R图被裁剪

Question

这是一个基本问题，你会认为R总会自动化。我正在制作一个热图（基本的东西，png（）到heatmap.2（）到dev.off（）），我的行标签在右侧被切掉了，还有一小部分的树状图。左：

手动调整边距最终会产生合理的输出，但问题在于这是考虑到生物学家用户的自动化管道的一部分。当然有一些自动化的方法，对吧？我的意思是，在OSX上的RGui中，图形窗口的快速重塑会自动修复布局，因此必须可行。谢谢，很抱歉打扰你。

编辑：重现此可视化的步骤：

输入数据：

Time,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48
CATMA1A23000,0.21129,0.48322,0.54234,0.93714,0.51816,0.11103,0.38304,0.97183,0.61381,-0.13775,0.32575,0.85221,0.1921,1.8692,0.4117,0.51977,0.74019,0.98932,0.023536,0.8849,0.75141,0.42846,0.03839,0.50295,0.38849,-0.95087,0.55017,-0.14813,0.79036,0.40978,-0.33048,0.81173,0.60585,0.014413,0.86586,0.063947,1.1195,0.25425,-0.090325,1.3035,0.90609,0.62866,0.83168,0.88655,0.4843,0.60098,0.26669,0.66605,0.78468,-0.76709,0.29615,-0.8911,0.5022,-0.93834,-0.065904,0.58003,0.41217,-0.99012,-0.032054,0.69119,1.1791,-0.0059458,0.81002,0.76421,1.302,0.77637,0.7824,1.192,-0.27005,-0.24698,1.8706,0.33513,0.38592,1.1987,0.48569,0.7104,2.4307,0.68148,0.11407,0.65619,0.94468,1.245,0.44146,0.71048,0.96389,1.7647,0.22729,0.96875,-0.2738,1.2975,2.0503,0.52507,2.282,1.0773,0.44489,0.22504
CATMA1A30870,3.9909,5.1844,5.2522,5.5482,5.665,5.4666,5.4456,5.5456,5.0014,5.5408,3.9324,3.9288,4.3624,3.0828,5.4821,5.1446,4.5638,4.6449,5.2604,4.2607,4.0942,3.9892,5.1361,3.8625,3.9454,5.3148,5.188,6.088,5.2085,5.3073,5.5652,4.8358,4.6111,4.9911,3.1497,4.3796,4.2456,3.9712,5.0998,5.4383,5.0908,4.5155,4.6486,5.1233,4.4259,4.7218,3.7928,4.0384,4.1085,6.2787,5.4937,5.9637,5.4085,5.188,5.3057,5.1963,4.3807,4.8352,3.9584,3.5859,3.8535,3.9755,4.5199,5.1093,5.3526,4.1214,4.5787,3.4499,4.1962,4.6929,4.3379,4.6376,4.4774,5.2341,5.3061,5.6769,3.6244,5.1073,4.543,4.9929,4.9341,3.9829,4.4304,4.0021,3.7498,4.2972,5.3338,4.8094,4.5766,5.5171,3.1207,5.0926,3.0253,4.351,4.351,4.5253
CATMA1A65800,0.65615,0.54186,0.93488,0.2205,0.38134,0.95061,0.60157,0.66508,0.83971,1.3625,0.9037,1.1606,1.0143,0.91896,1.3587,1.2468,1.0147,0.44113,1.5196,0.60232,0.52456,0.82557,0.43697,1.3253,0.78614,0.73697,1.0593,0.010271,0.59042,0.58544,0.38307,1.0372,1.071,0.21915,1.1779,0.97341,0.95672,0.92057,1.3866,1.3884,0.99241,1.0546,1.0215,1.0144,1.1606,1.2421,0.89549,0.56747,0.99347,1.0706,1.3403,0.48719,0.30759,1.0215,0.76474,0.87313,0.47597,1.5028,1.2201,1.7923,0.64299,1.3612,1.0079,0.64145,1.0969,0.90254,0.9109,0.85213,0.55241,0.63797,1.5373,0.45586,0.59624,0.5717,0.13919,-0.012128,2.7367,0.83577,0.13422,0.13908,0.32377,0.013345,-0.017209,0.47044,1.034,1.4932,1.0067,0.57515,1.1405,0.95364,3.0214,0.14601,2.1645,1.1704,0.45205,0.83406
CATMA1C71184,4.2879,2.7256,3.306,2.2375,2.6575,4.6438,4.3899,3.8518,5.3494,3.8049,5.4095,4.5437,3.4362,4.0983,2.5059,2.7275,3.9432,3.5177,4.266,4.6446,4.9338,3.5188,3.7903,4.4867,3.9692,3.3382,3.2898,3.4103,3.3025,4.1279,4.3532,5.0625,5.756,4.7799,5.0303,4.8974,3.8698,2.887,2.7541,2.7837,3.0665,4.0168,3.7507,4.6273,5.2384,3.7049,4.5843,3.97,2.7142,3.6205,3.5394,3.3561,3.2672,4.4467,5.2044,5.2177,3.8496,5.7881,4.7594,5.0395,2.8281,2.8751,2.8322,2.6873,1.8326,3.042,3.834,4.7844,3.1947,3.2571,4.0826,4.8398,3.8147,2.7439,2.846,2.64,2.8055,3.421,3.8495,4.9367,4.6413,3.5281,4.0636,3.7144,3.4468,2.3466,1.7452,2.3151,4.022,2.9211,3.89,3.7213,4.1856,3.3613,4.0891,4.2135
CATMA1C71776,-2.0266,-0.77692,-1.3279,-0.40422,-0.38614,-0.34387,-0.44277,0.99775,1.0748,0.17831,-0.14209,-0.98905,-0.88619,0.40548,-0.37731,0.18112,-0.80473,-0.26957,0.49049,0.25413,0.30341,0.20203,-1.0343,-0.17877,-0.46107,-1.202,-0.58841,-1.0995,-1.1079,-0.10977,0.29428,0.33363,0.35537,0.55571,-0.11074,-0.69584,-0.052035,-0.18207,-0.45321,-0.2778,-0.81074,-0.27129,0.087758,0.52214,0.33791,0.51601,-0.30863,0.14386,-0.2922,-0.21013,-0.73268,-1.1732,-0.36599,0.4731,1.0357,0.62377,0.8219,0.6029,-0.27195,1.0677,-0.48423,-0.57601,-0.43393,-2.0519,-0.67433,-0.44234,0.0078619,0.40677,-0.47102,-0.59971,0.30058,-0.4604,-0.56523,-3.3913,-0.52856,-0.54137,1.0418,-0.26115,0.21246,0.37858,0.38716,-0.86708,-0.41297,-0.21536,-0.06004,-0.48526,-1.2651,-0.52592,0.23757,-0.73376,1.0272,0.59383,0.65704,-0.017658,-0.44128,-0.30226
CATMA2A41800,1.5057,1.8357,2.7851,2.9125,2.6421,2.3881,2.4772,2.3367,2.2988,3.0073,2.7659,2.8454,2.5939,2.6327,2.6184,2.3415,3.3473,2.7683,1.1123,1.9614,1.8795,2.2335,2.9227,3.1536,2.6255,2.5264,2.3874,3.3196,1.8572,2.3446,2.3358,1.683,2.1742,2.8082,2.8634,2.8607,2.6755,3.2567,2.0726,3.0746,2.8984,2.5235,2.9399,2.5731,1.9196,2.9845,2.965,2.8055,1.1878,-0.6181,2.9552,2.7814,3.0701,-0.42372,2.5897,2.6331,1.7218,-0.70788,2.9578,1.1506,3.3772,1.6571,3.3166,3.5001,2.6541,2.5367,2.8643,2.1034,2.6389,1.8915,2.4861,3.2271,1.7718,2.7359,2.391,2.7223,1.1594,2.4025,1.1524,2.1405,2.253,2.4368,2.8053,2.2955,2.2877,2.7792,3.4115,3.2464,-0.37629,3.0582,1.682,2.0598,1.8747,2.0158,2.4714,2.1816
CATMA2C47274,2.2048,1.6574,0.96502,0.15092,0.5251,0.40351,0.90106,-0.12415,0.48846,0.03794,0.86292,0.27027,0.71848,1.8535,0.47188,-0.067504,0.68578,0.28113,0.17559,0.29659,0.067618,0.79368,-0.36732,0.80945,2.4297,1.3272,1.3741,0.005024,0.57369,0.6195,0.17845,1.3991,0.71594,-0.76358,0.74421,0.078431,0.97596,0.14151,-0.77085,0.64926,-0.24602,1.3478,0.49879,0.90549,0.78024,0.94685,0.023589,0.07446,1.3597,0.19311,1.1883,-0.20756,0.59042,0.031659,0.3591,1.1757,0.97314,-1.0133,0.92409,1.2264,-0.0095851,-0.47315,1.3107,1.3967,0.80332,0.5494,1.0394,1.4519,0.50253,-0.65282,1.5689,0.17996,1.5938,0.28124,0.93511,0.10344,3.6906,0.56448,-0.40754,0.75218,0.10346,-0.37737,-0.53789,0.57109,0.29602,-0.64821,-0.52805,0.34899,0.50146,0.61456,2.1785,-0.41,2.135,0.7426,0.3307,0.64542
CATMA2C47710,3.9021,3.7272,3.709,3.494,3.7557,3.7883,3.8697,3.4952,3.6365,3.6948,4.0954,3.7629,4.1282,3.6108,4.2769,3.3689,3.5232,3.7488,3.6237,4.0805,3.855,3.8724,4.2706,3.5584,3.9576,4.1324,3.857,3.6508,3.7609,3.7885,3.6256,3.8022,3.7189,3.7417,3.6357,3.6448,4.2841,3.8731,3.6047,3.7792,3.5703,3.8284,3.8098,3.8824,4.2441,3.6127,3.8253,3.529,3.6078,4.0917,3.6794,3.7977,3.8231,3.9369,3.6087,3.7634,3.6419,4.0052,3.7083,4.0191,3.3211,3.9133,3.74,4.0801,4.0999,3.6312,3.7747,3.7768,3.7977,3.9409,3.9423,3.6708,4.1773,3.666,3.8267,3.8832,4.0462,3.8007,3.3932,4.0945,3.9901,4.1036,4.1064,3.8178,3.7936,3.8638,4.3395,3.5859,3.5698,3.7885,4.4263,4.0292,3.6857,4.1197,4.0262,3.7753
CATMA3A13690,5.2022,5.6481,5.7765,4.8253,6.0581,6.2026,5.2711,6.4481,6.0929,6.3395,5.3806,4.9156,5.3634,4.5556,5.3547,5.5214,5.6947,5.9289,5.6269,5.5406,6.0508,5.8498,5.6275,5.4422,5.3293,5.7543,5.1577,6.3626,5.429,5.7245,5.7554,5.4575,5.2244,6.2312,6.0425,5.0317,5.4494,5.5252,5.5124,5.6588,5.0015,5.7454,5.6711,6.132,5.4789,6.1668,5.6978,5.113,4.3572,5.6177,5.9557,6.0099,5.2522,5.5598,6.2427,5.4703,5.4275,5.9159,5.3029,4.1094,5.927,5.9223,5.1257,5.3835,5.6579,5.5849,5.8674,4.9425,5.2144,5.5382,4.7165,5.5688,5.2766,6.4298,5.9438,5.7105,4.757,5.9097,5.3665,5.8336,5.8393,5.6104,5.4702,5.4028,5.0756,5.632,5.9963,5.7889,5.7521,5.5561,4.0685,6.3026,4.9628,6.176,5.7256,4.8529
CATMA3A15560,0.23073,0.32331,0.37953,0.081038,-0.33446,0.18495,0.86901,0.71363,0.33531,1.4741,0.32824,0.18869,-0.34772,0.97628,0.62455,-0.14645,0.42603,-0.00031328,0.92441,0.14199,0.25522,0.55583,0.10067,1.2818,0.64424,-0.24454,0.33039,0.25975,1.1023,-0.5464,0.62174,-0.15397,0.78478,0.2999,-0.063974,0.55156,0.44076,0.17798,0.61707,0.9308,0.19809,1.2378,0.26328,0.19767,0.069484,0.76748,0.45386,0.4495,0.050625,0.99311,-0.10988,-0.070507,0.46274,0.19475,0.36696,-0.16537,1.0566,0.94446,0.85272,1.194,-0.41335,0.17202,0.38729,0.65495,-0.32063,0.60186,0.24444,1.3128,0.48551,0.55998,1.8149,0.36494,0.10693,-0.19085,0.25082,-0.10628,-0.38432,0.50117,0.97923,-0.31536,-0.2634,-0.82767,0.70017,-0.0093473,0.27653,0.67773,0.40978,0.3315,0.5179,0.32044,2.9356,-0.51529,2.7438,0.4153,0.32022,0.74311
CATMA3A21390,-0.54603,-0.32262,-0.29966,-0.22463,-0.49654,-1.0552,-1.0705,-0.93928,-0.71247,-2.7228,-0.67849,-0.24868,-1.5015,-0.22486,-0.26215,-0.34298,-0.73168,-0.33699,-0.3455,-0.5349,-0.68784,-0.47506,-1.2541,0.86942,-0.14503,-2.0603,-0.35647,-0.67731,0.20243,-1.1881,-1.3828,-1.0471,-0.20157,-2.5492,-0.7862,-0.21715,-0.20583,-0.067758,-0.86589,-0.75509,-0.62777,-0.57176,-2.0996,-0.72894,-0.56391,-1.1054,-0.94172,-0.98805,-0.20763,-0.42764,-2.0142,-1.4079,-0.66326,-0.10354,-1.6284,-1.9413,-0.77001,-0.58492,-0.99846,-0.013285,-0.31205,-0.10665,-1.2396,-1.7556,-0.40454,-0.26631,-1.2694,-0.32263,-1.2293,-0.93683,0.97994,-1.8696,-0.26859,-0.25661,-0.33193,-0.83889,-0.25944,-0.63826,0.3387,-1.4443,-0.93123,-0.84915,-0.24606,-0.63109,-0.78621,-0.40802,-0.6463,-0.84319,-1.0379,-1.1471,1.9932,-1.3029,1.5286,-0.19754,0.018446,-0.55479
CATMA3A53880,3.917,3.6689,3.7213,3.8812,3.8253,4.4861,4.258,4.7926,4.9737,4.0869,3.2183,3.5812,3.408,3.3128,3.3915,4.1923,3.9122,4.0586,4.2707,4.3077,4.8926,4.1982,3.4817,3.5267,3.6952,3.6632,3.9304,4.0793,3.9499,4.2175,4.8303,4.9599,4.6336,3.8998,3.7932,3.8572,3.2167,3.7749,4.3971,4.0662,3.9241,4.6407,4.2837,4.9644,4.972,4.2565,3.8796,3.383,3.2382,4.1017,4.058,4.0423,3.6033,4.0774,5.141,4.9736,4.4372,3.8969,3.7386,3.3618,3.539,4.2588,3.4726,3.7424,3.5818,4.9159,4.3567,4.1291,4.1108,4.4035,3.1374,3.4675,3.762,3.9264,3.7319,4.1205,2.0915,4.4192,4.5049,4.5427,4.6205,3.4653,3.6017,3.3376,3.266,3.5561,3.4538,3.761,4.2013,4.1787,4.017,4.7773,3.748,4.4977,3.8685,3.7464
CATMA5A09500,6.2838,5.1076,6.6209,5.7153,5.9395,5.3601,4.2366,5.189,3.3074,4.8701,5.0357,5.0951,6.2843,5.691,5.5054,5.9949,5.0834,5.1484,4.5884,4.805,4.458,5.0816,4.7264,5.3661,5.0645,5.8293,5.2877,5.6602,5.3336,4.7329,4.843,5.1901,3.8431,4.683,5.7106,4.0774,6.5689,5.8061,5.3445,5.2905,3.837,4.6271,4.2277,4.6165,4.0081,4.5176,4.259,4.6363,4.8557,3.9828,5.9728,5.4698,5.4102,4.5802,5.0247,4.8967,4.0116,2.6636,5.4684,4.3454,6.6893,6.5624,6.1464,5.4444,5.3309,5.6682,5.5012,4.3162,2.9028,3.3906,4.6684,4.914,5.3601,5.5138,6.2191,5.8043,5.8165,5.1155,3.8681,4.9268,4.0232,6.1699,4.6327,5.7364,6.1934,6.7188,5.0755,5.7058,5.3703,4.3921,3.2108,4.9503,4.1003,4.8225,4.6701,4.7166
CATMA5A12680,1.7891,1.362,1.4303,0.61973,0.54124,1.2733,0.7775,0.66788,1.7338,0.63125,1.5852,0.91616,1.0712,0.81919,0.90152,0.77799,1.0835,0.32735,2.0868,0.5895,1.1445,0.64545,0.71776,0.33929,1.42,1.0729,1.4879,0.86379,0.95453,1.2928,0.97753,1.1738,0.79397,0.31563,0.86345,0.67595,1.3501,1.079,1.2034,1.2432,1.3696,1.1473,0.72528,0.57199,0.85965,0.65339,0.47614,0.43219,1.363,2.4026,0.98947,0.85204,1.2591,2.3151,1.6775,1.6555,1.0371,2.5586,-0.097071,0.91744,1.068,1.6819,1.0122,0.99911,0.75267,1.2195,0.42175,0.2554,0.4819,0.80025,0.44517,0.32442,1.9863,1.5019,1.2893,1.0669,1.6881,1.7581,1.6505,1.943,2.141,1.018,0.68207,0.84392,1.1452,1.009,1.1376,1.0572,1.9258,1.7039,0.10261,1.4549,0.94693,0.77945,0.049658,0.84178
CATMA5A14990,0.41247,0.51378,0.375,-0.24526,0.027658,-0.015345,-0.028278,-0.2643,0.3905,0.12299,0.94334,0.11482,0.50109,-0.55162,0.10768,-0.26433,-0.31064,-0.76526,1.0147,-0.73178,0.3323,-0.13657,-0.14013,-0.17878,0.31259,0.36723,0.55499,-0.2664,0.31862,0.60225,0.078919,0.18282,0.23014,-0.27835,0.16392,0.58131,1.052,0.062394,0.064929,-0.11918,-0.2167,-0.26018,-0.21649,-0.032523,-0.05763,-0.62775,-0.29148,0.13633,0.72715,1.535,0.08501,0.76137,0.54934,1.5163,-0.26612,0.58127,0.30339,1.8464,-0.17161,0.30309,-0.070279,0.28016,-0.036628,0.67464,0.34753,0.26499,-0.17856,-0.61162,-0.17941,-0.01017,0.21112,0.026389,0.64566,-0.39685,0.31403,-0.21637,1.1253,0.41434,0.77759,0.20421,0.70657,0.53273,-0.67276,-0.65656,0.6997,-0.06428,-0.13546,-0.15055,0.99804,1.4673,-0.47155,-0.056436,0.84609,-0.23068,-0.55114,0.68975
CATMA5A25890,-0.23072,0.82252,0.32512,0.13284,0.14406,0.005071,0.40953,-0.11252,-0.6367,-0.048073,0.21325,-0.046316,-0.35078,1.1023,-0.019882,-0.55825,-0.34621,0.1114,0.030302,-0.08142,0.19157,0.5152,-0.034952,0.20984,1.0547,0.4816,0.31078,0.14731,0.31811,-0.27275,-0.47217,-0.043207,0.29109,0.41192,-1.069,0.23357,-0.17453,0.015661,-0.26869,0.14587,0.19336,0.5926,-0.1583,0.61242,0.18635,0.01207,-0.21772,0.13986,1.9305,0.3349,0.62954,-0.04455,1.121,-0.14155,-0.33772,-0.42633,0.41828,-0.29794,-0.7107,1.4786,-0.37442,-0.45371,0.16175,-0.057764,-0.11803,-0.037838,0.25868,0.88605,0.33225,-0.24331,0.93084,-0.33266,0.9762,0.24755,0.30857,0.14661,1.8351,0.40313,0.45084,-0.52105,-0.31271,-0.37122,-0.28615,-0.0023692,-0.43072,-0.24417,-0.5184,0.13874,-0.32606,-0.1705,2.1396,-0.77657,2.3056,0.32096,0.29337,-0.034746
CATMA5A31940,4.4307,4.8735,4.7911,5.8201,5.9587,5.576,5.9084,5.849,5.2832,5.5423,5.0275,4.5254,4.5054,3.0696,5.6512,4.3986,4.9856,4.9222,4.951,4.5506,4.2185,4.3184,5.4783,4.4515,3.9397,5.6269,5.0988,6.1254,5.7446,5.6146,5.452,5.2047,5.3527,5.93,4.8931,5.5529,3.9876,4.1072,4.0583,5.4324,5.4681,4.392,4.5189,5.0629,4.9347,5.2165,4.6681,4.7428,4.1539,6.3376,5.353,6.2896,5.5844,5.1654,5.4391,5.3933,5.261,5.6974,4.5142,3.9851,3.569,4.0946,4.6662,5.1085,5.0319,4.4598,4.8672,3.7326,5.3032,5.0448,4.7771,4.2209,4.1886,4.284,5.4681,5.8331,4.7683,5.6614,5.3313,5.2017,5.1002,5.0642,4.4867,4.8576,4.1454,4.0971,5.0368,4.845,4.753,5.5496,2.9838,5.1394,3.342,4.1246,5.0121,4.618

适当的代码（BHC来自Bioconductor）：

library(argparse)
library(RColorBrewer)
library(BHC)
library(parallel)
library(gplots)

#data prep and clustering, to get dendrograms etc as shown in plot
data = read.csv('input.csv',header=TRUE,row.names=1,check.names=FALSE)
genes = rownames(data)
samples = colnames(data)
data = data.matrix(data)
standardisedData = (data-mean(data))/sd(data)
samples = as.numeric(samples)
hc = bhc(standardisedData, genes, timePoints=samples, dataType='time-course', verbose=TRUE)

#the plotting proper
png('heatmap.png',width=6,height=6,units='in',res=300)
heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'))
#heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(3,10)) <- this fixes it on a single-case basis
dev.off()

Answer 1

我建议只给它一个相当宽的默认边距，这样即使标签较长也应该剪掉它，例如：

heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(14, 14))

默认边距大小为(5,5)。上面增加了列和行边距，但你也可以只增加一个或另一个。

如果您想更精确，可以尝试使用max(strwidth(rownames(standardisedData)))来确定最大标签所需的空间量，然后将其转换为par(mar=*)所需的单位（heatmap.2() 1}}用于指定绘图边距。）

我认为这应该可以解决问题：

# determine margins to use
png('/tmp/trash', width=6,height=6,units='in',res=300)
plot.new()
margin_width = max(strwidth(rownames(standardisedData), units='inches')) * par('fin')[1]
dev.off()

#the plotting proper
png('heatmap.png',width=6,height=6,units='in',res=300)
heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(5, margin_width))
dev.off()