text: user4001: I have been attempting to extract particular clusters, given by hierarchical clustering outputs from the pheatmap function (in R).
  Please find the dput output of the dataset in question below:
  structure(list(`72v24.logFC` = c(-1.47511280138092, -1.10386310802134, 
  -1.14476608274903, -1.63563574551239, -0.895377907265352, -1.35216488439027, 
  -2.04949381135359, -1.0344565728341, -0.967008696515716, -1.11233305998901, 
  -2.02663681865178, -1.74756562789736, -1.02076838668592, -1.27981009782201, 
  -1.13181804725663, -1.19537930856639, -2.23476188503608, -1.67500131867632, 
  -0.950059974858215, -2.3124598902615, -1.93757457440581, -3.24602437386808, 
  -0.839869104053795, -1.40329424193006, -1.63484798229567, -0.912148120310492, 
  -1.33467209346367, -1.27031027753064, -0.925498608058671, -0.802956638081314, 
  -0.85457796397113, -1.0591348681193, -0.825278459132589, -0.671570119524199, 
  -1.8439768319437, -0.947033608766851, -1.63849733567277, -1.40584263305038, 
  -1.1317958487115, -1.40724695083764, -1.21842141154588, -2.29248800050516, 
  -1.41699787526721, -0.879218050664484, -2.25064962332145, 1.4685855647974, 
  -2.02553848518381, 1.32808748053321, -2.46062484389627, -2.45830217362141, 
  -0.880536960021976, -0.689060222340137, -0.863262774594, -1.64961312646758, 
  1.10572346456398, -0.891760767302047, -1.22716047163938, -0.680697741299578, 
  -1.24551344420046, -0.891918251648935, -1.64722787848732, -0.832845262108387, 
  -0.937129577660045, -0.891684122691785, 1.96452911491088, -1.59420664438654, 
  -0.921295293242016, -1.8304480291305, -0.632859040349798, 1.69982819847455, 
  -0.982668795391973, -1.61816842714933, -1.23602172818196, -2.15356245206668, 
  -1.67961932563564, 1.15478114880933, 1.32665444151868, -1.04590896017973, 
  -2.29770026795487, -1.27498150009975, -1.36310217581123, -1.09169550738617, 
  1.5349413586602, -1.66842984591719, -0.760122936706606, -1.10054393155051, 
  -1.00344072779106, -0.993259123487476, -1.43136824963825, -1.07214189069438, 
  -0.990813303020613, -1.51324812740189, -1.23465012540084, -1.00098231964124, 
  -1.92195764952845, -1.00139179559519, -0.940118366042393, -2.35969198434574, 
  -0.574626090826994, -0.884870428965888, -0.87601460107501, 1.61336157755029, 
  -0.777670642457121, -0.7312214522498, -0.812926777785119, -1.13443421373561, 
  -1.56498420350444, -0.69126972981765, -1.44351026281231, -1.21962275860236, 
  -2.21155555407497, -1.02015250027788, -0.604620179871691, -1.53013572266942, 
  -0.790050747397837, -1.17950736026735, -0.781075150161975, -0.888554144538286, 
  3.59172865862026, -0.8665071699621, -2.97701792242157, -1.44424941630738, 
  -1.50528882788757, -0.772465957539335, -1.57664185213987, -1.02371443439054, 
  -0.931807409493221, 1.77728969821973, -1.05455101137715, -1.09765136526264, 
  -0.881436416213335, -0.985605985458853, -1.31644334991692, 2.26917914828263, 
  -1.43844640540614, -1.75106843701475, -1.22483991752173, -1.65032906954133, 
  -0.686319914242903, 2.45473055753775, -1.15594379837188, 1.46397122502826, 
  -0.91260428248088, -0.726540148411507, -1.18227838019011, -0.940722690371935, 
  -1.28074043595918, -0.629033607437977, 1.01053893402133, -0.735590704487842, 
  -2.0620695625823, -0.692251638781327, -0.717818968339447, -0.564023101160995, 
  1.51541391124355, -1.89444914881727, -0.737931396419173, -1.17763728235316, 
  -0.887605568116903, -2.8392997898765, -1.48018352596355, 1.60698486226092, 
  -1.96804216410227, -0.881437183709851, 3.08730764755417, -0.600282670155725, 
  -0.905719394102218, -1.05553935946213, -1.13508709782814, -0.613381276596874, 
  -0.642647139688194, -0.861929974132332, -1.30652597213552, -1.73647794867498, 
  -0.619909931049252, -0.880145154869759, -0.60084263914673, -1.16825573255754, 
  -0.942919502394457, -1.3709930239358, -0.80595477526712, -0.628115199442632, 
  -1.11502998682131, -1.01274335471793, -1.16595378001606, -3.36098944183559, 
  -1.19617345920841, -2.10811718229285, 3.33752122936, -1.67696701892834, 
  -1.90639199489612, -0.574737209544065, -1.66853541929234, -0.595093777485911, 
  -0.7964813653225, -0.791102813817634, -0.601987407016077, -1.52559881980829, 
  1.15480324851026, -0.830167728660421), `72v0.logFC` = c(-5.10937036648522, 
  -8.41670756910048, -8.18671783299995, -2.79415692883273, -3.62090016917187, 
  -8.37523504570539, -3.79100494829738, -7.20659380156151, -5.46135634576091, 
  3.43493215839382, -1.67650075643956, -2.99391647274475, -5.77357941089076, 
  -5.22675557853878, 3.26436094268851, -5.98693257837598, -5.85864442290848, 
  -2.39995052889286, -5.19221784614079, -4.72634343497625, -7.46407809296449, 
  -3.04588366694082, -3.85014181238163, 4.44756662720351, -4.42031795110716, 
  -2.58478993868624, -5.46121416816988, -2.09364835701952, -5.42397023596482, 
  -5.26192471384563, -4.48979100280513, -5.14171942073048, -5.5267515390142, 
  3.88762033289334, -5.88489034628499, -2.85490179670763, -5.31586479048071, 
  -2.64877712735579, -6.24766069294439, -5.35826818217055, -4.97204642950896, 
  -2.82989963758335, -4.75016577988789, -3.51684070536132, -3.20931950649022, 
  -3.62394584217955, -2.81449967053025, -5.68308664428684, -3.11500402887324, 
  -4.08965188145047, -5.43176189260205, -4.30737780091769, 2.52666133143524, 
  -3.88213803962076, -5.517506523237, -3.27502948978619, -5.37724717693793, 
  2.77090845859761, -4.22554364178978, -5.81944792042417, -2.23700806354102, 
  -1.81804660477942, -3.45613077773548, -4.88444075082709, -5.48877199958173, 
  -4.90077849970695, -3.79304730634383, -0.953597409660203, -5.573920008042, 
  -1.83250444732307, -1.73248469438834, -2.35460087734472, -4.43029236446579, 
  -3.37654864236982, -3.63410171518379, -2.78276966423079, -2.01664452557169, 
  -3.54834187597395, -2.04395822264753, -2.15693095907293, -4.04759665569609, 
  -4.87928960250415, 1.1358557257212, -4.89657506999093, -2.42698466771808, 
  -4.55703295523896, -2.53230009478764, -1.74571568381108, 1.93875826054123, 
  -2.29178704384166, -1.88631492984573, -4.17811684330152, -4.55155213716622, 
  1.93093495783903, -3.66429213603731, 2.73817157445051, -3.96977406502995, 
  -4.18487497756956, 2.17512996773018, -4.41168757499049, -2.96267804428878, 
  -4.60683474159913, -3.0573109426718, -1.59500391193586, -4.65882130908176, 
  -2.68903554919404, -4.44676809434802, 1.60275224879078, -3.83760729167497, 
  -3.09907199540008, -2.37905633686461, -4.29650784478684, -1.88615561094275, 
  -4.44026540480975, -2.01996858091239, -2.46842498723876, -4.24053886261736, 
  -4.32561109033911, -2.96097578889787, -3.76708395833968, -2.45229520135946, 
  -2.33856203921674, -4.23241140779399, -3.48627475173498, 2.25888018977625, 
  -3.85271202182208, -4.61317704601435, -1.95186634348091, 1.3205477461731, 
  -2.51561846705872, -1.7031812569795, -4.44717736673796, -3.88478215160905, 
  -3.27547652595564, -2.81690169904308, -4.83981492357284, -2.4486942125238, 
  -4.31360736969916, -4.22122930700826, -3.49045260391997, -2.87862947524065, 
  -4.14268228866617, -2.62252967420329, -4.23902905919912, -4.14777621540367, 
  -2.86056694414781, -1.70668584273452, 1.3624660569909, -2.59153842674144, 
  -4.12393693326418, -2.12959469550212, 1.46923996462969, -1.98633421258236, 
  3.22176343046404, -3.52110060349997, -2.69900299957347, -4.20126962458439, 
  -4.68116989520068, 1.57592717464553, -3.93999603065316, -2.79446235029201, 
  1.53128139579193, 2.65531461899762, -1.33692502254506, -1.40309746138702, 
  7.1503230589606, -3.03232696595877, -3.99799016693196, 1.36106448869886, 
  2.48321747034381, -1.81760324077147, -2.93792828398095, -4.24318581706171, 
  -5.02935968459404, -2.8067837982494, -3.18182441332852, -3.17383228514224, 
  -3.75210155230786, -3.87059449392306, -3.38923922246314, -3.8492188722049, 
  -4.54207754798088, -3.65594980956956, -4.083692310451, 1.30846845334021, 
  -2.14067263149232, 0.87594188820449, -2.36549598411797, -1.6026649015159, 
  3.06122694909985, -2.80125769402892, -1.21061533381979, 2.45621751938726, 
  -1.29479960958983, -1.32215076834374, -3.40665434275434, -3.87581533996246, 
  2.25817917663687, -4.47531796954113, -3.0627832955887), `24v0.logFC` = c(-5.63038870666508, 
  -6.44381761773614, -9.71855520117086, 2.83617729007977, -3.39220401105853, 
  -9.03206578896647, 4.72316302034493, 2.69600384046815, -3.70005627557764, 
  1.57004091545159, -2.69837465613229, -1.96398920017231, -6.78881951127235, 
  2.88395305274553, 2.2815237548239, 4.26299665984366, 1.80759581466942, 
  -6.13159865127454, 2.31984691801986, 2.42017005000243, 1.90522291464817, 
  -6.08799743507621, 1.93712248733409, -2.85900752558212, -2.53314737897312, 
  -5.39825301043452, -2.67723981805717, 1.99371094854688, -6.30018858053764, 
  -5.51269257077614, 1.22241656195939, 2.21258569930309, -3.34360626488873, 
  2.84622416535537, 1.62066860166637, -4.78372642162402, -5.70058663575352, 
  -5.38484766744183, -5.09622306588101, 1.4720608195385, 2.81999896316429, 
  -5.00082275569591, -4.22688753149231, 3.13575564914666, -3.65108053066376, 
  -4.96357882349085, 1.41296031244116, 2.02777799934303, -2.69828900301196, 
  3.3280993785528, -4.91524305899842, 1.33559456145784, -3.20704073441948, 
  3.4589509748052, -4.76220190139647, -5.41080867153898, -2.52368474702804, 
  2.35227625126478, -1.66843249760588, -5.98409816921998, 1.97783827997787, 
  -5.05713668502354, -5.66050145489872, -3.23578154397873, -5.47590590732768, 
  1.79478248294125, 1.53715323981994, 1.17924158724962, -3.38135082340585, 
  -6.0533528170201, 3.64133939415158, -5.18911327526881, 1.12836935335145, 
  -5.50962223997537, -5.13018380364927, 2.43347308480167, 3.09821960202745, 
  1.08371028206663, 1.15073045150599, 1.66618928654645, -4.57926216582183, 
  -4.39710926752864, 2.29767598663356, 1.11369483753166, 1.90655785334723, 
  -4.57402537033236, -1.64795888694238, -4.90903507231585, -4.69225607476014, 
  -3.78658812613927, 2.71158710397443, 2.0014280958994, 1.42976609883019, 
  1.69469179645011, 2.02542067939079, 1.29620189704961, -2.11262483065018, 
  -4.45917113273047, -5.00209626672923, -2.22313144605634, 2.28015100958449, 
  2.99018492359164, -4.55487718731015, -4.4548605761304, -2.74564764773372, 
  1.50453692418261, -1.80916071906589, -3.78464149018, 5.44303553967597, 
  1.63876298449708, -2.55262897048338, -4.52516489294599, 1.86420921266273, 
  1.92394285952202, -1.87942876800687, -4.72261410600152, -2.57805004195914, 
  -4.47016439150427, -2.79823793519691, 1.49664827810044, -5.12377787039451, 
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  -1.66914425228449, -5.67499677983564, -2.41648326328024, 1.4178331810756, 
  1.34477707145884, 1.6168542644666, 1.51101526992765, 2.85584943327062, 
  -4.19149110174371, 1.69988651757158, 2.42852927065545, 1.66468253437414, 
  3.21304236161755, 2.52923647014318, -3.32575501787469, 1.32217968706286, 
  -4.3404208961354, 1.60065358035513, 1.11559852847827, 2.24622871386089, 
  -2.07936338453629, -4.096641542765, -1.81072034410725, -1.71317603678557, 
  3.48120770906848, -3.87801910383696, -4.08020770103266, 1.11478378387699, 
  -3.46079055745071, 1.7322630648363, 1.54861321913459, 1.96850013686628, 
  2.50282552968501, -1.81077760463368, 2.02487013804019, 1.95047564703855, 
  -2.99930567848563, -1.79193606152703, -2.54724389366544, -4.15112678166129, 
  1.13069494609896, -1.43241741260756, 2.36383913233529, 1.65786717131242, 
  -2.29507370488367, 1.5786351022915, -3.31042999789919, 2.582031624397, 
  -3.62438687496853, -4.20056844288066, 1.59787844454997, -4.39077226372811, 
  -4.50758458577604, -3.5310616440773, 1.34960913912344, 1.56097908933761, 
  1.80910781056029, -4.1248594098749, 1.5318048796277, -3.97753680837585, 
  -2.80501778688795, -3.20129716412254, -1.98305552020422, -4.25045728757901, 
  -4.08742040090535, -4.31190449886363, 1.39895836419766, 1.67102855271528, 
  -5.13520809951127, -4.31701572736756, 0.832778953035371, 2.30899115735356, 
  -3.18620970041199, -3.80052092618969, 1.59131320240714)), row.names = c("ENSMUSG00000097417.1", 
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  "ENSMUSG00000002985.16", "ENSMUSG00000046145.7", "ENSMUSG00000038274.11", 
  "ENSMUSG00000087366.7", "ENSMUSG00000039452.5", "ENSMUSG00000087660.1", 
  "ENSMUSG00000087206.1", "ENSMUSG00000079355.3", "ENSMUSG00000086693.1", 
  "ENSMUSG00000030579.10", "ENSMUSG00000084878.1", "ENSMUSG00000108235.1", 
  "ENSMUSG00000097077.1", "ENSMUSG00000101438.1", "ENSMUSG00000087367.1", 
  "ENSMUSG00000064351.1", "ENSMUSG00000086312.1", "ENSMUSG00000097221.1", 
  "ENSMUSG00000107090.1", "ENSMUSG00000037982.16", "ENSMUSG00000095280.1", 
  "ENSMUSG00000017837.12", "ENSMUSG00000029422.14", "ENSMUSG00000102564.1", 
  "ENSMUSG00000026749.11", "ENSMUSG00000067288.12", "ENSMUSG00000025353.4", 
  "ENSMUSG00000109251.1", "ENSMUSG00000086600.8", "ENSMUSG00000052214.9", 
  "ENSMUSG00000090330.2", "ENSMUSG00000090009.1", "ENSMUSG00000059791.14", 
  "ENSMUSG00000101695.1", "ENSMUSG00000103698.1", "ENSMUSG00000097472.1", 
  "ENSMUSG00000084128.10", "ENSMUSG00000026156.8", "ENSMUSG00000075297.10", 
  "ENSMUSG00000055692.18", "ENSMUSG00000038502.16", "ENSMUSG00000015942.9", 
  "ENSMUSG00000106478.1", "ENSMUSG00000039307.16", "ENSMUSG00000054556.6", 
  "ENSMUSG00000045576.16", "ENSMUSG00000037936.15", "ENSMUSG00000087486.1", 
  "ENSMUSG00000082180.1", "ENSMUSG00000014470.4", "ENSMUSG00000056078.5", 
  "ENSMUSG00000049928.15", "ENSMUSG00000013997.10", "ENSMUSG00000105198.1", 
  "ENSMUSG00000086714.1", "ENSMUSG00000109274.1", "ENSMUSG00000100548.1", 
  "ENSMUSG00000053706.2", "ENSMUSG00000109854.1", "ENSMUSG00000060802.8", 
  "ENSMUSG00000093598.1"), class = "data.frame")
  
  Please note, I have checked out many posts regarding this, most notably: https://www.biostars.org/p/287512/#287518, which highlights how to perform this procedure. Regardless, there are some unanswered questions.
  The problem is the following: After running the code suggested in the post, I do indeed obtain x number of clusters, depending on the height I decide to cut the tree at. However, they are in an incomprehensible order, making it extremely difficult to extract the clusters as they are observed in the heatmap. Please note, the dataframe I have uploaded is only a snippet of the true data - and is called logFC_mat, in the code below:
  pheatmap(logFC_mat, 
           show_rownames=F, cluster_cols=F, cluster_rows=T, scale="row",
           cex=1, clustering_distance_rows="euclidean", cex=1,
           clustering_distance_cols="euclidean", 
           clustering_method="complete", border_color=FALSE) -> heatof
  
  #make clusters based on h=1.5
  sort(cutree(heatof$tree_row, h=1.5)) -> hi_clusters
  
  #check if clusters are in same order as in heatmap
  hi_clusters[hi_clusters==1] %>% names() -> clust1
  hi_clusters[hi_clusters==2] %>% names() -> clust2
  
  length(clust1) #56
  length(clust2) #78
  all(clust1 %in% 
        rownames(logFC_mat[heatof$tree_row$order[1:56],])) #TRUE
  
  all(clust2 %in%
        rownames(logFC_mat[heatof$tree_row$order[57:134],])) #FALSE
  
  Now, from visual inspection of the heatmap, it becomes clear that cluster 2 is in fact the last 78 genes rather than the middle cluster. The problem is, why is it labeled as cluster 2 then !? In addition, this is a snippet of the data. The real data contains in fact thousands of rows, and so such visual deductions can simply be impossible.
  Now for the question: How to extract the clusters, such that they are in the SAME ORDER, as what is seen in the heatmap (Top to bottom)?
  Thanks.
  
  user15731: I would recommend not to use h to cut the tree but to use k, as k instructs the number of clusters to obtain, and then leaves it to the function to find the correct height for that. From there on you can easily extract the genes per cluster, for example with this code obtaining the first three clusters:
  
  heatof <- 
  pheatmap(logFC_mat, 
           show_rownames=F, cluster_cols=F, cluster_rows=T, scale="row",
           cex=1, clustering_distance_rows="euclidean", cex=1,
           clustering_distance_cols="euclidean", 
           clustering_method="complete", border_color=FALSE)
  
  #/ extract the top three clusters
  k <- 3
  sort(cutree(heatof$tree_row, k=3)) -> hi_clusters
  
  genes_per_cluster <- do.call(rbind, lapply(unique(hi_clusters), function(x){
    
    data.frame(cluster=x, gene=names(hi_clusters[hi_clusters %in% x]))
               
    
  }))
  
  genes_per_cluster
  #>     cluster                  gene
  #> 1         1  ENSMUSG00000097417.1
  #> 2         1  ENSMUSG00000084950.7
  #> 3         1 ENSMUSG00000021824.12
  #> 4         1 ENSMUSG00000018381.15
  #> 5         1  ENSMUSG00000098716.1
  #> 6         1 ENSMUSG00000039206.13
  #> 7         1 ENSMUSG00000047880.14
  #> 8         1  ENSMUSG00000094127.1
  #> 9         1  ENSMUSG00000098609.1
  #> 10        1  ENSMUSG00000106093.1
  #> 11        1 ENSMUSG00000009585.17
  #> 12        1  ENSMUSG00000027950.7
  #> 13        1 ENSMUSG00000004071.12
  #> 14        1  ENSMUSG00000104208.1
  #> 15        1 ENSMUSG00000047369.15
  #> 16        1  ENSMUSG00000097660.1
  #> 17        1 ENSMUSG00000002109.14
  #> 18        1  ENSMUSG00000108524.1
  #> 19        1 ENSMUSG00000067786.16
  #> 20        1  ENSMUSG00000085437.8
  #> 21        1  ENSMUSG00000086220.1
  #> 22        1  ENSMUSG00000102299.1
  #> 23        1 ENSMUSG00000079293.11
  #> 24        1  ENSMUSG00000085425.1
  #> 25        1  ENSMUSG00000006517.5
  #> 26        1 ENSMUSG00000049775.16
  #> 27        1  ENSMUSG00000109881.1
  #> 28        1  ENSMUSG00000102349.1
  #> 29        1  ENSMUSG00000089636.1
  #> 30        1  ENSMUSG00000086360.1
  #> 31        1 ENSMUSG00000036138.16
  #> 32        1  ENSMUSG00000045382.6
  #> 33        1 ENSMUSG00000030720.16
  #> 34        1 ENSMUSG00000027398.13
  #> 35        1  ENSMUSG00000104823.1
  #> 36        1  ENSMUSG00000100783.1
  #> 37        1  ENSMUSG00000082848.1
  #> 38        1  ENSMUSG00000110148.1
  #> 39        1  ENSMUSG00000085754.7
  #> 40        1  ENSMUSG00000108321.1
  #> 41        1 ENSMUSG00000032363.15
  #> 42        1 ENSMUSG00000003868.14
  #> 43        1  ENSMUSG00000107075.1
  #> 44        1  ENSMUSG00000074136.9
  #> 45        1  ENSMUSG00000089875.1
  #> 46        1 ENSMUSG00000055725.11
  #> 47        1 ENSMUSG00000028451.12
  #> 48        1  ENSMUSG00000078786.9
  #> 49        1  ENSMUSG00000087442.1
  #> 50        1  ENSMUSG00000053442.4
  #> 51        1  ENSMUSG00000101674.6
  #> 52        1  ENSMUSG00000097748.1
  #> 53        1  ENSMUSG00000050010.8
  #> 54        1 ENSMUSG00000029623.14
  #> 55        1  ENSMUSG00000097060.1
  #> 56        1 ENSMUSG00000050627.13
  #> 57        1  ENSMUSG00000085471.1
  #> 58        1 ENSMUSG00000039753.16
  #> 59        1  ENSMUSG00000027706.8
  #> 60        1  ENSMUSG00000032487.8
  #> 61        1 ENSMUSG00000002985.16
  #> 62        1 ENSMUSG00000038274.11
  #> 63        1  ENSMUSG00000087206.1
  #> 64        1  ENSMUSG00000079355.3
  #> 65        1  ENSMUSG00000086693.1
  #> 66        1 ENSMUSG00000030579.10
  #> 67        1  ENSMUSG00000108235.1
  #> 68        1  ENSMUSG00000097077.1
  #> 69        1  ENSMUSG00000087367.1
  #> 70        1 ENSMUSG00000037982.16
  #> 71        1 ENSMUSG00000029422.14
  #> 72        1 ENSMUSG00000026749.11
  #> 73        1 ENSMUSG00000067288.12
  #> 74        1  ENSMUSG00000090330.2
  #> 75        1 ENSMUSG00000059791.14
  #> 76        1  ENSMUSG00000103698.1
  #> 77        1  ENSMUSG00000097472.1
  #> 78        1  ENSMUSG00000026156.8
  #> 79        1 ENSMUSG00000075297.10
  #> 80        1 ENSMUSG00000055692.18
  #> 81        1 ENSMUSG00000039307.16
  #> 82        1 ENSMUSG00000045576.16
  #> 83        1  ENSMUSG00000087486.1
  #> 84        1  ENSMUSG00000014470.4
  #> 85        1  ENSMUSG00000056078.5
  #> 86        1 ENSMUSG00000049928.15
  #> 87        1  ENSMUSG00000086714.1
  #> 88        1  ENSMUSG00000109274.1
  #> 89        1  ENSMUSG00000109854.1
  #> 90        1  ENSMUSG00000060802.8
  #> 91        2  ENSMUSG00000085505.1
  #> 92        2  ENSMUSG00000092134.1
  #> 93        2  ENSMUSG00000097272.1
  #> 94        2  ENSMUSG00000087700.1
  #> 95        2  ENSMUSG00000101162.2
  #> 96        2  ENSMUSG00000107317.1
  #> 97        2  ENSMUSG00000102451.1
  #> 98        2  ENSMUSG00000109669.1
  #> 99        2  ENSMUSG00000086836.1
  #> 100       2  ENSMUSG00000092545.7
  #> 101       2  ENSMUSG00000090625.1
  #> 102       2  ENSMUSG00000047988.1
  #> 103       2  ENSMUSG00000086430.1
  #> 104       2  ENSMUSG00000105941.1
  #> 105       2  ENSMUSG00000022223.8
  #> 106       2 ENSMUSG00000031145.15
  #> 107       2  ENSMUSG00000086680.2
  #> 108       2 ENSMUSG00000021485.13
  #> 109       2  ENSMUSG00000097768.1
  #> 110       2 ENSMUSG00000075576.12
  #> 111       2  ENSMUSG00000090952.2
  #> 112       2 ENSMUSG00000040723.14
  #> 113       2  ENSMUSG00000027329.9
  #> 114       2  ENSMUSG00000106005.1
  #> 115       2 ENSMUSG00000046027.17
  #> 116       2 ENSMUSG00000004221.16
  #> 117       2  ENSMUSG00000023988.8
  #> 118       2  ENSMUSG00000087611.1
  #> 119       2  ENSMUSG00000092103.2
  #> 120       2  ENSMUSG00000090081.1
  #> 121       2  ENSMUSG00000107999.1
  #> 122       2 ENSMUSG00000041774.14
  #> 123       2  ENSMUSG00000090246.1
  #> 124       2  ENSMUSG00000032528.4
  #> 125       2 ENSMUSG00000021250.13
  #> 126       2 ENSMUSG00000009292.17
  #> 127       2  ENSMUSG00000109491.1
  #> 128       2  ENSMUSG00000090252.1
  #> 129       2  ENSMUSG00000087443.1
  #> 130       2  ENSMUSG00000064339.1
  #> 131       2  ENSMUSG00000091160.1
  #> 132       2  ENSMUSG00000108332.1
  #> 133       2  ENSMUSG00000048721.2
  #> 134       2  ENSMUSG00000102961.1
  #> 135       2  ENSMUSG00000096957.1
  #> 136       2  ENSMUSG00000093006.2
  #> 137       2 ENSMUSG00000027774.16
  #> 138       2 ENSMUSG00000012126.16
  #> 139       2  ENSMUSG00000092190.1
  #> 140       2  ENSMUSG00000074213.2
  #> 141       2  ENSMUSG00000086564.9
  #> 142       2  ENSMUSG00000092655.1
  #> 143       2  ENSMUSG00000098482.1
  #> 144       2  ENSMUSG00000108574.1
  #> 145       2  ENSMUSG00000087669.1
  #> 146       2  ENSMUSG00000078653.4
  #> 147       2  ENSMUSG00000108353.1
  #> 148       2  ENSMUSG00000092386.1
  #> 149       2  ENSMUSG00000087607.1
  #> 150       2 ENSMUSG00000061607.14
  #> 151       2  ENSMUSG00000026729.9
  #> 152       2  ENSMUSG00000064330.9
  #> 153       2  ENSMUSG00000103864.1
  #> 154       2  ENSMUSG00000085208.3
  #> 155       2  ENSMUSG00000073628.5
  #> 156       2  ENSMUSG00000102776.1
  #> 157       2  ENSMUSG00000086998.1
  #> 158       2 ENSMUSG00000006728.12
  #> 159       2  ENSMUSG00000021273.9
  #> 160       2  ENSMUSG00000062591.5
  #> 161       2 ENSMUSG00000040936.14
  #> 162       2  ENSMUSG00000046145.7
  #> 163       2  ENSMUSG00000087366.7
  #> 164       2  ENSMUSG00000039452.5
  #> 165       2  ENSMUSG00000087660.1
  #> 166       2  ENSMUSG00000084878.1
  #> 167       2  ENSMUSG00000101438.1
  #> 168       2  ENSMUSG00000064351.1
  #> 169       2  ENSMUSG00000086312.1
  #> 170       2  ENSMUSG00000097221.1
  #> 171       2  ENSMUSG00000107090.1
  #> 172       2  ENSMUSG00000095280.1
  #> 173       2 ENSMUSG00000017837.12
  #> 174       2  ENSMUSG00000109251.1
  #> 175       2  ENSMUSG00000086600.8
  #> 176       2  ENSMUSG00000090009.1
  #> 177       2  ENSMUSG00000101695.1
  #> 178       2 ENSMUSG00000084128.10
  #> 179       2 ENSMUSG00000038502.16
  #> 180       2  ENSMUSG00000015942.9
  #> 181       2  ENSMUSG00000106478.1
  #> 182       2  ENSMUSG00000054556.6
  #> 183       2  ENSMUSG00000082180.1
  #> 184       2 ENSMUSG00000013997.10
  #> 185       2  ENSMUSG00000100548.1
  #> 186       2  ENSMUSG00000053706.2
  #> 187       2  ENSMUSG00000093598.1
  #> 188       3  ENSMUSG00000097860.1
  #> 189       3  ENSMUSG00000079179.9
  #> 190       3  ENSMUSG00000097347.1
  #> 191       3  ENSMUSG00000092371.1
  #> 192       3  ENSMUSG00000109754.1
  #> 193       3  ENSMUSG00000090016.1
  #> 194       3  ENSMUSG00000097854.1
  #> 195       3  ENSMUSG00000029360.3
  #> 196       3  ENSMUSG00000102564.1
  #> 197       3  ENSMUSG00000025353.4
  #> 198       3  ENSMUSG00000052214.9
  #> 199       3 ENSMUSG00000037936.15
  #> 200       3  ENSMUSG00000105198.1
  
  Created on 2022-07-07 by the reprex package (v2.0.1)
  
  ```
  
  
original_text: 4001: <p>I have been attempting to extract particular clusters, given by hierarchical clustering outputs from the <code>pheatmap</code> function (in R).</p>
  <p>Please find the <code>dput</code> output of the dataset in question below:</p>
  <pre><code>structure(list(`72v24.logFC` = c(-1.47511280138092, -1.10386310802134, 
  -1.14476608274903, -1.63563574551239, -0.895377907265352, -1.35216488439027, 
  -2.04949381135359, -1.0344565728341, -0.967008696515716, -1.11233305998901, 
  -2.02663681865178, -1.74756562789736, -1.02076838668592, -1.27981009782201, 
  -1.13181804725663, -1.19537930856639, -2.23476188503608, -1.67500131867632, 
  -0.950059974858215, -2.3124598902615, -1.93757457440581, -3.24602437386808, 
  -0.839869104053795, -1.40329424193006, -1.63484798229567, -0.912148120310492, 
  -1.33467209346367, -1.27031027753064, -0.925498608058671, -0.802956638081314, 
  -0.85457796397113, -1.0591348681193, -0.825278459132589, -0.671570119524199, 
  -1.8439768319437, -0.947033608766851, -1.63849733567277, -1.40584263305038, 
  -1.1317958487115, -1.40724695083764, -1.21842141154588, -2.29248800050516, 
  -1.41699787526721, -0.879218050664484, -2.25064962332145, 1.4685855647974, 
  -2.02553848518381, 1.32808748053321, -2.46062484389627, -2.45830217362141, 
  -0.880536960021976, -0.689060222340137, -0.863262774594, -1.64961312646758, 
  1.10572346456398, -0.891760767302047, -1.22716047163938, -0.680697741299578, 
  -1.24551344420046, -0.891918251648935, -1.64722787848732, -0.832845262108387, 
  -0.937129577660045, -0.891684122691785, 1.96452911491088, -1.59420664438654, 
  -0.921295293242016, -1.8304480291305, -0.632859040349798, 1.69982819847455, 
  -0.982668795391973, -1.61816842714933, -1.23602172818196, -2.15356245206668, 
  -1.67961932563564, 1.15478114880933, 1.32665444151868, -1.04590896017973, 
  -2.29770026795487, -1.27498150009975, -1.36310217581123, -1.09169550738617, 
  1.5349413586602, -1.66842984591719, -0.760122936706606, -1.10054393155051, 
  -1.00344072779106, -0.993259123487476, -1.43136824963825, -1.07214189069438, 
  -0.990813303020613, -1.51324812740189, -1.23465012540084, -1.00098231964124, 
  -1.92195764952845, -1.00139179559519, -0.940118366042393, -2.35969198434574, 
  -0.574626090826994, -0.884870428965888, -0.87601460107501, 1.61336157755029, 
  -0.777670642457121, -0.7312214522498, -0.812926777785119, -1.13443421373561, 
  -1.56498420350444, -0.69126972981765, -1.44351026281231, -1.21962275860236, 
  -2.21155555407497, -1.02015250027788, -0.604620179871691, -1.53013572266942, 
  -0.790050747397837, -1.17950736026735, -0.781075150161975, -0.888554144538286, 
  3.59172865862026, -0.8665071699621, -2.97701792242157, -1.44424941630738, 
  -1.50528882788757, -0.772465957539335, -1.57664185213987, -1.02371443439054, 
  -0.931807409493221, 1.77728969821973, -1.05455101137715, -1.09765136526264, 
  -0.881436416213335, -0.985605985458853, -1.31644334991692, 2.26917914828263, 
  -1.43844640540614, -1.75106843701475, -1.22483991752173, -1.65032906954133, 
  -0.686319914242903, 2.45473055753775, -1.15594379837188, 1.46397122502826, 
  -0.91260428248088, -0.726540148411507, -1.18227838019011, -0.940722690371935, 
  -1.28074043595918, -0.629033607437977, 1.01053893402133, -0.735590704487842, 
  -2.0620695625823, -0.692251638781327, -0.717818968339447, -0.564023101160995, 
  1.51541391124355, -1.89444914881727, -0.737931396419173, -1.17763728235316, 
  -0.887605568116903, -2.8392997898765, -1.48018352596355, 1.60698486226092, 
  -1.96804216410227, -0.881437183709851, 3.08730764755417, -0.600282670155725, 
  -0.905719394102218, -1.05553935946213, -1.13508709782814, -0.613381276596874, 
  -0.642647139688194, -0.861929974132332, -1.30652597213552, -1.73647794867498, 
  -0.619909931049252, -0.880145154869759, -0.60084263914673, -1.16825573255754, 
  -0.942919502394457, -1.3709930239358, -0.80595477526712, -0.628115199442632, 
  -1.11502998682131, -1.01274335471793, -1.16595378001606, -3.36098944183559, 
  -1.19617345920841, -2.10811718229285, 3.33752122936, -1.67696701892834, 
  -1.90639199489612, -0.574737209544065, -1.66853541929234, -0.595093777485911, 
  -0.7964813653225, -0.791102813817634, -0.601987407016077, -1.52559881980829, 
  1.15480324851026, -0.830167728660421), `72v0.logFC` = c(-5.10937036648522, 
  -8.41670756910048, -8.18671783299995, -2.79415692883273, -3.62090016917187, 
  -8.37523504570539, -3.79100494829738, -7.20659380156151, -5.46135634576091, 
  3.43493215839382, -1.67650075643956, -2.99391647274475, -5.77357941089076, 
  -5.22675557853878, 3.26436094268851, -5.98693257837598, -5.85864442290848, 
  -2.39995052889286, -5.19221784614079, -4.72634343497625, -7.46407809296449, 
  -3.04588366694082, -3.85014181238163, 4.44756662720351, -4.42031795110716, 
  -2.58478993868624, -5.46121416816988, -2.09364835701952, -5.42397023596482, 
  -5.26192471384563, -4.48979100280513, -5.14171942073048, -5.5267515390142, 
  3.88762033289334, -5.88489034628499, -2.85490179670763, -5.31586479048071, 
  -2.64877712735579, -6.24766069294439, -5.35826818217055, -4.97204642950896, 
  -2.82989963758335, -4.75016577988789, -3.51684070536132, -3.20931950649022, 
  -3.62394584217955, -2.81449967053025, -5.68308664428684, -3.11500402887324, 
  -4.08965188145047, -5.43176189260205, -4.30737780091769, 2.52666133143524, 
  -3.88213803962076, -5.517506523237, -3.27502948978619, -5.37724717693793, 
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  1.53128139579193, 2.65531461899762, -1.33692502254506, -1.40309746138702, 
  7.1503230589606, -3.03232696595877, -3.99799016693196, 1.36106448869886, 
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  -2.14067263149232, 0.87594188820449, -2.36549598411797, -1.6026649015159, 
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  2.25817917663687, -4.47531796954113, -3.0627832955887), `24v0.logFC` = c(-5.63038870666508, 
  -6.44381761773614, -9.71855520117086, 2.83617729007977, -3.39220401105853, 
  -9.03206578896647, 4.72316302034493, 2.69600384046815, -3.70005627557764, 
  1.57004091545159, -2.69837465613229, -1.96398920017231, -6.78881951127235, 
  2.88395305274553, 2.2815237548239, 4.26299665984366, 1.80759581466942, 
  -6.13159865127454, 2.31984691801986, 2.42017005000243, 1.90522291464817, 
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  1.13069494609896, -1.43241741260756, 2.36383913233529, 1.65786717131242, 
  -2.29507370488367, 1.5786351022915, -3.31042999789919, 2.582031624397, 
  -3.62438687496853, -4.20056844288066, 1.59787844454997, -4.39077226372811, 
  -4.50758458577604, -3.5310616440773, 1.34960913912344, 1.56097908933761, 
  1.80910781056029, -4.1248594098749, 1.5318048796277, -3.97753680837585, 
  -2.80501778688795, -3.20129716412254, -1.98305552020422, -4.25045728757901, 
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  -5.13520809951127, -4.31701572736756, 0.832778953035371, 2.30899115735356, 
  -3.18620970041199, -3.80052092618969, 1.59131320240714)), row.names = c(&quot;ENSMUSG00000097417.1&quot;, 
  &quot;ENSMUSG00000084950.7&quot;, &quot;ENSMUSG00000021824.12&quot;, &quot;ENSMUSG00000085505.1&quot;, 
  &quot;ENSMUSG00000018381.15&quot;, &quot;ENSMUSG00000098716.1&quot;, &quot;ENSMUSG00000092134.1&quot;, 
  &quot;ENSMUSG00000097272.1&quot;, &quot;ENSMUSG00000039206.13&quot;, &quot;ENSMUSG00000097860.1&quot;, 
  &quot;ENSMUSG00000047880.14&quot;, &quot;ENSMUSG00000087700.1&quot;, &quot;ENSMUSG00000094127.1&quot;, 
  &quot;ENSMUSG00000101162.2&quot;, &quot;ENSMUSG00000079179.9&quot;, &quot;ENSMUSG00000107317.1&quot;, 
  &quot;ENSMUSG00000102451.1&quot;, &quot;ENSMUSG00000098609.1&quot;, &quot;ENSMUSG00000109669.1&quot;, 
  &quot;ENSMUSG00000086836.1&quot;, &quot;ENSMUSG00000092545.7&quot;, &quot;ENSMUSG00000106093.1&quot;, 
  &quot;ENSMUSG00000090625.1&quot;, &quot;ENSMUSG00000009585.17&quot;, &quot;ENSMUSG00000047988.1&quot;, 
  &quot;ENSMUSG00000027950.7&quot;, &quot;ENSMUSG00000086430.1&quot;, &quot;ENSMUSG00000105941.1&quot;, 
  &quot;ENSMUSG00000004071.12&quot;, &quot;ENSMUSG00000104208.1&quot;, &quot;ENSMUSG00000022223.8&quot;, 
  &quot;ENSMUSG00000031145.15&quot;, &quot;ENSMUSG00000047369.15&quot;, &quot;ENSMUSG00000097347.1&quot;, 
  &quot;ENSMUSG00000086680.2&quot;, &quot;ENSMUSG00000097660.1&quot;, &quot;ENSMUSG00000002109.14&quot;, 
  &quot;ENSMUSG00000108524.1&quot;, &quot;ENSMUSG00000067786.16&quot;, &quot;ENSMUSG00000021485.13&quot;, 
  &quot;ENSMUSG00000097768.1&quot;, &quot;ENSMUSG00000085437.8&quot;, &quot;ENSMUSG00000086220.1&quot;, 
  &quot;ENSMUSG00000075576.12&quot;, &quot;ENSMUSG00000102299.1&quot;, &quot;ENSMUSG00000079293.11&quot;, 
  &quot;ENSMUSG00000090952.2&quot;, &quot;ENSMUSG00000040723.14&quot;, &quot;ENSMUSG00000027329.9&quot;, 
  &quot;ENSMUSG00000106005.1&quot;, &quot;ENSMUSG00000085425.1&quot;, &quot;ENSMUSG00000046027.17&quot;, 
  &quot;ENSMUSG00000006517.5&quot;, &quot;ENSMUSG00000004221.16&quot;, &quot;ENSMUSG00000049775.16&quot;, 
  &quot;ENSMUSG00000109881.1&quot;, &quot;ENSMUSG00000023988.8&quot;, &quot;ENSMUSG00000092371.1&quot;, 
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  &quot;ENSMUSG00000089636.1&quot;, &quot;ENSMUSG00000086360.1&quot;, &quot;ENSMUSG00000036138.16&quot;, 
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  &quot;ENSMUSG00000087669.1&quot;, &quot;ENSMUSG00000053442.4&quot;, &quot;ENSMUSG00000101674.6&quot;, 
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  &quot;ENSMUSG00000087607.1&quot;, &quot;ENSMUSG00000061607.14&quot;, &quot;ENSMUSG00000026729.9&quot;, 
  &quot;ENSMUSG00000097854.1&quot;, &quot;ENSMUSG00000064330.9&quot;, &quot;ENSMUSG00000039753.16&quot;, 
  &quot;ENSMUSG00000027706.8&quot;, &quot;ENSMUSG00000029360.3&quot;, &quot;ENSMUSG00000103864.1&quot;, 
  &quot;ENSMUSG00000085208.3&quot;, &quot;ENSMUSG00000073628.5&quot;, &quot;ENSMUSG00000102776.1&quot;, 
  &quot;ENSMUSG00000032487.8&quot;, &quot;ENSMUSG00000086998.1&quot;, &quot;ENSMUSG00000006728.12&quot;, 
  &quot;ENSMUSG00000021273.9&quot;, &quot;ENSMUSG00000062591.5&quot;, &quot;ENSMUSG00000040936.14&quot;, 
  &quot;ENSMUSG00000002985.16&quot;, &quot;ENSMUSG00000046145.7&quot;, &quot;ENSMUSG00000038274.11&quot;, 
  &quot;ENSMUSG00000087366.7&quot;, &quot;ENSMUSG00000039452.5&quot;, &quot;ENSMUSG00000087660.1&quot;, 
  &quot;ENSMUSG00000087206.1&quot;, &quot;ENSMUSG00000079355.3&quot;, &quot;ENSMUSG00000086693.1&quot;, 
  &quot;ENSMUSG00000030579.10&quot;, &quot;ENSMUSG00000084878.1&quot;, &quot;ENSMUSG00000108235.1&quot;, 
  &quot;ENSMUSG00000097077.1&quot;, &quot;ENSMUSG00000101438.1&quot;, &quot;ENSMUSG00000087367.1&quot;, 
  &quot;ENSMUSG00000064351.1&quot;, &quot;ENSMUSG00000086312.1&quot;, &quot;ENSMUSG00000097221.1&quot;, 
  &quot;ENSMUSG00000107090.1&quot;, &quot;ENSMUSG00000037982.16&quot;, &quot;ENSMUSG00000095280.1&quot;, 
  &quot;ENSMUSG00000017837.12&quot;, &quot;ENSMUSG00000029422.14&quot;, &quot;ENSMUSG00000102564.1&quot;, 
  &quot;ENSMUSG00000026749.11&quot;, &quot;ENSMUSG00000067288.12&quot;, &quot;ENSMUSG00000025353.4&quot;, 
  &quot;ENSMUSG00000109251.1&quot;, &quot;ENSMUSG00000086600.8&quot;, &quot;ENSMUSG00000052214.9&quot;, 
  &quot;ENSMUSG00000090330.2&quot;, &quot;ENSMUSG00000090009.1&quot;, &quot;ENSMUSG00000059791.14&quot;, 
  &quot;ENSMUSG00000101695.1&quot;, &quot;ENSMUSG00000103698.1&quot;, &quot;ENSMUSG00000097472.1&quot;, 
  &quot;ENSMUSG00000084128.10&quot;, &quot;ENSMUSG00000026156.8&quot;, &quot;ENSMUSG00000075297.10&quot;, 
  &quot;ENSMUSG00000055692.18&quot;, &quot;ENSMUSG00000038502.16&quot;, &quot;ENSMUSG00000015942.9&quot;, 
  &quot;ENSMUSG00000106478.1&quot;, &quot;ENSMUSG00000039307.16&quot;, &quot;ENSMUSG00000054556.6&quot;, 
  &quot;ENSMUSG00000045576.16&quot;, &quot;ENSMUSG00000037936.15&quot;, &quot;ENSMUSG00000087486.1&quot;, 
  &quot;ENSMUSG00000082180.1&quot;, &quot;ENSMUSG00000014470.4&quot;, &quot;ENSMUSG00000056078.5&quot;, 
  &quot;ENSMUSG00000049928.15&quot;, &quot;ENSMUSG00000013997.10&quot;, &quot;ENSMUSG00000105198.1&quot;, 
  &quot;ENSMUSG00000086714.1&quot;, &quot;ENSMUSG00000109274.1&quot;, &quot;ENSMUSG00000100548.1&quot;, 
  &quot;ENSMUSG00000053706.2&quot;, &quot;ENSMUSG00000109854.1&quot;, &quot;ENSMUSG00000060802.8&quot;, 
  &quot;ENSMUSG00000093598.1&quot;), class = &quot;data.frame&quot;)
  </code></pre>
  <p>Please note, I have checked out many posts regarding this, most notably: <a href="https://www.biostars.org/p/287512/#287518" rel="nofollow noreferrer">https://www.biostars.org/p/287512/#287518</a>, which highlights how to perform this procedure. Regardless, there are some unanswered questions.</p>
  <p>The problem is the following: After running the code suggested in the post, I do indeed obtain x number of clusters, depending on the height I decide to cut the tree at. However, they are in an incomprehensible order, making it extremely difficult to extract the clusters as they are observed in the heatmap. Please note, the dataframe I have uploaded is only a snippet of the true data - and is called logFC_mat, in the code below:</p>
  <pre><code>pheatmap(logFC_mat, 
           show_rownames=F, cluster_cols=F, cluster_rows=T, scale=&quot;row&quot;,
           cex=1, clustering_distance_rows=&quot;euclidean&quot;, cex=1,
           clustering_distance_cols=&quot;euclidean&quot;, 
           clustering_method=&quot;complete&quot;, border_color=FALSE) -&gt; heatof
  
  #make clusters based on h=1.5
  sort(cutree(heatof$tree_row, h=1.5)) -&gt; hi_clusters
  
  #check if clusters are in same order as in heatmap
  hi_clusters[hi_clusters==1] %&gt;% names() -&gt; clust1
  hi_clusters[hi_clusters==2] %&gt;% names() -&gt; clust2
  
  length(clust1) #56
  length(clust2) #78
  all(clust1 %in% 
        rownames(logFC_mat[heatof<span class="math-container">$tree_row$</span>order[1:56],])) #TRUE
  
  all(clust2 %in%
        rownames(logFC_mat[heatof<span class="math-container">$tree_row$</span>order[57:134],])) #FALSE
  </code></pre>
  <p>Now, from visual inspection of the heatmap, it becomes clear that cluster 2 is in fact the last 78 genes rather than the middle cluster. The problem is, why is it labeled as cluster 2 then !? In addition, this is a snippet of the data. The real data contains in fact thousands of rows, and so such visual deductions can simply be impossible.</p>
  <p>Now for the question: How to extract the clusters, such that they are in the SAME ORDER, as what is seen in the heatmap (Top to bottom)?</p>
  <p>Thanks.</p>
   15731: <p>I would recommend not to use <code>h</code> to cut the tree but to use <code>k</code>, as <code>k</code> instructs the number of clusters to obtain, and then leaves it to the function to find the correct height for that. From there on you can easily extract the genes per cluster, for example with this code obtaining the first three clusters:</p>
  <pre class="lang-r prettyprint-override"><code>
  heatof &lt;- 
  pheatmap(logFC_mat, 
           show_rownames=F, cluster_cols=F, cluster_rows=T, scale=&quot;row&quot;,
           cex=1, clustering_distance_rows=&quot;euclidean&quot;, cex=1,
           clustering_distance_cols=&quot;euclidean&quot;, 
           clustering_method=&quot;complete&quot;, border_color=FALSE)
  
  #/ extract the top three clusters
  k &lt;- 3
  sort(cutree(heatof$tree_row, k=3)) -&gt; hi_clusters
  
  genes_per_cluster &lt;- do.call(rbind, lapply(unique(hi_clusters), function(x){
    
    data.frame(cluster=x, gene=names(hi_clusters[hi_clusters %in% x]))
               
    
  }))
  
  genes_per_cluster
  #&gt;     cluster                  gene
  #&gt; 1         1  ENSMUSG00000097417.1
  #&gt; 2         1  ENSMUSG00000084950.7
  #&gt; 3         1 ENSMUSG00000021824.12
  #&gt; 4         1 ENSMUSG00000018381.15
  #&gt; 5         1  ENSMUSG00000098716.1
  #&gt; 6         1 ENSMUSG00000039206.13
  #&gt; 7         1 ENSMUSG00000047880.14
  #&gt; 8         1  ENSMUSG00000094127.1
  #&gt; 9         1  ENSMUSG00000098609.1
  #&gt; 10        1  ENSMUSG00000106093.1
  #&gt; 11        1 ENSMUSG00000009585.17
  #&gt; 12        1  ENSMUSG00000027950.7
  #&gt; 13        1 ENSMUSG00000004071.12
  #&gt; 14        1  ENSMUSG00000104208.1
  #&gt; 15        1 ENSMUSG00000047369.15
  #&gt; 16        1  ENSMUSG00000097660.1
  #&gt; 17        1 ENSMUSG00000002109.14
  #&gt; 18        1  ENSMUSG00000108524.1
  #&gt; 19        1 ENSMUSG00000067786.16
  #&gt; 20        1  ENSMUSG00000085437.8
  #&gt; 21        1  ENSMUSG00000086220.1
  #&gt; 22        1  ENSMUSG00000102299.1
  #&gt; 23        1 ENSMUSG00000079293.11
  #&gt; 24        1  ENSMUSG00000085425.1
  #&gt; 25        1  ENSMUSG00000006517.5
  #&gt; 26        1 ENSMUSG00000049775.16
  #&gt; 27        1  ENSMUSG00000109881.1
  #&gt; 28        1  ENSMUSG00000102349.1
  #&gt; 29        1  ENSMUSG00000089636.1
  #&gt; 30        1  ENSMUSG00000086360.1
  #&gt; 31        1 ENSMUSG00000036138.16
  #&gt; 32        1  ENSMUSG00000045382.6
  #&gt; 33        1 ENSMUSG00000030720.16
  #&gt; 34        1 ENSMUSG00000027398.13
  #&gt; 35        1  ENSMUSG00000104823.1
  #&gt; 36        1  ENSMUSG00000100783.1
  #&gt; 37        1  ENSMUSG00000082848.1
  #&gt; 38        1  ENSMUSG00000110148.1
  #&gt; 39        1  ENSMUSG00000085754.7
  #&gt; 40        1  ENSMUSG00000108321.1
  #&gt; 41        1 ENSMUSG00000032363.15
  #&gt; 42        1 ENSMUSG00000003868.14
  #&gt; 43        1  ENSMUSG00000107075.1
  #&gt; 44        1  ENSMUSG00000074136.9
  #&gt; 45        1  ENSMUSG00000089875.1
  #&gt; 46        1 ENSMUSG00000055725.11
  #&gt; 47        1 ENSMUSG00000028451.12
  #&gt; 48        1  ENSMUSG00000078786.9
  #&gt; 49        1  ENSMUSG00000087442.1
  #&gt; 50        1  ENSMUSG00000053442.4
  #&gt; 51        1  ENSMUSG00000101674.6
  #&gt; 52        1  ENSMUSG00000097748.1
  #&gt; 53        1  ENSMUSG00000050010.8
  #&gt; 54        1 ENSMUSG00000029623.14
  #&gt; 55        1  ENSMUSG00000097060.1
  #&gt; 56        1 ENSMUSG00000050627.13
  #&gt; 57        1  ENSMUSG00000085471.1
  #&gt; 58        1 ENSMUSG00000039753.16
  #&gt; 59        1  ENSMUSG00000027706.8
  #&gt; 60        1  ENSMUSG00000032487.8
  #&gt; 61        1 ENSMUSG00000002985.16
  #&gt; 62        1 ENSMUSG00000038274.11
  #&gt; 63        1  ENSMUSG00000087206.1
  #&gt; 64        1  ENSMUSG00000079355.3
  #&gt; 65        1  ENSMUSG00000086693.1
  #&gt; 66        1 ENSMUSG00000030579.10
  #&gt; 67        1  ENSMUSG00000108235.1
  #&gt; 68        1  ENSMUSG00000097077.1
  #&gt; 69        1  ENSMUSG00000087367.1
  #&gt; 70        1 ENSMUSG00000037982.16
  #&gt; 71        1 ENSMUSG00000029422.14
  #&gt; 72        1 ENSMUSG00000026749.11
  #&gt; 73        1 ENSMUSG00000067288.12
  #&gt; 74        1  ENSMUSG00000090330.2
  #&gt; 75        1 ENSMUSG00000059791.14
  #&gt; 76        1  ENSMUSG00000103698.1
  #&gt; 77        1  ENSMUSG00000097472.1
  #&gt; 78        1  ENSMUSG00000026156.8
  #&gt; 79        1 ENSMUSG00000075297.10
  #&gt; 80        1 ENSMUSG00000055692.18
  #&gt; 81        1 ENSMUSG00000039307.16
  #&gt; 82        1 ENSMUSG00000045576.16
  #&gt; 83        1  ENSMUSG00000087486.1
  #&gt; 84        1  ENSMUSG00000014470.4
  #&gt; 85        1  ENSMUSG00000056078.5
  #&gt; 86        1 ENSMUSG00000049928.15
  #&gt; 87        1  ENSMUSG00000086714.1
  #&gt; 88        1  ENSMUSG00000109274.1
  #&gt; 89        1  ENSMUSG00000109854.1
  #&gt; 90        1  ENSMUSG00000060802.8
  #&gt; 91        2  ENSMUSG00000085505.1
  #&gt; 92        2  ENSMUSG00000092134.1
  #&gt; 93        2  ENSMUSG00000097272.1
  #&gt; 94        2  ENSMUSG00000087700.1
  #&gt; 95        2  ENSMUSG00000101162.2
  #&gt; 96        2  ENSMUSG00000107317.1
  #&gt; 97        2  ENSMUSG00000102451.1
  #&gt; 98        2  ENSMUSG00000109669.1
  #&gt; 99        2  ENSMUSG00000086836.1
  #&gt; 100       2  ENSMUSG00000092545.7
  #&gt; 101       2  ENSMUSG00000090625.1
  #&gt; 102       2  ENSMUSG00000047988.1
  #&gt; 103       2  ENSMUSG00000086430.1
  #&gt; 104       2  ENSMUSG00000105941.1
  #&gt; 105       2  ENSMUSG00000022223.8
  #&gt; 106       2 ENSMUSG00000031145.15
  #&gt; 107       2  ENSMUSG00000086680.2
  #&gt; 108       2 ENSMUSG00000021485.13
  #&gt; 109       2  ENSMUSG00000097768.1
  #&gt; 110       2 ENSMUSG00000075576.12
  #&gt; 111       2  ENSMUSG00000090952.2
  #&gt; 112       2 ENSMUSG00000040723.14
  #&gt; 113       2  ENSMUSG00000027329.9
  #&gt; 114       2  ENSMUSG00000106005.1
  #&gt; 115       2 ENSMUSG00000046027.17
  #&gt; 116       2 ENSMUSG00000004221.16
  #&gt; 117       2  ENSMUSG00000023988.8
  #&gt; 118       2  ENSMUSG00000087611.1
  #&gt; 119       2  ENSMUSG00000092103.2
  #&gt; 120       2  ENSMUSG00000090081.1
  #&gt; 121       2  ENSMUSG00000107999.1
  #&gt; 122       2 ENSMUSG00000041774.14
  #&gt; 123       2  ENSMUSG00000090246.1
  #&gt; 124       2  ENSMUSG00000032528.4
  #&gt; 125       2 ENSMUSG00000021250.13
  #&gt; 126       2 ENSMUSG00000009292.17
  #&gt; 127       2  ENSMUSG00000109491.1
  #&gt; 128       2  ENSMUSG00000090252.1
  #&gt; 129       2  ENSMUSG00000087443.1
  #&gt; 130       2  ENSMUSG00000064339.1
  #&gt; 131       2  ENSMUSG00000091160.1
  #&gt; 132       2  ENSMUSG00000108332.1
  #&gt; 133       2  ENSMUSG00000048721.2
  #&gt; 134       2  ENSMUSG00000102961.1
  #&gt; 135       2  ENSMUSG00000096957.1
  #&gt; 136       2  ENSMUSG00000093006.2
  #&gt; 137       2 ENSMUSG00000027774.16
  #&gt; 138       2 ENSMUSG00000012126.16
  #&gt; 139       2  ENSMUSG00000092190.1
  #&gt; 140       2  ENSMUSG00000074213.2
  #&gt; 141       2  ENSMUSG00000086564.9
  #&gt; 142       2  ENSMUSG00000092655.1
  #&gt; 143       2  ENSMUSG00000098482.1
  #&gt; 144       2  ENSMUSG00000108574.1
  #&gt; 145       2  ENSMUSG00000087669.1
  #&gt; 146       2  ENSMUSG00000078653.4
  #&gt; 147       2  ENSMUSG00000108353.1
  #&gt; 148       2  ENSMUSG00000092386.1
  #&gt; 149       2  ENSMUSG00000087607.1
  #&gt; 150       2 ENSMUSG00000061607.14
  #&gt; 151       2  ENSMUSG00000026729.9
  #&gt; 152       2  ENSMUSG00000064330.9
  #&gt; 153       2  ENSMUSG00000103864.1
  #&gt; 154       2  ENSMUSG00000085208.3
  #&gt; 155       2  ENSMUSG00000073628.5
  #&gt; 156       2  ENSMUSG00000102776.1
  #&gt; 157       2  ENSMUSG00000086998.1
  #&gt; 158       2 ENSMUSG00000006728.12
  #&gt; 159       2  ENSMUSG00000021273.9
  #&gt; 160       2  ENSMUSG00000062591.5
  #&gt; 161       2 ENSMUSG00000040936.14
  #&gt; 162       2  ENSMUSG00000046145.7
  #&gt; 163       2  ENSMUSG00000087366.7
  #&gt; 164       2  ENSMUSG00000039452.5
  #&gt; 165       2  ENSMUSG00000087660.1
  #&gt; 166       2  ENSMUSG00000084878.1
  #&gt; 167       2  ENSMUSG00000101438.1
  #&gt; 168       2  ENSMUSG00000064351.1
  #&gt; 169       2  ENSMUSG00000086312.1
  #&gt; 170       2  ENSMUSG00000097221.1
  #&gt; 171       2  ENSMUSG00000107090.1
  #&gt; 172       2  ENSMUSG00000095280.1
  #&gt; 173       2 ENSMUSG00000017837.12
  #&gt; 174       2  ENSMUSG00000109251.1
  #&gt; 175       2  ENSMUSG00000086600.8
  #&gt; 176       2  ENSMUSG00000090009.1
  #&gt; 177       2  ENSMUSG00000101695.1
  #&gt; 178       2 ENSMUSG00000084128.10
  #&gt; 179       2 ENSMUSG00000038502.16
  #&gt; 180       2  ENSMUSG00000015942.9
  #&gt; 181       2  ENSMUSG00000106478.1
  #&gt; 182       2  ENSMUSG00000054556.6
  #&gt; 183       2  ENSMUSG00000082180.1
  #&gt; 184       2 ENSMUSG00000013997.10
  #&gt; 185       2  ENSMUSG00000100548.1
  #&gt; 186       2  ENSMUSG00000053706.2
  #&gt; 187       2  ENSMUSG00000093598.1
  #&gt; 188       3  ENSMUSG00000097860.1
  #&gt; 189       3  ENSMUSG00000079179.9
  #&gt; 190       3  ENSMUSG00000097347.1
  #&gt; 191       3  ENSMUSG00000092371.1
  #&gt; 192       3  ENSMUSG00000109754.1
  #&gt; 193       3  ENSMUSG00000090016.1
  #&gt; 194       3  ENSMUSG00000097854.1
  #&gt; 195       3  ENSMUSG00000029360.3
  #&gt; 196       3  ENSMUSG00000102564.1
  #&gt; 197       3  ENSMUSG00000025353.4
  #&gt; 198       3  ENSMUSG00000052214.9
  #&gt; 199       3 ENSMUSG00000037936.15
  #&gt; 200       3  ENSMUSG00000105198.1
  
  Created on 2022-07-07 by the reprex package (v2.0.1)
  
  <span class="math-container">```</span>
  </code></pre>
  