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")))
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