I have done a Heat Map using the function heatmap.2 of gplots in R, but I don't have an idea of how to coloring the branches and tick labels per groups (Eg. if I cut the tree to have four gruops like in my second figure). I have checked that it is possible to color the dendrogram alone using dendextend package.
Also there is a heatmap here: selecting number of leaf nodes of dendrogram in heatmap.2 in R with a colored dendrogram, but I can't implement it in my example.
Somebody can help me with this issue?
Update
This is my Heat Map:
and I would like to have one like this with branches and tick labels in color according their four groups (this figure was edited with Illustrator to explain this question):
这是我使用的数据和代码:
数据
YEAR varA varB varC varD varE varF var1 var2 var3 var4 var5 var6 var7 var8 var9 var10 var11 var12 var13 var14 var15 var16 var17 2005 1.175290887 1.535846033 1.531113178 -1.10297075 0.0284 26 -25.5470 -24.2101 24.7900 3.3345 0.0468 0.5058 0.0087 1.7378 0.0703 2.7070 0.0183 0.0340 0.0177 0.0176 0.0240 0.0015 0.0292 2004 0.834733204 0.64917365 -0.403174087 0.116169692 0.033 50 -24.4170 -22.2574 27.3400 3.4106 0.1151 0.5822 0.0085 1.8133 0.0762 3.2604 0.0114 0.0178 0.0086 0.0086 0.0824 0.0018 0.0308 2003 1.297607635 1.224946337 0.4486378 0.227557968 0.0544 181 -24.5080 -23.2790 27.4200 3.5092 0.1052 0.5239 0.0038 0.9815 0.0681 2.7465 0.0074 0.0099 0.0025 0.0025 0.0142 0.0015 0.0298 2002 1.043780072 0.650695815 -0.337133061 0.016766696 0.0374 227 -22.6110 -21.7828 30.0200 3.6270 0.1119 0.5753 0.0106 0.7916 0.0805 3.0434 0.0069 0.0086 0.0109 0.0108 0.0313 0.0017 0.0288 2001 0.781864124 0.534881678 -0.740527443 0.171745261 0.0074 20 -23.9170 -23.2327 3.8007 0.1243 0.6216 0.0553 1.2333 0.3414 2.9606 0.0074 0.0384 0.0079 0.0082 0.0570 0.0018 0.0360 2000 0.742528229 0.667207042 -0.614740091 0.189253192 0.0257 88 -22.6420 -21.4066 30.8900 3.1693 0.0287 0.6244 0.0070 1.0256 0.1336 2.7033 0.0063 0.0102 0.0185 0.0186 0.0248 0.0015 0.0278 1999 0.701222612 1.059869033 0.772334853 0.290190993 0.0476 312 -22.4730 -21.8328 26.6600 3.0578 0.0719 0.6363 0.0032 0.7183 0.0649 2.5445 0.0066 0.0070 0.0063 0.0063 0.0095 0.0016 0.0252 1998 0.904634938 1.16455833 0.646654191 0.086214161 0.0546 332 -23.2070 -22.4399 26.1400 3.2344 0.0656 0.7096 0.0046 0.6709 0.0718 2.5656 0.0072 0.0166 0.0132 0.0131 0.0144 0.0016 0.0275 1997 0.965775183 1.362520795 0.653268963 0.007038426 0.0791 509 -23.4830 -22.4253 26.0400 3.0278 0.0438 0.7575 0.0081 0.5002 0.0657 2.5755 0.0077 0.0072 0.0083 0.0083 0.0108 0.0017 0.0252 1996 0.956113049 1.439534042 0.618648101 -0.334351083 0.0411 245 -23.4290 -23.0417 27.3000 2.9331 0.0363 0.9229 0.0050 0.4819 0.1306 2.7239 0.0072 0.0166 0.0027 0.0026 0.0174 0.0018 0.0240 1995 1.786742729 1.732091021 2.654237394 0.190377371 0.0842 646 -22.7600 -22.0212 24.2100 3.1562 0.0202 1.1728 0.0072 0.6133 0.0772 3.1313 0.0080 0.0051 0.0035 0.0035 0.0055 0.0022 0.0266 1994 0.811695681 0.670904284 0.76646691 2.163378723 0.0394 203 -22.4920 -21.3677 28.6500 3.2475 0.0132 1.7476 0.0084 0.9386 0.1880 3.8856 0.0082 0.0120 0.0129 0.0129 0.0151 0.0026 0.0280 1993 0.754876913 0.302624208 -0.927234708 -0.108263802 0.017 66 -22.3880 -21.2900 32.8400 3.5853 0.0008 1.6626 0.0221 1.2307 0.4173 3.8864 0.0079 0.0379 0.0199 0.0196 0.0225 0.0028 0.0319 1992 0.723058507 0.818965047 -0.52053294 0.384656566 0.0345 155 -21.4920 -20.8724 32.2000 3.3116 0.0068 1.5673 0.0104 0.9411 0.2245 4.0228 0.0075 0.0123 0.0308 0.0306 0.0112 0.0027 0.0287 1991 1.024225427 0.71537408 0.22672288 -0.029575009 0.0297 235 -23.4850 -22.7000 27.8400 4.4024 0.0097 1.6126 0.0698 0.6344 0.2832 4.4160 0.0108 0.0127 0.0184 0.0184 0.0122 0.0030 0.0356 1990 0.873807193 1.168599747 1.317306687 -0.335682786 0.0533 172 -23.7170 -23.5029 25.8100 4.0497 0.0170 1.5207 0.0065 0.5232 0.1734 4.6765 0.0104 0.0164 0.0131 0.0130 0.0093 0.0030 0.0332 1989 0.71498833 1.065965836 0.650281646 -0.048038841 0.0663 214 -23.5000 -23.1053 26.3500 4.1139 0.0159 1.6162 0.0096 0.5199 0.1426 4.7752 0.0106 0.0083 0.0098 0.0099 0.0076 0.0031 0.0341 1988 1.188282778 1.133076429 -0.167816244 0.448030288 0.007 64 -23.3750 -21.9900 29.3900 3.6893 0.0278 1.8392 0.0939 0.5658 1.2390 5.1103 0.0086 0.0775 0.0203 0.0202 0.0339 0.0034 0.0340 1987 0.788798159 0.276008942 -0.934596308 -0.039259431 0.012 65 -22.9540 -22.7758 28.3800 3.6375 0.0011 1.8331 0.0768 0.6187 0.6081 5.0475 0.0088 0.0554 0.0183 0.0180 0.0159 0.0038 0.0381 1986 0.757757883 1.395817348 0.455252572 -0.001274532 0.0125 47 -22.6120 -22.9011 29.7400 3.7060 0.0172 1.5279 0.0151 0.5897 0.6168 4.4917 0.0085 0.0160 0.0257 0.0256 0.0276 0.0033 0.0410 1985 1.128413419 0.321849225 -0.904189697 -0.05362552 0.0705 291 -22.7200 -21.9357 28.4100 3.5887 0.0100 1.4955 0.0022 0.3538 0.1471 4.3125 0.0091 0.0157 0.0042 0.0042 0.0041 0.0029 0.0292 1984 1.015352865 1.014625668 0.39294569 -0.267936245 0.0419 121 -23.5170 -23.1678 25.6200 4.5018 0.0353 1.8985 0.0022 0.3420 0.2620 4.9867 0.0113 0.0069 0.0058 0.0058 0.0051 0.0033 0.0356 1983 0.393985784 0.474743555 -0.368393191 -0.222845745 0.0161 49 -24.5600 -23.9514 30.5300 3.0978 0.0270 0.9467 0.0421 0.3287 0.5616 3.1256 0.0075 0.0553 0.0154 0.0155 0.0084 0.0022 0.0323 1982 0.503744901 0.524683063 -0.946225504 0.016766696 0.0118 10 -23.5970 -24.0037 30.3100 2.7288 0.0011 1.2154 0.0097 0.3022 0.8415 4.3594 0.0083 0.0254 0.0075 0.0076 0.0134 0.0029 0.0304 1981 0.872025585 1.496555573 0.658923526 -0.175816424 0.0489 343 -23.8320 -23.4716 28.1100 4.6585 0.0128 1.9205 0.0031 0.2999 0.2278 5.6588 0.0134 0.0067 0.0072 0.0071 0.0087 0.0036 0.0437 1980 2.165460373 3.419095697 3.741300435 0.250364758 0.0644 626 -24.5010 -24.0323 28.7300 3.8474 0.0122 1.4827 0.0019 0.2164 0.1859 4.3602 0.0104 0.0056 0.0050 0.0050 0.0064 0.0028 0.0337 1979 1.00201444 0.453601121 0.109577407 0.73158507 0.0281 301 -23.6070 -22.9149 27.9100 4.5765 0.0467 1.6919 0.0344 0.1940 0.3453 5.1064 0.0132 0.0162 0.0078 0.0077 0.0554 0.0032 0.0389 1978 0.829984787 0.2021646 -0.724630653 -0.178430782 0.0000 1977 0.939170906 0.192142351 -1.029656979 0.50745842 0.0068 30 -24.3510 -22.5760 29.4900 6.1029 0.3417 2.4069 0.0938 0.2824 1.3937 6.6441 0.0136 0.0609 0.0395 0.0391 0.6074 0.0045 0.0591 1976 0.741090851 0.151474404 -0.439448642 0.359471579 0.056 396 -23.7450 -22.7680 28.3700 4.3464 0.0431 1.6901 0.0234 0.2937 0.2160 5.1366 0.0113 0.0147 0.0082 0.0081 0.0317 0.0034 0.0389 1975 1.061884929 0.396763153 -1.075320241 0.433356946 0.0299 322 -23.4320 -22.9732 25.7800 5.0301 0.1740 2.2028 0.0311 0.3131 0.4254 5.8683 0.0131 0.0160 0.0182 0.0182 0.2093 0.0038 0.0443 1974 1.052548763 0.491883924 0.28198823 -0.562241025 0.0215 267 -23.3350 -22.7075 26.4100 5.3407 0.1187 2.2436 0.0231 0.2984 0.5378 5.8795 0.0127 0.0208 0.0127 0.0128 0.0821 0.0038 0.0466 1973 0.519163031 1.120525721 0.960322396 -0.84893256 0.0129 49 -23.4350 -23.0556 31.3500 6.4341 0.1105 2.4298 0.0484 0.2783 0.9249 5.8779 0.0129 0.0428 0.0124 0.0123 0.1293 0.0038 0.0499 1972 0.703961551 1.359485416 -0.306513069 -1.150818704 0.0228 247 -23.7840 -23.3257 28.3000 6.3520 0.1096 2.6043 0.0439 0.4126 0.5335 6.3320 0.0154 0.0279 0.0061 0.0062 0.0874 0.0042 0.0593 1971 0.714252707 1.621333793 -1.065184704 0.003023451 0.0274 196 -23.2140 -22.2731 31.3800 5.1332 0.0873 1.9259 0.0872 0.3598 0.4714 4.9337 0.0112 0.0234 0.0073 0.0073 0.0688 0.0034 0.0426 1970 1.022643019 1.491401283 0.088239434 -0.973528472 0.025 206 -22.9870 -21.9506 30.6200 5.0770 0.0698 2.1145 0.1825 0.3537 0.4990 5.3274 0.0129 0.0873 0.0098 0.0098 0.0316 0.0040 0.0479 1969 2.157784838 1.796722133 0.731152565 -0.193891705 0.0547 505 -24.2820 -23.9048 26.2400 5.0183 0.0637 2.2673 0.0127 0.2893 0.2420 5.1038 0.0129 0.0244 0.0069 0.0069 0.0154 0.0037 0.0440 1968 0.913026742 1.271215847 0.196849717 -1.068149218 0.0132 112 -22.9850 -21.9397 32.2300 4.0568 0.0498 2.0576 0.0965 0.2188 0.9468 5.3597 0.0080 0.0513 0.0157 0.0154 0.0507 0.0039 0.0371 1967 0.749350643 0.439194622 -1.316546028 0.306149455 0.0209 196 -23.7020 -22.8580 30.5400 4.5873 0.0703 1.9639 0.4981 0.2136 0.6086 5.1528 0.0100 0.0934 0.0103 0.0102 0.0235 0.0042 0.0415 1966 0.732785384 0.74795644 -0.681581292 1.265096245 0.0189 204 -23.3746 -22.7452 30.0600 4.8598 0.0542 1.8172 0.0437 0.2605 0.6557 5.2782 0.0131 0.0118 0.0081 0.0080 0.0203 0.0036 0.0418 1965 0.613725701 0.507953446 -1.91048851 0.825418348 0.0073 75 -24.2131 -22.5251 30.1900 5.5445 0.0691 1.9367 0.9303 0.2240 1.6461 5.5971 0.0119 0.1519 0.0318 0.0322 0.0436 0.0053 0.0467 1964 0.761469549 0.591007527 -0.715988774 -0.038091331 0.0000 1963 0.863218851 0.888615198 -0.331691877 -0.251436807 0.0123 121 -25.0690 -24.5964 27.4600 6.3232 0.0777 2.0383 0.1999 0.2465 0.9724 5.8291 0.0133 0.0349 0.0130 0.0131 0.0240 0.0044 0.0519 1962 1.194332086 1.123299319 1.400311402 -0.006545299 0.0296 250 -23.6850 -23.4588 29.3800 5.7280 0.0771 1.8900 0.0077 0.1952 0.4429 5.7635 0.0122 0.0047 0.0064 0.0063 0.0121 0.0041 0.0471 1961 0.685968021 0.396586649 -0.75076967 0.0168 201 -26.3352 -26.3457 5.5119 0.0726 1.9270 0.0180 0.1741 0.7887 5.7523 0.0121 0.0080 0.0119 0.0119 0.0208 0.0043 0.0496 1960 0.881343621 0.681729796 -0.466014418 0.0242 250 -25.5025 -25.2769 29.1200 6.5630 0.1133 2.2199 0.1176 0.2603 0.5894 6.4430 0.0159 0.0392 0.0062 0.0061 0.0308 0.0051 0.0647 1959 0.976463783 0.856497076 -0.769653776 0.0046 109 -24.9889 -25.0234 28.1000 7.4239 0.0760 3.3692 3.7315 0.4288 2.8041 7.8173 0.0178 0.6213 0.0559 0.0554 0.0902 0.0115 0.0722 1958 1.267054108 0.846073161 -0.698278256 0.0069 41 -24.5183 -25.8900 24.7200 8.4312 0.0602 3.1824 0.6086 0.4111 1.6313 7.3141 0.0165 0.0977 0.0280 0.0279 0.0575 0.0046 0.0709 1957 0.811849325 0.818326511 -1.087269506 0.0126 95 -23.4967 -23.5870 32.4900 5.6488 0.0761 2.6156 0.2207 0.4425 1.0305 7.3572 0.0159 0.0726 0.0380 0.0377 0.0437 0.0059 0.0573 1956 0.837065839 1.0007592 0.424525891 0.0115 76 -23.4403 -22.9419 32.1500 5.6087 0.0844 2.8347 0.3853 0.3125 1.1162 8.0455 0.0167 0.0696 0.0158 0.0157 0.0306 0.0058 0.0565 1955 2.044375189 1.828578166 0.0218 128 -24.9729 -24.2108 26.9000 7.4702 0.1659 4.0858 0.2619 0.3952 0.7023 9.7602 0.0222 0.0635 0.0111 0.0111 0.0338 0.0070 0.0731 1954 0.737033129 1.060103924 0.0029 8 -25.6604 -25.1068 28.9700 7.8034 0.0884 4.0907 1.8003 0.4834 5.0243 8.9409 0.0243 0.4037 0.0541 0.0529 0.2932 0.0091 0.0813 1953 0.619590578 0.647436408 0.0075 109 31.0400 1952 0.671851137 1.325676852 0.00562 41 33.1100 1951 0.894632264 1.397998867 0.00374 95 35.1800 1950 0.793048089 0.55195169 0.00186 76 -24.6750 -24.0405 37.2500 6.8214 0.1632 3.3876 1.0452 0.4622 1.7704 7.9556 0.0223 0.2316 0.0594 0.0592 0.3935 0.0066 0.0673 1949 0.70029018 1.053010492 0.0061 23 -25.2148 -26.0272 31.0900 5.8770 0.0532 3.0895 0.1231 0.4304 2.1365 7.9355 0.0165 0.1047 0.0204 0.0201 0.0735 0.0060 0.0578 1948 1.051413064 0.611568416 0.0105 86 -25.9116 -25.3761 29.6500 4.0905 0.0930 2.3578 0.7431 0.1757 1.3103 7.2889 0.0122 0.1378 0.0138 0.0136 0.0408 0.0056 0.0441 1947 0.706745895 0.323498221 0.0108 129 -26.5485 -25.8733 29.7700 5.7245 0.1294 3.2072 0.0524 0.2021 1.2550 9.1257 0.0150 0.1170 0.0155 0.0155 0.0393 0.0060 0.0588 1946 1.550656194 1.598435187 0.0164 381 -27.4603 -26.6368 28.0600 5.8659 0.1405 2.7682 0.0353 0.2424 0.3504 8.4089 0.0130 0.0437 0.0075 0.0075 0.0176 0.0057 0.0516 1945 0.877065687 0.539494611 0.0199 169 -26.7543 -26.0271 24.5700 6.2789 0.1407 2.9213 0.0309 0.3404 0.2888 7.9661 0.0131 0.0460 0.0079 0.0079 0.0185 0.0054 0.0507 1944 0.630508563 0.833959181 0.0116 20 -26.8748 -25.0203 29.4600 7.8427 0.0963 3.3664 0.8484 0.4187 0.4954 6.6868 0.0172 0.1799 0.0114 0.0114 0.0185 0.0066 0.0697 1943 0.948762137 0.552892235 0.0392 309 -24.8697 -26.9799 24.9700 7.2577 0.1020 3.2354 0.1611 0.3774 0.7706 8.0918 0.0196 0.0457 0.0060 0.0060 0.0120 0.0055 0.0699 1942 0.950673449 1.135547963 0.0148 18 -22.5094 -22.8155 28.5600 7.6926 0.1348 3.3979 0.6492 0.3347 1.3499 8.7744 0.0190 0.1142 0.0095 0.0095 0.0208 0.0072 0.0710 1941 1.185071356 1.263733805 0.0107 10 -24.3510 -22.5329 29.8200 6.2710 0.1459 3.3306 0.0560 0.3519 1.0068 9.4886 0.0179 0.0185 0.0196 0.0198 0.1190 0.0066 0.0613 1940 1.262322422 0.924262914 0.0168 133 -25.2962 -25.0828 26.2600 7.9568 0.1977 3.2329 0.0803 0.3561 3.2999 9.5743 0.0200 0.0232 0.0125 0.0125 0.0538 0.0065 0.0702 1939 1.114823086 1.548939022 0.0158 25 -25.5439 -24.3820 27.9800 4.2674 0.1624 2.3578 0.4553 0.3042 2.2656 7.3905 0.0087 0.0741 0.0100 0.0100 0.3075 0.0059 0.0413 1938 0.639727143 0.569847918 0.0115 5 -23.4696 -22.7480 5.0000 0.0751 2.6663 0.4021 0.2049 0.4997 7.9594 0.0121 0.0753 0.0093 0.0092 0.0819 0.0068 0.0485 1937 0.844930794 1.201811673 0.0269 13 -24.2616 -24.5915 25.9500 4.5623 0.0912 2.3393 0.0227 0.3172 0.2136 7.5512 0.0108 0.0093 0.0080 0.0079 0.1586 0.0049 0.0397 1936 0.603048989 0.528796963 0.0167 4 -23.4819 -23.1849 29.0200 7.1722 0.0600 2.7679 0.0126 0.2080 1.1025 7.5967 0.0175 0.0076 0.0094 0.0095 0.0608 0.0052 0.0569 1935 0.739921482 0.980951812 0.0369 402 -25.3542 -25.7692 30.5500 4.8218 0.0563 2.1489 0.0084 0.2337 1.3120 6.8994 0.0154 0.0044 0.0081 0.0081 0.0329 0.0047 0.0404 1934 0.936808475 1.350050919 0.0289 166 -26.1766 -24.8557 26.5700 4.2794 0.0626 2.1503 0.0112 0.3330 1.5501 6.8375 0.0072 0.0045 0.0248 0.0249 0.0818 0.0046 0.0362 1933 0.822006233 0.980858486 0.0187 215 -25.2825 -24.7483 27.0600 4.0682 0.0719 2.1376 0.0170 0.3042 3.6465 6.7130 0.0085 0.0074 0.0071 0.0071 0.0790 0.0047 0.0380 1932 1.128679304 1.122260931 0.0302 318 -26.5160 -24.7148 29.8100 3.4429 0.0475 2.1194 0.0111 0.2919 2.6147 7.5700 0.0093 0.0039 0.0069 0.0071 0.0472 0.0047 0.0336 1931 1.013960586 0.485124456 0.0189 13 -24.7074 -24.9517 30.7100 3.9828 0.0677 2.2806 0.0183 0.2268 3.7269 9.1548 0.0074 0.0089 0.0073 0.0073 0.0687 0.0057 0.0383 1930 1.148649752 1.029163891 0.0203 175 -26.8323 -26.0809 29.1800 3.0899 0.0697 3.5321 0.0158 0.3735 1.8765 13.0435 0.0121 0.0145 0.0103 0.0104 0.0397 0.0086 0.0506 1929 0.99387758 1.204846613 0.0376 104 -26.6411 -26.0890 28.1500 4.2733 0.0412 2.6675 0.0078 0.2893 0.1528 9.4824 0.0094 0.0112 0.0075 0.0075 0.0083 0.0064 0.0354 1928 0.905609551 0.772378969 0.0331 233 -25.8461 -26.2246 32.3600 5.8361 0.0440 2.8293 0.0095 0.2231 0.1736 8.7255 0.0186 0.0087 0.0074 0.0075 0.0091 0.0063 0.0476 1927 0.85672722 0.215215241 0.0171 152 -25.9555 -25.9299 28.1500 8.1915 0.1054 2.9585 0.0298 0.2692 0.3361 7.8459 0.0158 0.0135 0.0113 0.0112 0.2221 0.0057 0.0717 1926 0.932350398 0.425876672 0.0165 132 -27.7161 -26.9161 22.1900 7.5864 0.0875 3.2115 0.0256 0.2381 0.3483 8.4859 0.0152 0.0123 0.0127 0.0127 0.1256 0.0061 0.0618 1925 0.809324244 0.603492919 0.0174 48 -24.5765 -24.8562 28.9600 6.3520 0.0226 2.7524 0.0175 0.2355 0.3303 7.8838 0.0120 0.0130 0.0096 0.0096 0.0174 0.0058 0.0534 1924 1.735408827 1.991986688 0.027 253 -25.9985 -24.8571 31.4900 6.1000 0.1097 2.6762 0.0284 0.2676 2.2755 7.9132 0.0158 0.0089 0.0107 0.0106 0.2161 0.0054 0.0668 1923 0.787925712 1.573404755 0.0203 150 -24.6288 -25.1568 29.9300 5.6860 0.0967 2.5993 0.0231 0.2137 3.8395 9.0800 0.0128 0.0101 0.0098 0.0098 0.1010 0.0060 0.0536 1922 0.799163043 0.0208 334 -24.4215 -24.3729 28.8900 5.3341 0.0924 2.6394 0.0133 0.2462 3.8226 7.8138 0.0114 0.0069 0.0149 0.0150 0.0729 0.0054 0.0497 1921 0.77243578 0.0226 443 -23.4421 -23.8877 29.4300 6.1139 0.0805 3.2761 0.0156 0.2522 4.2754 10.1551 0.0128 0.0040 0.0195 0.0197 0.1065 0.0067 0.0623 1920 0.787155209 0.0385 278 -24.2587 -23.9798 29.2400 5.9896 0.0727 3.0804 0.0110 0.2266 3.7709 9.9680 0.0133 0.0038 0.0268 0.0269 0.0544 0.0067 0.0567 1919 0.836725864 0.0276 341 -24.7950 -24.8537 27.3900 6.5779 0.0798 3.1646 0.0126 0.2276 4.7733 10.8125 0.0149 0.0052 0.0154 0.0154 0.0604 0.0073 0.0629 1918 0.838156697 0.0058 392 -25.9260 -24.5236 30.6200 6.0259 0.0939 3.5283 0.0448 0.4603 6.5956 12.5834 0.0114 0.0238 0.0598 0.0605 0.2763 0.0095 0.0823 1917 0.966249549 0.0208 58 -25.5352 -24.7604 28.3400 5.8498 0.0925 2.8573 0.0143 0.2275 3.3143 9.2387 0.0118 0.0090 0.0238 0.0239 0.0445 0.0065 0.0535 1916 1.352618036 0.0152 567 -24.0530 -23.6626 27.6400 6.3964 0.0549 3.1876 0.0166 0.2559 6.1909 11.3232 0.0119 0.0088 0.0303 0.0302 0.0696 0.0078 0.0620 1915 0.56838431 0.0354 153 -23.6817 -23.9420 29.7600 5.9449 0.0494 3.1254 0.0118 0.2632 3.6600 10.8684 0.0125 0.0096 0.0234 0.0234 0.0455 0.0075 0.0580 1914 1.653698335 0.0096 355 -25.3230 -25.5543 30.4100 6.1042 0.0305 3.3067 0.0310 0.3592 11.7772 11.9468 0.0103 0.0189 0.0230 0.0230 0.0825 0.0083 0.0603 1913 0.673176646 0.018 479 -25.2734 -25.9128 31.0800 6.1167 0.1001 3.5575 0.0227 0.3392 8.3156 12.0722 0.0131 0.0069 0.0294 0.0291 0.0844 0.0083 0.0681 1912 1.168563731 0.0026 57 -25.4911 -25.0984 30.9900 8.2413 0.1793 5.4744 0.1320 0.7542 53.7132 17.0050 0.0120 0.1196 0.0562 0.0570 0.3436 0.0120 0.1118 1911 1.458277945 0.0119 43 -25.0742 -25.1744 29.2000 8.5525 0.0326 4.2884 0.0276 0.4920 13.5179 14.3376 0.0117 0.0126 0.0152 0.0153 0.0453 0.0096 0.0817 1910 1.653698335 0.0096 355 -25.3230 -25.5543 30.4100 6.1042 0.0305 3.3067 0.0310 0.3592 11.7772 11.9468 0.0103 0.0189 0.0230 0.0230 0.0825 0.0083 0.0603
码
# reading data
test <- read.delim("clipboard", sep="")
rnames <- test[,1]
test <- data.matrix(test[,2:ncol(test)]) # to matrix
rownames(test) <- rnames
test <- scale(test, center=T, scale=T) # data standarization
test <- t(test) # transpose
## Creating a color palette & color breaks
my_palette <- colorRampPalette(c("forestgreen", "yellow", "red"))(n = 299)
col_breaks = c(seq(-1,-0.5,length=100), # forestgreen
seq(-0.5,0.5,length=100), # yellow
seq(0.5,1,length=100)) # red
# distance & hierarchical clustering
distance= dist(test, method ="euclidean")
hcluster = hclust(distance, method ="ward.D")
# Creating Heat Map
heatmap.2(test,
main = paste( "test"),
trace="none",
margins =c(5,7),
col=my_palette,
breaks=col_breaks,
dendrogram="row",
Rowv = as.dendrogram(hcluster),
Colv = "NA",
key.xlab = "Concentration (index)",
cexRow =0.6,
cexCol = 0.8,
na.rm = TRUE )
Tal Galili.. 7
解决方法:使用color_branches从功能dendextend包(或set功能,用"branches_k_color","K"和"值"参数).
首先,我们需要将数据导入R并准备好相关对象(这部分与问题中的代码相同):
test <- read.delim("clipboard", sep="")
rnames <- test[,1]
test <- data.matrix(test[,2:ncol(test)]) # to matrix
rownames(test) <- rnames
test <- scale(test, center=T, scale=T) # data standarization
test <- t(test) # transpose
## Creating a color palette & color breaks
my_palette <- colorRampPalette(c("forestgreen", "yellow", "red"))(n = 299)
col_breaks = c(seq(-1,-0.5,length=100), # forestgreen
seq(-0.5,0.5,length=100), # yellow
seq(0.5,1,length=100)) # red
# distance & hierarchical clustering
distance= dist(test, method ="euclidean")
hcluster = hclust(distance, method ="ward.D")
接下来,我们准备好树形图和热图:
dend1 <- as.dendrogram(hcluster)
# Get the dendextend package
if(!require(dendextend)) install.packages("dendextend")
library(dendextend)
# get some colors
cols_branches <- c("darkred", "forestgreen", "orange", "blue")
# Set the colors of 4 branches
dend1 <- color_branches(dend1, k = 4, col = cols_branches)
# or with:
# dend1 <- set(dend1, "branches_k_color", k = 4, value = cols_branches)
# get the colors of the tips of the dendrogram:
# col_labels <- cols_branches[cutree(dend1, k = 4)] # this may need tweaking in various cases - the following is a more general solution.
# The following code will work on its own once I uplode dendextend 0.18.6 to CRAN - but that can
# take several good weeks until that happens. In the meantime
# Either use devtools::install_github('talgalili/dendextend')
# Or just the following:
source("https://raw.githubusercontent.com/talgalili/dendextend/master/R/attr_access.R")
col_labels <- get_leaves_branches_col(dend1)
# But due to the way heatmap.2 works - we need to fix it to be in the
# order of the data!
col_labels <- col_labels[order(order.dendrogram(dend1))]
# Creating Heat Map
if(!require(gplots)) install.packages("gplots")
library(gplots)
heatmap.2(test,
main = paste( "test"),
trace="none",
margins =c(5,7),
col=my_palette,
breaks=col_breaks,
dendrogram="row",
Rowv = dend1,
Colv = "NA",
key.xlab = "Concentration (index)",
cexRow =0.6,
cexCol = 0.8,
na.rm = TRUE,
RowSideColors = col_labels, # to add nice colored strips
colRow = col_labels # to add nice colored labels - only for qplots 2.17.0 and higher
)
这产生了这个情节:
有关包装的更多详细信息,您可以查看其小插图.
ps:使标签着色取决于heatmap.2的参数,这应该从gplots的维护者那里询问(即:来自warnes.net的greg)
更新:此答案现在包含qplots 2.17.0中的新"colRow"参数.
解决方法:使用color_branches从功能dendextend包(或set功能,用"branches_k_color","K"和"值"参数).
首先,我们需要将数据导入R并准备好相关对象(这部分与问题中的代码相同):
test <- read.delim("clipboard", sep="")
rnames <- test[,1]
test <- data.matrix(test[,2:ncol(test)]) # to matrix
rownames(test) <- rnames
test <- scale(test, center=T, scale=T) # data standarization
test <- t(test) # transpose
## Creating a color palette & color breaks
my_palette <- colorRampPalette(c("forestgreen", "yellow", "red"))(n = 299)
col_breaks = c(seq(-1,-0.5,length=100), # forestgreen
seq(-0.5,0.5,length=100), # yellow
seq(0.5,1,length=100)) # red
# distance & hierarchical clustering
distance= dist(test, method ="euclidean")
hcluster = hclust(distance, method ="ward.D")
接下来,我们准备好树形图和热图:
dend1 <- as.dendrogram(hcluster)
# Get the dendextend package
if(!require(dendextend)) install.packages("dendextend")
library(dendextend)
# get some colors
cols_branches <- c("darkred", "forestgreen", "orange", "blue")
# Set the colors of 4 branches
dend1 <- color_branches(dend1, k = 4, col = cols_branches)
# or with:
# dend1 <- set(dend1, "branches_k_color", k = 4, value = cols_branches)
# get the colors of the tips of the dendrogram:
# col_labels <- cols_branches[cutree(dend1, k = 4)] # this may need tweaking in various cases - the following is a more general solution.
# The following code will work on its own once I uplode dendextend 0.18.6 to CRAN - but that can
# take several good weeks until that happens. In the meantime
# Either use devtools::install_github('talgalili/dendextend')
# Or just the following:
source("https://raw.githubusercontent.com/talgalili/dendextend/master/R/attr_access.R")
col_labels <- get_leaves_branches_col(dend1)
# But due to the way heatmap.2 works - we need to fix it to be in the
# order of the data!
col_labels <- col_labels[order(order.dendrogram(dend1))]
# Creating Heat Map
if(!require(gplots)) install.packages("gplots")
library(gplots)
heatmap.2(test,
main = paste( "test"),
trace="none",
margins =c(5,7),
col=my_palette,
breaks=col_breaks,
dendrogram="row",
Rowv = dend1,
Colv = "NA",
key.xlab = "Concentration (index)",
cexRow =0.6,
cexCol = 0.8,
na.rm = TRUE,
RowSideColors = col_labels, # to add nice colored strips
colRow = col_labels # to add nice colored labels - only for qplots 2.17.0 and higher
)
这产生了这个情节:
有关包装的更多详细信息,您可以查看其小插图.
ps:使标签着色取决于heatmap.2的参数,这应该从gplots的维护者那里询问(即:来自warnes.net的greg)
更新:此答案现在包含qplots 2.17.0中的新"colRow"参数.
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