Sunny Srivastava
2010-Sep-17 01:30 UTC
[R] Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
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]]
Michael Bedward
2010-Sep-17 06:32 UTC
[R] Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
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.baba at 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 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.
>
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