M02B P04A P04B M06A M06B P08A
P08B M10A
P00B 0.9678
M02A 1.0054 1.0349
M02B 1.0258 1.0052 1.2106
P04A 1.0247 0.9928 1.0145 0.9260
P04B 0.9898 0.9769 0.9875 0.9855 0.6075
M06A 1.0159 0.9893 1.0175 0.9521 0.9266 0.9660
M06B 0.9837 0.9912 1.0124 1.0402 1.0272 1.0367 1.5693
P08A 1.0279 1.0303 0.9865 0.9748 1.0184 1.0452 0.9799 1.0400
P08B 1.0248 1.0299 0.9717 0.9673 1.0048 1.0329 1.0280 0.9907 0.2158
M10A 0.9850 0.9603 1.0246 0.9708 1.0231 0.9771 0.9916 1.0168 0.9722
0.9525
M10B 1.0150 1.0397 0.9754 1.0292 0.9769 1.0229 1.0084 0.9832 1.0278
1.0475 2.0000
On Fri, May 28, 2010 at 3:39 PM, Ayesha Khan <ayesha.diamond...@gmail.com>wrote:
> v <- dput(x,"sampledata.txt")
> dim(v)
> q <- v[1:10,1:10]
> f =as.matrix(dist(t(q)))
>
> distB=NULL
> for(k in 1:(nrow(f)-1)) for( m in (k+1):ncol(f)) {
> if(f[k,m] <2) distB=rbind(distB,c(k,m,f[k,m]))
> }
> #now distB looks like this
>
> > distB
> [,1] [,2] [,3]
> [1,] 1 2 1.6275568
> [2,] 1 3 0.5252058
> [3,] 1 4 0.7323116
> [4,] 1 5 1 .9966001
> [5,] 1 6 1.6664110
> [6,] 1 7 1.0800540
> [7,] 1 8 1.8698925
> [8,] 1 10 0.5161808
> [9,] 2 3 1.7325811
> [10,] 2 5 0.8267843
> [11,] 2 6 0.5963280
> [12,] 2 7 0.8787230
>
> #now from this output< i want to cluster all 1's, friedns of 1 and friends
> of friends of 1 in one cluster. The same goes for 2,3 and so on
> But when i do that using hclust, i get the following error. I think what I
> need to do is convert my cureent matrix somehow into a format that would be
> accepted by the hclust function but I dont know how to achieve that.
> distclust <- hclust(distB,method="single")
>
> Error in if (n < 2) stop("must have n >= 2 objects to cluster") :
> argument is of length zero
>
> P.S: Please let me know if this makes things more clear? "cuz i dont know
> how looking at the original data set would help becuase the matrix under
> consdieration right now is the distance matrix and how it can be altered. I
> have tried as.dist, doesnt work because my matrix as i mentioned eralier is
> not a square matrix.
>
> On Fri, May 28, 2010 at 2:37 PM, Tal Galili <tal.gal...@gmail.com>wrote:
>
>> Hi Ayesha,
>> I wish to help you, but without a simple self contained example that shows
>> your issue, I will not be able to help.
>> Try using the ?dput command to create some simple data, and let us see
>> what you are doing.
>>
>> Best,
>> Tal
>> ----------------Contact
>> Details:-------------------------------------------------------
>> Contact me: tal.gal...@gmail.com | 972-52-7275845
>> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
>> www.r-statistics.com (English)
>>
>> ----------------------------------------------------------------------------------------------
>>
>>
>>
>>
>> On Fri, May 28, 2010 at 9:04 PM, Ayesha Khan <
>> ayesha.diamond...@gmail.com> wrote:
>>
>>> Thanks Tal & Joris!
>>> I created my distance matrix distA by using the dist() function in R
>>> manipulating my output in order to get a matrix.
>>> distA =as.matrix(dist(t(x2))) # x2 being my original dataset
>>> as according to the documentaion on dist()
>>>
>>> For the default method, a "dist" object, or a matrix (of distances) or
>>> an object which can be coerced to such a matrix using as.matrix()
>>>
>>> On Fri, May 28, 2010 at 6:34 AM, Joris Meys <jorism...@gmail.com>wrote:
>>>
>>>> As Tal said.
>>>>
>>>> Next to that, I read that column1 (and column2?) are supposed to be seen
>>>> as factors, not as numerical variables. Did you take that into account
>>>> somehow?
>>>>
>>>> It's easy to reproduce the error code :
>>>> > n <- NULL
>>>> > if(n<2)print("This is OK")
>>>> Error in if (n < 2) print("This is OK") : argument is of length zero
>>>>
>>>> In the hclust code, you find following line :
>>>> n <- as.integer(attr(d, "Size"))
>>>> where d is the distance object entered in the hclust function. Looking
>>>> at the error you get, this means that the size attribute of your distance
>>>> is
>>>> NULL. Which tells me that distA is not a dist-object.
>>>>
>>>> > A <- matrix(1:4,ncol=2)
>>>> > A
>>>> [,1] [,2]
>>>> [1,] 1 3
>>>> [2,] 2 4
>>>> > hclust(A,method="single")
>>>>
>>>> Error in if (n < 2) stop("must have n >= 2 objects to cluster") :
>>>> argument is of length zero
>>>>
>>>> Did you actually put in a distance object? see also ?dist or ?as.dist.
>>>>
>>>> Cheers
>>>> Joris
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, May 28, 2010 at 1:41 AM, Ayesha Khan <
>>>> ayesha.diamond...@gmail.com> wrote:
>>>>
>>>>> i have a matrix with the following dimensions
>>>>> 136 3
>>>>>
>>>>> and it looks something like
>>>>>
>>>>> [,1] [,2] [,3]
>>>>> [1,] 402 675 1.802758
>>>>> [2,] 402 696 1.938902
>>>>> [3,] 402 699 1.994253
>>>>> [4,] 402 945 1.898619
>>>>> [5,] 424 470 1.812857
>>>>> [6,] 424 905 1.816345
>>>>> [7,] 470 905 1.871252
>>>>> [8,] 504 780 1.958191
>>>>> [9,] 504 848 1.997111...............
>>>>>
>>>>> ................................................................................
>>>>> so you get the idea. I want to group similar items in one group/cluster
>>>>> following the "friends of friends" approach. I tried doing
>>>>>
>>>>> distclust <- hclust(distA,method="single")
>>>>> However, I got the following error.
>>>>>
>>>>> Error in if (n < 2) stop("must have n >= 2 objects to cluster") :
>>>>> argument
>>>>> is of length zero
>>>>> which probably means there's something wrong with my input here. Is
>>>>> there
>>>>> another way of doing this kind of clustering without getting into all
>>>>> the
>>>>> looping and ifelse etc. Basically, if 402 is close to 675,696,and699
>>>>> and
>>>>> thus fall in cluster A then all items close to 675,696,and 699 should
>>>>> also
>>>>> fall into the same cluster A following a friends of friedns strategy.
>>>>> Any help would be highly appreciated.
>>>>>
>>>>> --
>>>>> Ayesha Khan
>>>>>
>>>>> MS Bioengineering
>>>>> Dept. of Bioengineering
>>>>> Rice University, TX
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> R-help@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<http://www.r-project.org/posting-guide.html>
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Joris Meys
>>>> Statistical Consultant
>>>>
>>>> Ghent University
>>>> Faculty of Bioscience Engineering
>>>> Department of Applied mathematics, biometrics and process control
>>>>
>>>> Coupure Links 653
>>>> B-9000 Gent
>>>>
>>>> tel : +32 9 264 59 87
>>>> joris.m...@ugent.be
>>>> -------------------------------
>>>> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>>>>
>>>
>>>
>>>
>>> --
>>> Ayesha Khan
>>>
>>> MS Bioengineering
>>> Dept. of Bioengineering
>>> Rice University, TX
>>>
>>
>>
>
>
> --
> Ayesha Khan
>
> MS Bioengineering
> Dept. of Bioengineering
> Rice University, TX
>
--
Ayesha Khan
MS Bioengineering
Dept. of Bioengineering
Rice University, TX
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