[BioC] Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
January Weiner
january.weiner at mpiib-berlin.mpg.de
Thu Sep 16 13:46:13 CEST 2010
Dear Sunny,
I think a better approach would be to use a package like pvclust.
Pvclust creates a hierarchical clustering (a tree), and at each node
computes a p-value; therefore, the criterion to choose certain
clusters can be defined by a threshold p value.
See http://www.is.titech.ac.jp/~shimo/prog/pvclust/ for details.
Best regards,
January
On Thu, Sep 16, 2010 at 12:57 PM, Sunny Srivastava
<research.baba at gmail.com> wrote:
> Hello Bioconductor 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 I am not clear. Please let me know if you need any further
> clarifications. Thanks in advance for your help.
>
> Best Regards,
> S.
>
>
> 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")))
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------
> Dump of the object ht4 obtained by using heatmap.2 on a given data set
> (matrix) of dimension 47 x 4
> ---------------------------------------------------------------------------------------------------------------------------------------------------
> ht4 <-
> structure(list(rowInd = c(7L, 34L, 6L, 20L, 13L, 18L, 3L, 40L,
> 15L, 19L, 42L, 44L, 1L, 21L, 43L, 45L, 14L, 5L, 39L, 29L,
> 27L,
> 30L, 28L, 8L, 9L, 41L, 10L, 38L, 26L, 23L, 24L, 25L, 32L,
> 33L,
> 47L, 31L, 46L, 22L, 17L, 16L, 37L, 35L, 12L, 2L, 11L, 4L,
> 36L
> ), colInd = 1:4, call = quote(heatmap.2(x =
> row.scaled.fc2, Colv = FALSE,
> dendrogram = "row", scale = "none",
> breaks = breaks.fc2,
> col = blue.red.fc2, trace = "none",
> cexRow = 0.8, cexCol = 2,
> labCol = colnames(row.scaled.fc2), key =
> FALSE, density.info = "none",
> main = expression("Heatmap of " * log[2]
> * "Int. of Genes (with Adjusted P Value <0.01 & FC>1.5or<0.7) for
> Treatments"),
> xlab = "Treatments", ylab = "Genes in
> the Microarray Adjusted P Value less than 0.01 and Fold Change above 1.5 or
> below 0.7",
> lmat = rbind(c(0, 3), c(2, 1), c(0, 4)),
> lhei = c(0.25, 4,
>
> 0.25), cex = 1.5)), carpet = structure(c(-0.72130612803134,
>
> -0.966047927590969, 0.595799016736027, 1.09155503888627,
> -1.33532716080095,
>
> -0.194585070239614, 0.698917086441383,
> 0.830995144599174, -1.26811754842825,
>
> -0.215733545477378, 0.392333008215492, 1.09151808569014,
> -1.37364737258546,
>
> 0.297815716619546, 0.0658502505817462, 1.00998140538417,
> -0.81506628597585,
>
> 1.45704025225707, -0.263387651214153,
> -0.378586315067078, -1.31512789127346,
>
> 1.00819322156949, 0.475088705288397, -0.168154035584431,
> -1.36708804887146,
>
> 1.03174081073449, 0.0957282195118376, 0.239619018625132,
> -1.46614749631243,
>
> 0.362539212141846, 0.786326226622549, 0.317282057548041,
> -1.02514155647985,
>
> 1.07113369815538, 0.609736001727743, -0.655728143403281,
> -1.03419747081316,
>
> 1.14148232415467, 0.503896215545131, -0.611181068886636,
> -0.943184299406566,
>
> 0.778492522245523, 0.945708813261833, -0.78101703610078,
> 1.25047276064487,
>
> -0.113538768459753, 0.0548777607029143,
> -1.19181175288804, 1.28370586906697,
>
> 0.254354524536168, -0.540351240198989,
> -0.997709153404147, 1.25426184614502,
>
> 0.143195107796418, -0.235112572720005,
> -1.16234438122143, 1.03714731356991,
>
> 0.406650195058153, -0.123281411659495,
> -1.32051609696858, 0.851530489918317,
>
> 0.596257630693658, -0.0638457887809093,
> -1.38394233183106, 0.9281945227055,
>
> 0.57691754078049, -0.172495725682589, -1.33261633780340,
> 0.931917365795697,
>
> 0.653353551741362, -0.319287162711085,
> -1.26598375482597, 1.19372966187956,
>
> 0.453501818870319, -0.903176468889435,
> -0.744055011860442, 1.19698274357976,
>
> 0.441487949431983, -0.941766151100918,
> -0.696704541910826, 1.19407808189758,
>
> 0.447251122498145, -0.9372047007794, -0.704124503616327,
> 1.18155526998177,
>
> 0.465093691295555, -0.949595224394993,
> -0.697053736882326, 1.2218547353343,
>
> 0.400521563178456, -0.93488345268835,
> -0.687492845824406, 0.997233560332114,
>
> 0.652368565446036, -0.493631246722725,
> -1.15597087905543, 1.10914280037357,
>
> 0.536560120952493, -0.570129842719142,
> -1.07557307860692, 1.05871763558761,
>
> 0.64658837487362, -0.793466237636563,
> -0.911839772824668, 0.906822512746599,
>
> 0.807139899513123, -0.687622802632555,
> -1.02633960962716, 0.77912190137299,
>
> 0.947182223637108, -0.809524028729025,
> -0.91678009628107, 1.33893188130515,
>
> 0.178377570495840, -0.86894723087327,
> -0.648362220927723, 1.39208493297302,
>
> 0.062650188298147, -0.73223360450103,
> -0.722501516770135, 1.46330419386939,
>
> -0.177601977084224, -0.661334598551208,
> -0.624367618233957, 1.46904838309704,
>
> -0.437288024655434, -0.759202304177765,
> -0.272558054263839, 0.747807260442244,
>
> 0.657576754588525, -1.41712359913304,
> 0.0117395841022768, 0.714318042078153,
>
> 0.832332574891687, -1.32146222297309,
> -0.225188393996755, 0.776853817614179,
>
> 0.731202922578465, -1.35599301451107,
> -0.152063725681571, 0.841732283108634,
>
> 0.754248218272813, -1.27181485347646,
> -0.324165647904986, 0.97326112450597,
>
> 0.652082611403661, -1.20425833446000,
> -0.421085401449625, -0.901983912371582,
>
> -0.0065855621849476, 1.39599392995549,
> -0.487424455398969, 0.610771143828774,
>
> -0.762088920575592, 1.08430415610192,
> -0.932986379355095, -0.0148828263869010,
>
> 0.610158458070122, 0.809229072877685, -1.40450470456092,
> -0.116351310506438,
>
> 0.583290457043162, 0.892855986235108, -1.35979513277183,
> -0.313607205847584,
>
> 1.09572866565514, 0.444155476463272, -1.22627693627083,
> 0.243716750638903,
>
> 1.28335333872251, -0.510913960310597, -1.01615612905082,
> 0.045882176168387,
>
> 1.31978778177031, -0.280636135117373, -1.08503382282132,
> 0.124305385892705,
>
> 1.26763097889282, -0.243797611378268, -1.14813875340725,
> 0.521861081643557,
>
> 1.03284070831524, -0.301771114678491, -1.25293067528031,
> 0.355541486307312,
>
> 1.04256940502540, -0.0629413619565949,
> -1.33516952937611), .Dim = c(4L,
>
>
> 47L), .Dimnames = list(c("l1", "d1", "l13", "d13"), c("sll0685",
>
>
> "slr0853", "sll0327", "sll1796", "sll0790", "sll1694", "pSysX_49",
>
>
> "slr1675", "sll1450", "sll1695", "slr1984", "ssl2148",
> "pSysX_130",
>
>
> "sll1814", "smr0003", "ssl2245", "sll1130", "sll0108", "slr1634",
>
>
> "slr0146", "slr0144", "slr0147", "slr0145", "sll0735", "sll0781",
>
>
> "slr1930", "sll0783", "slr1603", "slr0044", "slr0041", "slr0042",
>
>
> "slr0043", "slr0749", "slr0750", "ssr1251", "slr0737", "ssr0390",
>
>
> "sll1891", "sll1621", "sll1507", "slr1251", "slr0898", "sll0789",
>
>
> "pSysX_48", "sll0788", "pSysX_50", "slr1236"))), rowDendrogram =
> structure(list(
>
>
>
> structure(list(structure(list(structure(7L, members = 1L, height = 0, label
> = "sll0685", leaf = TRUE, value = structure(-2.3037127760972e-15, .Names =
> "sll0685")),
>
>
>
> structure(list(structure(list(structure(34L, label = "slr0853",
> members = 1L, height = 0, leaf = TRUE, value =
> structure(-2.11636264069170e-15, .Names = "slr0853")),
>
>
>
> structure(6L, label = "sll0327",
> members = 1L, height = 0, leaf = TRUE, value =
> structure(-1.38777878078145e-17, .Names = "sll0327"))), members = 2L,
> midpoint = 0.5, height = 0.408448760380633, value = -2.13024042849952e-15),
>
>
>
> structure(20L, members = 1L, height = 0, label =
> "sll1796", leaf = TRUE, value = structure(1.05818132034585e-15, .Names =
> "sll1796"))), members = 3L, midpoint = 1.25, height = 0.822640063299773,
> value = -1.07205910815367e-15)), members = 4L, midpoint = 1.125, height =
> 1.5200001193864, value = -3.37577188425087e-15),
>
>
>
> structure(list(structure(13L, members = 1L, height = 0, label = "sll0790",
> leaf = TRUE, value = structure(-2.12330153459561e-15, .Names = "sll0790")),
>
>
>
> structure(list(structure(list(structure(list(structure(18L,
> label = "sll1694", members = 1L, height = 0, leaf = TRUE, value =
> structure(-1.06165076729781e-15, .Names = "sll1694")),
>
>
>
> structure(3L, label
> = "pSysX_49", members = 1L, height = 0, leaf = TRUE, value =
> structure(3.12250225675825e-17, .Names = "pSysX_49"))), members = 2L,
> midpoint = 0.5, height = 0.55986390207006, value = -1.03042574473022e-15),
>
>
>
> structure(40L, members = 1L,
> height = 0, label = "slr1675", leaf = TRUE, value =
> structure(2.59514632006130e-15, .Names = "slr1675"))), members = 3L,
> midpoint = 1.25, height = 0.96984571387736, value = 1.56472057533108e-15),
>
>
>
> structure(list(structure(list(structure(15L,
> label = "sll1450", members = 1L, height = 0, leaf = TRUE, value =
> structure(-7.4940054162198e-16, .Names = "sll1450")),
>
>
>
> structure(19L,
> label = "sll1695", members = 1L, height = 0, leaf = TRUE, value =
> structure(1.72084568816899e-15, .Names = "sll1695"))), members = 2L,
> midpoint = 0.5, height = 0.134972000620768, value = 9.71445146547012e-16),
>
>
>
> structure(42L, members = 1L,
> height = 0, label = "slr1984", leaf = TRUE, value =
> structure(2.35922392732846e-15, .Names = "slr1984"))), members = 3L,
> midpoint = 1.25, height = 0.603396735921129, value = 3.33066907387547e-15)),
> members = 6L, midpoint = 2.75, height = 1.41703706740193, value =
> 4.89538964920655e-15)), members = 7L, midpoint = 1.875, height =
> 1.79108103853389, value = 2.77208811461094e-15)), members = 11L, midpoint =
> 3.5, height = 2.96304988576369, value = -6.03683769639929e-16),
>
>
>
> structure(list(structure(list(structure(list(structure(list(
>
>
>
> structure(list(structure(44L,
> members = 1L, height = 0, label = "ssl2148", leaf = TRUE, value =
> structure(-2.68535194081210e-15, .Names = "ssl2148")),
>
>
>
>
> structure(list(structure(1L, label = "pSysX_130", members = 1L, height = 0,
> leaf = TRUE, value = structure(-3.88578058618805e-16, .Names =
> "pSysX_130")),
>
>
>
>
> structure(21L, label = "sll1814", members = 1L, height = 0, leaf = TRUE,
> value = structure(2.77555756156289e-17, .Names = "sll1814"))), members = 2L,
> midpoint = 0.5, height = 0.36537483325832, value = -3.60822483003176e-16)),
> members = 3L, midpoint = 0.75, height = 0.72692729840601, value =
> -3.04617442381527e-15),
>
>
>
>
> structure(list(structure(list(structure(43L, members = 1L, height = 0, label
> = "smr0003", leaf = TRUE, value = structure(-3.63598040564739e-15, .Names =
> "smr0003")),
>
>
>
>
> structure(list(structure(45L, label = "ssl2245", members = 1L, height = 0,
> leaf = TRUE, value = structure(8.22258927613007e-16, .Names = "ssl2245")),
>
>
>
>
> structure(14L, label = "sll1130", members = 1L, height = 0, leaf
> = TRUE, value = structure(1.38083988687754e-15, .Names = "sll1130"))),
> members = 2L, midpoint = 0.5, height = 0.143842203308732, value =
> 2.20309881449055e-15)), members = 3L, midpoint = 0.75, height =
> 0.279213297331223, value = -1.43288159115684e-15),
>
>
>
> structure(5L,
> members = 1L, height = 0, label = "sll0108", leaf = TRUE, value =
> structure(1.19348975147204e-15, .Names = "sll0108"))), members = 4L,
> midpoint = 1.875, height = 0.336642122872617, value =
> -2.39391839684799e-16)), members = 7L, midpoint = 2.8125, height =
> 0.913839289019599, value = -3.28556626350007e-15),
>
>
>
>
> structure(list(structure(list(structure(list(structure(39L, members = 1L,
> height = 0, label = "slr1634", leaf = TRUE, value =
> structure(-3.46944695195361e-16, .Names = "slr1634")),
>
>
>
>
> structure(list(structure(list(structure(29L, label = "slr0146", members =
> 1L, height = 0, leaf = TRUE, value = structure(-2.22044604925031e-16, .Names
> = "slr0146")),
>
>
>
>
> structure(27L, label = "slr0144", members = 1L,
> height = 0, leaf = TRUE, value = structure(1.94289029309402e-16, .Names =
> "slr0144"))), members = 2L, midpoint = 0.5, height = 0.0108403820977512,
> value = -2.77555756156289e-17),
>
>
>
>
> structure(30L, members = 1L, height = 0, label = "slr0147", leaf
> = TRUE, value = structure(2.35922392732846e-16, .Names = "slr0147"))),
> members = 3L, midpoint = 1.25, height = 0.0292686575762982, value =
> 2.08166817117217e-16)), members = 4L, midpoint = 1.125, height =
> 0.068164565843679, value = -1.38777878078145e-16),
>
>
>
> structure(28L,
> members = 1L, height = 0, label = "slr0145", leaf = TRUE, value =
> structure(0, .Names = "slr0145"))), members = 5L, midpoint = 2.5625, height
> = 0.088331980043033, value = -1.38777878078145e-16),
>
>
>
>
> structure(list(structure(list(structure(list(structure(8L, label =
> "sll0735", members = 1L, height = 0, leaf = TRUE, value =
> structure(-1.65145674912992e-15, .Names = "sll0735")),
>
>
>
>
> structure(9L, label = "sll0781", members = 1L, height = 0, leaf =
> TRUE, value = structure(4.9960036108132e-16, .Names = "sll0781"))), members
> = 2L, midpoint = 0.5, height = 0.195578923529741, value =
> -1.1518563880486e-15),
>
>
>
>
> structure(41L, members = 1L, height = 0, label = "slr1930", leaf = TRUE,
> value = structure(7.7715611723761e-16, .Names = "slr1930"))), members = 3L,
> midpoint = 1.25, height = 0.39155423751868, value = -3.7470027081099e-16),
>
>
>
>
> structure(list(structure(10L, label = "sll0783", members = 1L, height = 0,
> leaf = TRUE, value = structure(4.16333634234434e-16, .Names = "sll0783")),
>
>
>
>
> structure(38L, label = "slr1603", members = 1L, height = 0, leaf = TRUE,
> value = structure(6.10622663543836e-16, .Names = "slr1603"))), members = 2L,
> midpoint = 0.5, height = 0.250564352172644, value = 1.02695629777827e-15)),
> members = 5L, midpoint = 2.375, height = 0.600040909040007, value =
> 6.5225602696728e-16)), members = 10L, midpoint = 4.96875, height =
> 0.750425125084372, value = 5.13478148889135e-16)), members = 17L, midpoint =
> 7.390625, height = 1.47313730565769, value = -2.77208811461094e-15),
>
>
>
> structure(list(structure(list(structure(list(structure(list(
>
>
>
>
> structure(26L, label = "slr0044", members = 1L, height = 0, leaf = TRUE,
> value = structure(-6.59194920871187e-16, .Names = "slr0044")),
>
>
>
>
> structure(23L, label = "slr0041", members = 1L, height = 0, leaf = TRUE,
> value = structure(2.42861286636753e-17, .Names = "slr0041"))), members = 2L,
> midpoint = 0.5, height = 0.201010757711608, value = -6.34908792207511e-16),
>
>
>
> structure(24L,
> members = 1L, height = 0, label = "slr0042", leaf = TRUE, value =
> structure(0, .Names = "slr0042"))), members = 3L, midpoint = 1.25, height =
> 0.431124873425334, value = -6.34908792207511e-16),
>
>
>
> structure(25L, members = 1L,
> height = 0, label = "slr0043", leaf = TRUE, value =
> structure(6.66133814775094e-16, .Names = "slr0043"))), members = 4L,
> midpoint = 2.125, height = 0.741112103334488, value =
> 3.12250225675825e-17),
>
>
>
> structure(list(structure(32L, members = 1L,
> height = 0, label = "slr0749", leaf = TRUE, value =
> structure(2.59774840527527e-16, .Names = "slr0749")),
>
>
>
>
> structure(list(structure(list(structure(list(
>
>
>
>
> structure(33L, label = "slr0750", members = 1L, height = 0, leaf
> = TRUE, value = structure(-2.84494650060196e-16, .Names = "slr0750")),
>
>
>
>
> structure(47L, label = "ssr1251", members = 1L, height = 0, leaf
> = TRUE, value = structure(2.08166817117217e-17, .Names = "ssr1251"))),
> members = 2L, midpoint = 0.5, height = 0.143796809698028, value =
> -2.63677968348475e-16),
>
>
>
>
> structure(31L, members = 1L, height = 0, label = "slr0737", leaf = TRUE,
> value = structure(-4.16333634234434e-17, .Names = "slr0737"))), members =
> 3L, midpoint = 1.25, height = 0.203581274597441, value =
> -3.05311331771918e-16),
>
>
>
> structure(46L,
> members = 1L, height = 0, label = "ssr0390", leaf = TRUE, value =
> structure(1.81799020282369e-15, .Names = "ssr0390"))), members = 4L,
> midpoint = 2.125, height = 0.38942773178888, value = 1.51267887105178e-15)),
> members = 5L, midpoint = 1.5625, height = 0.532455368507944, value =
> 1.77245371157930e-15)), members = 9L, midpoint = 3.84375, height =
> 1.58111810294058, value = 1.80367873414689e-15)), members = 26L, midpoint =
> 14.1171875, height = 2.11249037373193, value = -9.68409380464053e-16),
>
>
>
> structure(list(structure(list(structure(22L, label = "sll1891", members =
> 1L, height = 0, leaf = TRUE, value = structure(-1.26287869051112e-15, .Names
> = "sll1891")),
>
>
>
> structure(17L, label = "sll1621", members = 1L,
> height = 0, leaf = TRUE, value = structure(1.08246744900953e-15, .Names =
> "sll1621"))), members = 2L, midpoint = 0.5, height = 1.77620075661612, value
> = -1.80411241501588e-16),
>
>
>
> structure(list(structure(list(structure(list(structure(16L,
> label = "sll1507", members = 1L, height = 0, leaf = TRUE, value =
> structure(-2.86055901188575e-15, .Names = "sll1507")),
>
>
>
> structure(37L,
> label = "slr1251", members = 1L, height = 0, leaf = TRUE, value =
> structure(1.68962066560141e-15, .Names = "slr1251"))), members = 2L,
> midpoint = 0.5, height = 0.141457234512609, value = -1.17093834628434e-15),
>
>
>
> structure(35L, members = 1L,
> height = 0, label = "slr0898", leaf = TRUE, value =
> structure(-1.12410081243297e-15, .Names = "slr0898"))), members = 3L,
> midpoint = 1.25, height = 0.721569166579802, value =
> -2.29503915871732e-15),
>
>
>
> structure(list(structure(list(structure(12L,
> members = 1L, height = 0, label = "sll0789", leaf = TRUE, value =
> structure(-6.93889390390723e-18, .Names = "sll0789")),
>
>
>
>
> structure(list(structure(2L, label = "pSysX_48", members = 1L, height = 0,
> leaf = TRUE, value = structure(-3.98986399474666e-17, .Names =
> "pSysX_48")),
>
>
>
>
> structure(11L, label = "sll0788", members = 1L, height = 0, leaf = TRUE,
> value = structure(5.93275428784068e-16, .Names = "sll0788"))), members = 2L,
> midpoint = 0.5, height = 0.119205037667866, value = 5.53376788836601e-16)),
> members = 3L, midpoint = 0.75, height = 0.321367116594267, value =
> 5.46437894932694e-16),
>
>
>
> structure(list(structure(4L, label
> = "pSysX_50", members = 1L, height = 0, leaf = TRUE, value =
> structure(-8.04911692853238e-16, .Names = "pSysX_50")),
>
>
>
> structure(36L,
> label = "slr1236", members = 1L, height = 0, leaf = TRUE, value =
> structure(3.21270787750905e-15, .Names = "slr1236"))), members = 2L,
> midpoint = 0.5, height = 0.302588392442079, value = 2.40779618465581e-15)),
> members = 5L, midpoint = 2.125, height = 0.610680499686294, value =
> 2.9542340795885e-15)), members = 8L, midpoint = 3.1875, height =
> 1.64572016900367, value = 6.59194920871187e-16)), members = 10L, midpoint =
> 2.84375, height = 2.62534326555191, value = 4.78783679369599e-16)), members
> = 36L, midpoint = 21.48046875, height = 3.36537033143646, value =
> -4.89625701094454e-16)), members = 47L, midpoint = 17.990234375, height =
> 3.46289882269828, class = "dendrogram", value = -1.09330947073438e-15),
> breaks = structure(c(-1.46614749631243,
> -1.32889829952663,
> -1.17216683844364, -0.966047927590969,
> -0.890971685205478,
> -0.721704590944272, -0.611181068886636,
> -0.317393843756585,
> -0.0065855621849476, 0, 0.247262675271325,
> 0.446219240486521,
> 0.596257630693658, 0.719946335578257, 0.831886764794183,
> 0.997233560332114, 1.09153040342218, 1.25299881764497,
> 1.46904838309704
> ), .Names = c("0%", "11.111%", "22.222%", "33.333%",
> "44.444%",
> "55.556%", "66.667%", "77.778%", "100%", "",
> "11.111%", "22.222%",
> "33.333%", "44.444%", "55.556%", "66.667%", "77.778%",
> "88.889%",
> "100%")), col = c("#0000FF", "#2020FF", "#4040FF",
> "#6060FF",
> "#8080FF", "#9F9FFF", "#BFBFFF", "#DFDFFF",
> "#FFFFFF", "#FFFFFF",
> "#FFDFDF", "#FFBFBF", "#FF9F9F", "#FF8080",
> "#FF6060", "#FF4040",
> "#FF2020", "#FF0000"), colorTable =
> structure(list(low = c(-1.46614749631243,
>
> -1.32889829952663, -1.17216683844364, -0.966047927590969,
>
> -0.890971685205478, -0.721704590944272, -0.611181068886636,
>
> -0.317393843756585, -0.0065855621849476, 0, 0.247262675271325,
>
> 0.446219240486521, 0.596257630693658, 0.719946335578257,
>
> 0.831886764794183, 0.997233560332114, 1.09153040342218,
> 1.25299881764497
>
> ), high = c(-1.32889829952663, -1.17216683844364, -0.966047927590969,
>
> -0.890971685205478, -0.721704590944272, -0.611181068886636,
>
> -0.317393843756585, -0.0065855621849476, 0, 0.247262675271325,
>
> 0.446219240486521, 0.596257630693658, 0.719946335578257,
>
> 0.831886764794183, 0.997233560332114, 1.09153040342218,
> 1.25299881764497,
>
> 1.46904838309704), color = structure(c(1L, 2L, 3L, 4L, 5L,
>
> 6L, 7L, 8L, 17L, 17L, 16L, 15L, 14L, 13L, 12L,
> 11L, 10L,
>
> 9L), .Label = c("#0000FF", "#2020FF", "#4040FF",
> "#6060FF",
>
> "#8080FF", "#9F9FFF", "#BFBFFF", "#DFDFFF",
> "#FF0000", "#FF2020",
>
> "#FF4040", "#FF6060", "#FF8080", "#FF9F9F",
> "#FFBFBF", "#FFDFDF",
>
> "#FFFFFF"), class = "factor")), .Names =
> c("low", "high",
>
> "color"),
> row.names = c(NA, -18L), class = "data.frame")), .Names = c("rowInd",
>
>
> "colInd", "call", "carpet",
> "rowDendrogram", "breaks", "col",
>
>
> "colorTable"))
>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>
--
-------- Dr. January Weiner 3 --------------------------------------
Max Planck Institute for Infection Biology
Charitéplatz 1
D-10117 Berlin, Germany
Web : www.mpiib-berlin.mpg.de
Tel : +49-30-28460514
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