Thanks Michael for your help. At least its good to know that there is no
function which does what I wanted. I will definitely try to code something
that fulfills my requirements.
Regards,
S.
On Fri, Sep 17, 2010 at 2:32 AM, Michael Bedward
<michael.bedw...@gmail.com>wrote:
> Hello Sunny,
>
> Defining groups at a given height can be done with the cut function
> (see ?cut.dendrogram).
>
> Unfortunately, cut doesn't give you the option of specifying a number
> of clusters rather than a height in the way that cutree does for
> "hclust" objects. Perhaps someone else here knows of a package that
> includes a function to do this (I did a quick sos search but didn't
> find anything obvious). Otherwise you could examine the cut function
> and try to hack a version that takes number of groups as an argument.
> You can see the function's code with the command getS3method("cut",
> "dendrogram").
>
> Sorry I can't help more. Being a simple soul I find hclust objects so
> much easier to deal with !
>
> Michael
>
>
> On 17 September 2010 11:30, Sunny Srivastava <research.b...@gmail.com>
> wrote:
> > Hello R-Helpers,
> > I have a question about extracting the clusters of genes after we make
> the
> > heatmap (say ht4) using the heatmap.2 function. Basically, I want to get
> the
> > clusters which are shown as row dendrogram in the heatmap.
> >
> > I understand that ht4$rowDendrogram is an object of dendrogram and it
> > containes details of all the nodes and branches, but lets say I want to
> know
> > the number of clusters and the genes in each cluster if I terminated the
> > tree (dendrogram) at a particular height. Also, if I know that I want 12
> > clusters, how do I know which height I should terminate the tree (or
> > branching structure)
> >
> > I am sorry if I am not clear. Please let me know if you need any further
> > clarifications. Thanks in advance for your help.
> >
> > Best Regards,
> > S.
> >
> > PS: I had posted this question on the Bioconductor mailing list, but no
> one
> > responded with the answer about my problem (some suggested to use other
> > package). Probably this is more related to R, so I am reposting here.
> >
> >
> >
> > Below is the dump of the matrix *row.scaled.fc2* and the object *ht4*
> which
> > was obtained by using the heatmap.2 function.
> >
> >
> -------------------------------------------------------------------------------------------------------------------------------------------------
> > Dump of the matrix row.scaled.fc2 of dimension 47X4 for which I need to
> get
> > the cluster
> >
> -------------------------------------------------------------------------------------------------------------------------------------------------
> > row.scaled.fc2 <-
> > structure(c(1.28370586906697, 0.045882176168387, -1.36708804887146,
> > 0.521861081643557, 0.931917365795697, -1.26811754842825,
> > -0.72130612803134,
> > 0.997233560332114, 1.10914280037357, 0.906822512746599,
> > 0.124305385892705,
> > 0.243716750638903, -0.81506628597585, 0.9281945227055,
> > -1.02514155647985,
> > -0.0148828263869010, 0.610771143828774, -1.31512789127346,
> > -1.03419747081316,
> > -1.37364737258546, 1.25426184614502, -0.901983912371582,
> > 1.39208493297302,
> > 1.46330419386939, 1.46904838309704, 1.33893188130515,
> > 1.19407808189758,
> > 1.2218547353343, 1.19698274357976, 1.18155526998177,
> > 0.841732283108634,
> > 0.747807260442244, 0.714318042078153, -1.33532716080095,
> > -0.313607205847584,
> > 0.355541486307312, -0.116351310506438, 0.77912190137299,
> > 1.19372966187956,
> > -1.46614749631243, 1.05871763558761, -0.943184299406566,
> > 1.03714731356991,
> > 1.25047276064487, 0.851530489918317, 0.97326112450597,
> > 0.776853817614179,
> > 0.254354524536168, 1.31978778177031, 1.03174081073449,
> > 1.03284070831524,
> > 0.653353551741362, -0.215733545477378, -0.966047927590969,
> > 0.652368565446036,
> > 0.536560120952493, 0.807139899513123, 1.26763097889282,
> > 1.28335333872251,
> > 1.45704025225707, 0.57691754078049, 1.07113369815538,
> > 0.610158458070122,
> > -0.762088920575592, 1.00819322156949, 1.14148232415467,
> > 0.297815716619546,
> > 0.143195107796418, -0.0065855621849476, 0.062650188298147,
> > -0.177601977084224,
> > -0.437288024655434, 0.178377570495840, 0.447251122498145,
> > 0.400521563178456,
> > 0.441487949431983, 0.465093691295555, 0.754248218272813,
> > 0.657576754588525,
> > 0.832332574891687, -0.194585070239614, 1.09572866565514,
> > 1.04256940502540,
> > 0.583290457043162, 0.947182223637108, 0.453501818870319,
> > 0.362539212141846,
> > 0.64658837487362, 0.778492522245523, 0.406650195058153,
> > -0.113538768459753,
> > 0.596257630693658, 0.652082611403661, 0.731202922578465,
> > -0.540351240198989,
> > -0.280636135117373, 0.0957282195118376,
> -0.301771114678491,
> > -0.319287162711085,
> > 0.392333008215492, 0.595799016736027, -0.493631246722725,
> > -0.570129842719142,
> > -0.687622802632555, -0.243797611378268,
> -0.510913960310597,
> > -0.263387651214153,
> > -0.172495725682589, 0.609736001727743, 0.809229072877685,
> > 1.08430415610192,
> > 0.475088705288397, 0.503896215545131, 0.0658502505817462,
> > -0.235112572720005,
> > 1.39599392995549, -0.73223360450103, -0.661334598551208,
> > -0.759202304177765,
> > -0.86894723087327, -0.9372047007794, -0.93488345268835,
> > -0.941766151100918,
> > -0.949595224394993, -1.27181485347646, -1.41712359913304,
> > -1.32146222297309,
> > 0.698917086441383, 0.444155476463272, -0.0629413619565949,
> > 0.892855986235108,
> > -0.809524028729025, -0.903176468889435, 0.786326226622549,
> > -0.793466237636563,
> > 0.945708813261833, -0.123281411659495, 0.0548777607029143,
> > -0.0638457887809093,
> > -1.20425833446000, -1.35599301451107, -0.997709153404147,
> > -1.08503382282132,
> > 0.239619018625132, -1.25293067528031, -1.26598375482597,
> > 1.09151808569014,
> > 1.09155503888627, -1.15597087905543, -1.07557307860692,
> > -1.02633960962716,
> > -1.14813875340725, -1.01615612905082, -0.378586315067078,
> > -1.33261633780340,
> > -0.655728143403281, -1.40450470456092, -0.932986379355095,
> > -0.168154035584431,
> > -0.611181068886636, 1.00998140538417, -1.16234438122143,
> > -0.487424455398969,
> > -0.722501516770135, -0.624367618233957,
> -0.272558054263839,
> > -0.648362220927723,
> > -0.704124503616327, -0.687492845824406,
> -0.696704541910826,
> > -0.697053736882326,
> > -0.324165647904986, 0.0117395841022768,
> -0.225188393996755,
> > 0.830995144599174,
> > -1.22627693627083, -1.33516952937611, -1.35979513277183,
> > -0.91678009628107,
> > -0.744055011860442, 0.317282057548041, -0.911839772824668,
> > -0.78101703610078,
> > -1.32051609696858, -1.19181175288804, -1.38394233183106,
> > -0.421085401449625,
> > -0.152063725681571), .Dim = c(47L, 4L), .Dimnames =
> > list(c("pSysX_130",
> > "pSysX_48",
> > "pSysX_49", "pSysX_50", "sll0108", "sll0327", "sll0685",
> > "sll0735",
> > "sll0781", "sll0783", "sll0788", "sll0789", "sll0790",
> > "sll1130",
> > "sll1450", "sll1507", "sll1621", "sll1694", "sll1695",
> > "sll1796",
> > "sll1814", "sll1891", "slr0041", "slr0042", "slr0043",
> > "slr0044",
> > "slr0144", "slr0145", "slr0146", "slr0147", "slr0737",
> > "slr0749",
> > "slr0750", "slr0853", "slr0898", "slr1236", "slr1251",
> > "slr1603",
> > "slr1634", "slr1675", "slr1930", "slr1984", "smr0003",
> > "ssl2148",
> > "ssl2245", "ssr0390", "ssr1251"), c("l1", "d1", "l13",
> >
> > "d13")))
> >
> > [[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
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
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