Question: how to obtain the clusters of genes (basically the ones in the row dendrograms) from an object obtained by heatmap.2 function
2
0
Entering edit mode
@sunny-srivastava-3793
Last seen 9.6 years ago
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]]
Microarray Microarray • 1.3k views
ADD COMMENT
0
Entering edit mode
@january-weiner-3999
Last seen 9.6 years ago
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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514
ADD COMMENT
0
Entering edit mode
Hi January, Thanks for the answer and help. I have already tried this package, but unfortunately it gives me an error due to some singularity related issues in the LAPACK routine. I have not seen people using the biclustering package, but I don't know if it will give me what I want (basically the clustering pattern in the heatmap). Thanks, S. On Thu, Sep 16, 2010 at 7:46 AM, January Weiner < january.weiner@mpiib-berlin.mpg.de> wrote: > 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@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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > -------- 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Sunny the function "cut.dendrogram" from the "stats" package does what you want. It's described in the manual page of the "dendrogram" class. Try typing, in R: ? dendrogram Best wishes Wolfgang On Sep/16/10 12:57 PM, Sunny Srivastava 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. > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENT
0
Entering edit mode
Dear Dr. Huber, Thanks for your reply, but I had looked at this function. What I understood from the documentation was: if give the height at which I want to cut, then it gives me $upper and $lower, but I guess I have to "hack" to get the height which gives me a specific number of clusters? I am I thinking correctly? Best Regards, S. On Fri, Sep 17, 2010 at 10:11 AM, Wolfgang Huber <whuber@embl.de> wrote: > Sunny > > the function "cut.dendrogram" from the "stats" package does what you want. > It's described in the manual page of the "dendrogram" class. Try typing, in > R: > > ? dendrogram > > Best wishes > Wolfgang > > > > > On Sep/16/10 12:57 PM, Sunny Srivastava wrote: > >> Hello Bioconductor Helpers, >> I have a question about extracting the clusters of genes after we make the >> heatmap (say ht4) using the heatmap.2 function. Basically, I want to get >> the >> clusters which are shown as row dendrogram in the heatmap. >> >> I understand that ht4$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. >> >> -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
On Fri, Sep 17, 2010 at 1:17 PM, Sunny Srivastava <research.baba@gmail.com>wrote: > Dear Dr. Huber, > Thanks for your reply, but I had looked at this function. What I understood > from the documentation was: if give the height at which I want to cut, then > it gives me $upper and $lower, but I guess I have to "hack" to get the > height which gives me a specific number of clusters? > > I am I thinking correctly? > > You could also try the cutree() function. Sean > On Fri, Sep 17, 2010 at 10:11 AM, Wolfgang Huber <whuber@embl.de> wrote: > > > Sunny > > > > the function "cut.dendrogram" from the "stats" package does what you > want. > > It's described in the manual page of the "dendrogram" class. Try typing, > in > > R: > > > > ? dendrogram > > > > Best wishes > > Wolfgang > > > > > > > > > > On Sep/16/10 12:57 PM, Sunny Srivastava wrote: > > > >> Hello Bioconductor Helpers, > >> I have a question about extracting the clusters of genes after we make > the > >> heatmap (say ht4) using the heatmap.2 function. Basically, I want to get > >> the > >> clusters which are shown as row dendrogram in the heatmap. > >> > >> I understand that ht4$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. > >> > >> -- > > > > > > Wolfgang Huber > > EMBL > > http://www.embl.de/research/units/genome_biology/huber > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
thank you very much Sean, this is exactly what I needed! On Fri, Sep 17, 2010 at 1:26 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Fri, Sep 17, 2010 at 1:17 PM, Sunny Srivastava <research.baba@gmail.com> > wrote: > >> Dear Dr. Huber, >> Thanks for your reply, but I had looked at this function. What I >> understood >> from the documentation was: if give the height at which I want to cut, >> then >> it gives me $upper and $lower, but I guess I have to "hack" to get the >> height which gives me a specific number of clusters? >> >> I am I thinking correctly? >> >> > You could also try the cutree() function. > > Sean > > >> On Fri, Sep 17, 2010 at 10:11 AM, Wolfgang Huber <whuber@embl.de> wrote: >> >> > Sunny >> > >> > the function "cut.dendrogram" from the "stats" package does what you >> want. >> > It's described in the manual page of the "dendrogram" class. Try typing, >> in >> > R: >> > >> > ? dendrogram >> > >> > Best wishes >> > Wolfgang >> > >> > >> > >> > >> > On Sep/16/10 12:57 PM, Sunny Srivastava wrote: >> > >> >> Hello Bioconductor Helpers, >> >> I have a question about extracting the clusters of genes after we make >> the >> >> heatmap (say ht4) using the heatmap.2 function. Basically, I want to >> get >> >> the >> >> clusters which are shown as row dendrogram in the heatmap. >> >> >> >> I understand that ht4$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. >> >> >> >> -- >> > >> > >> > Wolfgang Huber >> > EMBL >> > http://www.embl.de/research/units/genome_biology/huber >> > >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLY

Login before adding your answer.

Traffic: 736 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6