使用 ggbiplot 向 PCA 的变量名称添加下标？
Adding subscripts to the variable names of a PCA using ggbiplot?
我有以下包含 7 个变量的 PCA 图（请参阅下面的数据和代码），我希望将变量名称放在下标中。
然而，在 ggbiplot() 中，变量名称自动取自用于生成 PCA 的矩阵的列名称，并且（据我所知）没有可用于手动添加这些选项的选项。
因此我尝试使用
在我的实际列名中创建下标
c(expression("j"["d"]),expression("k"["1"]), etc.)
这只会导致变量名称在 PCA 图上变成 "j"["d"]、"k"["1"]。
这个问题有解决办法吗？例如让第二个字符变小或类似的东西？
该图是使用以下数据生成的：
Param.clean <- structure(c(0.314689287410068, 0.279479887056815, 0.448790689537864,
0.25336455455925, 0.289008161177184, 0.314501392595033, 0.291144087910652,
0.30630205659933, 0.283940162753961, 0.293902791758693, 0.384490609026053,
0.287376099118374, 0.308181312257512, 0.295516976083076, 0.299962079750977,
0.377418190053724, 0.577708482228635, 0.548861542714413, 0.445100820783724,
0.454234613160057, 0.509303280474031, 0.485557486397235, 0.512794671011103,
0.438809386918853, 0.584488774396788, 0.485077847448695, 0.54242611837146,
0.50295109738886, 0.462140343335828, 0.482811895512131, 0.505123975906175,
0.454883826310242, 0.270198900375524, 0.375171915727647, 0.415330703464691,
0.335520417496773, 0.337301727971001, 0.414448624199441, 0.413407199816623,
0.480251511263297, 0.381597639419929, 0.299997369191106, 0.716363262901133,
0.334190348030789, 0.339749957548872, 0.615860520668703, 0.399995858493781,
0.290916481482953, 0.271565709782391, 0.434971269297489, 0.426102875513371,
0.245620918873499, 0.350757895503111, 0.314711831388176, 0.233155192989713,
0.248289747469244, 0.260316266382216, 0.435133707574921, 0.270357707406285,
0.460714026041302, 0.300202262584418, 0.283894965208827, 0.286731230742906,
0.476076636930455, 0.496419713185873, 0.449716335449948, 0.414301742272173,
0.517741851053675, 0.452096411019313, 0.503619428840069, 0.46590684730812,
0.426164828533173, 0.526710272381684, 0.60162289738927, 0.501571299694807,
0.5204289094248, 0.501944294148778, 0.420989057029306, 0.486676941655541,
0.581232141136961, 0.388451077003248, 0.348575471498664, 0.541637601056563,
0.280529225927791, 0.474527715587717, 0.427368925204716, 0.247233045036043,
0.371205006512827, 0.350378420436755, 0.334934610173675, 0.672485054825788,
0.387370130421541, 0.442394016641109, 0.410245000087745, 0.554591956294395,
0.292541225836523, 4.53967830833669, 4.07671677879989, 6.31220323958745,
5.53951495559886, 6.14831664270411, 2.49250044245273, 3.56566691364472,
0.905669305473566, 5.65883946946512, 2.64297457644716, 3.05508165226008,
3.18054619676744, 6.40823390030613, 3.37302493648604, 3.66350222987433,
2.54057804516827, 8.20203100920965, 2.71440979468947, 2.91087136765321,
1.99383332931126, 2.54861955298111, 2.76731871856997, 2.8168199171933,
1.87471640761942, 2.36744814319536, 2.70068269921467, 3.73984078429639,
3.14727020682767, 2.44860090082511, 2.96811391366646, 3.15924824448302,
2.75038693333045, 0.571991651163747, 0.0795687369691844, 0.199285715352744,
0.278876264579594, 0.0878147967159748, 0.776516450569034, 0.109050695318729,
0.214585168287158, 0.0733157177455723, 4.99666969059035, 0.681611322797835,
0.511083496330927, 0.103351746220142, 2.09765716294448, 0.163525143420944,
1.15420421690991, 3.94337840843946, 3.16239102048179, 5.81127347030366,
5.75235136287908, 2.48392526193832, 2.46317023644224, 1.81044878205284,
4.65439113788307, 5.15721979085356, 2.87866174476221, 2.5224589696154,
5.64499958222732, 1.54218871717652, 2.67105548409745, 3.03890538634732,
4.12773523628712, 2.30713835917413, 1.77077499361088, 2.28220948716626,
2.27822186658159, 2.22687301691622, 2.78089357145751, 2.10296940756962,
1.62778628757223, 2.64038743038351, 2.90401477599517, 2.85171007970348,
2.15843657962978, 2.22618574043736, 2.01146884588525, 7.50444248911614,
2.78893498703837, 0.369707935024053, 0.640407053288072, 1.16690336726606,
1.19069673353806, 0.369720328599215, 0.222492094617337, 1.97003725056226,
0.0771822298566498, 0.0491951033473015, 1.58942595124245, 0.56345314020291,
3.61783248605207, 0.470429616980255, 4.25140980218227, 0.416233133369436,
0.838344213552773, 2.73752116598189, 3.02740207407624, 1.11222450388595,
2.30047973571345, 2.45276295114309, 2.64581680834914, 2.78265510452911,
3.27471463242546, 3.1145193031989, 2.56884276599934, 3.15895244479179,
3.14939826028422, 2.39397626441593, 3.8150685878781, 2.75754480964194,
2.56850058445707, 1.10134650183221, 1.90155507440989, 1.71837465837598,
2.29802527697757, 1.24960316416497, 1.95164571283385, 1.49695883272216,
2.51760663697496, 1.04954799870029, 1.59203378250822, 1.33138975808397,
1.30761714885011, 1.6880701482296, 1.33289409801364, 1.18721167324111,
2.10289117880166, 4.97532397741452, 4.08132408546905, 4.83296488539005,
5.65673472359776, 1.52374835970501, 4.90433675702661, 6.09970323707287,
4.9611738567551, 4.98475494328886, 1.58062443907062, 6.51368894614279,
5.82539446347704, 4.37618843046948, 6.41044923532754, 1.36502551613376,
2.11988553637639, 2.87185357650742, 1.99067048101375, 2.6186517810449,
1.56325603065391, 3.18718514405191, 2.67383103277534, 3.39795261013011,
3.97267814834292, 3.7929962793986, 2.75519806658849, 2.67046403462688,
1.61068025619412, 3.21088001991933, 2.72053461754695, 2.89008031133562,
2.44437138317153, 1.87622146913782, 2.30537068654473, 1.77740855213876,
1.46343538770452, 2.23820108221844, 1.83238286990672, 1.70535395620391,
3.20611382601783, 1.42552105011418, 1.35411406867206, 1.67505901074037,
1.27963638935859, 1.50879823369905, 3.20626547553887, 1.34457757696509,
1.4350421866402, 3.01776180580879, 4.42168406192213, 2.68915122840554,
5.10021819965914, 5.7995775481686, 3.69961343705654, 5.6582765411896,
5.42690238449723, 4.12574668414891, 2.88072699628149, 7.37651169135546,
0.877918794285506, 3.48383912583813, 7.16048748052369, 1.10681456684445,
2.0056554214408, 0.843951161950827, 0.892569730058312, 1.82299897540361,
1.4852886760508, 1.34192016645273, 1.12837524153292, 0.788718643598258,
2.59369957595567, 1.03540072683245, 0.767321502789855, 1.23622662722568,
0.784033099189401, 0.784212271682918, 1.25203002375116, 0.76296656858176,
0.985467154532671, -0.220396793447435, 0.106205735355616, 0.124459093059103,
-0.00892141033460625, -0.10377890299509, 0.0926174888437004,
-0.0549866305664182, 0.278899986296892, 0.0474233353460836, -0.109990653581917,
0.0474225463395319, 0.0338427349925041, 0.0972763542085886, 0.114185092970729,
-0.00886052381247282, -0.0589170539751649, -2.3298938000525,
-1.84932016064972, -3.90579685030132, -6.07330848347147, 1.8304963277777,
-2.75582764982432, -4.77531149517745, -3.8228796642224, 1.27799427995086,
-5.45959737020979, -2.00253919902196, -2.22745593055834, -2.6610222319141,
-3.21496389806271, -6.01237997648368, -3.13309627585113, 0.733061715583007,
1.04009207207213, 1.51182846035312, 1.92732659168541, 1.29081471823156,
0.809032674878836, 0.954354595015446, 1.5407008677721, 0.961584224718311,
0.949504360179106, 1.17135864682496, 0.758904917165637, 1.27744460012764,
1.13802453503013, 1.12143621314317, 0.923086409457028, -0.207958693792422,
-0.112425229889651, -0.114883695351581, -0.0418341891790419,
0.00953924376517534, 0.0761805102229118, 0.06189932115376, -0.279747098684311,
-0.139795616269112, -0.0957655208185315, -0.211875131353736,
0.15934879556795, -0.307479116310674, -0.171517195557555, -0.147559982724488,
-0.151702696457505, -3.2736393770054, -3.77255320500831, -2.50166923739016,
-3.38403152301908, -3.54271008856346, -5.98730765748769, -3.46145537216216,
4.08535061942786, -5.5706409165586, -5.12871207815409, -2.00980313849697,
-1.74987012389551, -4.99012113984178, -5.52220372986048, -4.09768380224705,
-2.65192667357127, 0.368457175791264, 0.276677635120849, 0.660357913002372,
0.536901503801346, 0.122066596522927, 0.248441367586455, 0.326834246516228,
0.414462564513087, 0.374505277723074, 0.157977417111397, 0.147561579942703,
0.327407247386873, 0.481645831460754, 0.471423282288015, 0.402634991332889,
0.600018523255984, -0.754529740661383, -0.333761049988369, -0.479209786502022,
-0.338527356651923, -1.15156446321805, -0.187009451910853, -1.59113974179576,
-0.26058504227052, -0.629410240799189, -1.30694395600756, -0.916838761041562,
-1.07011808082461, -1.22627768199891, -0.492068426683545, -1.54347744450718,
-0.104520670138299, 1.40759190544486, 7.8479420303603, 2.75170721710225,
3.93423731307934, 9.85715725720922, 5.37083122879267, 6.15668724537641,
4.96914687916388, 6.46718368138125, 1.0871206430619, 9.84838488511741,
9.75057146977633, 1.26769720241924, 9.92010527290404, 9.98543933499604,
9.69677802640945, 0.169932479038835, 0.409494925844172, 0.409328970126808,
0.740250064991415, 0.193447070196271, 0.51206505260865, 0.250175041146576,
0.391306541860104, 0.295244073495269, 0.243191891349852, 0.293793072924018,
0.408511371351779, 0.281213674316803, 0.680068365474543, 0.41473192628473,
0.371123384684324, -0.753847653398911, -0.768953422084451, -1.10839967615902,
-0.771105247549713, -0.155546843451758, -0.282887876386441, -0.444554830901325,
-0.305730849504471, -0.499526713974774, -0.561585665126642, -0.731248073279858,
-0.888600847683847, -0.92906893696636, -0.32135354558875, -0.635939710773528,
-0.817948141487935, 1.6278464008073, 3.22130429296692, 3.22974945083757,
7.91888088977089, 9.00321571025501, 2.45285976212472, 6.25077115575721,
5.03100211266428, 2.74867731204381, 1.44042827261984, 5.0080717401579,
9.99481210485101, 1.47605382240812, 5.14414160776883, 7.90287723037352,
9.74082155153155, 6.49911883796255, 4.32981192308168, 8.23767292803774,
4.77091148030013, 9.32961360147844, 2.72199803938468, 3.16884732668598,
0.829324850315849, 5.05701699654261, 2.34405943658203, 3.72586945071816,
2.25735736116767, 6.09207524452358, 4.18884709620227, 3.34469041476647,
2.58207156453282, 0.749518116253117, 10.288818734698, 4.99554592402031,
12.6404861267656, 7.78458069656044, 5.22634824855874, 19.4536860734845,
18.1442198018854, 2.79630955830216, 9.58980514369905, 7.07662330872069,
2.31912315823138, 4.37504726642122, 10.6357821771254, 4.86855507971098,
15.2487045279394, 2.38136078696698, 2.2241358395045, 2.6578728514413,
2.00018415475885, 14.3105512278154, 2.79016453381628, 2.82581362407655,
3.00503022968769, 0.867751725018024, 19.840897029452, 2.76507987820854,
2.18780075665563, 2.29634886607528, 5.24806297849864, 3.00219499040395,
3.75070014856756, 4.70993515464167, 2.90138749877612, 7.88213442545384,
6.81599063475927, 2.61536476109177, 2.09377944457034, 1.96296699593464,
5.57947221212089, 5.20963124415527, 3.33875400945544, 2.79699660371989,
4.58355573223283, 1.3866287143901, 2.73741390556097, 3.83854200132191,
3.64578404258937, 8.6152262147516, 7.4471927308167, 10.7907397029921,
3.60064423537503, 2.21575071569532, 13.2584175148358, 6.69871457573026,
7.57425001679609, 10.597095658568, 6.29717063158751, 19.982005469501,
4.82507357889165, 12.0198037318264, 12.1128156222403, 0.971864601969719,
7.90290065680941, 2.69096855397026, 3.41408452807615, 3.34672867252181,
3.73752327635884, 2.59765107041846, 3.69969989638776, 6.49256678763777,
1.34200508563469, 2.58853476804991, 6.08448572133978, 2.86518771201372,
8.80958803463727, 3.21931545517097, 13.9356314451744, 3.31248219124973,
2.6213849833856, 6.81703055885931, 4.57180783512692, 0.800920105539262,
1.6915382258594, 1.97274463716894, 8.35091653894633, 4.07009290065616,
4.70143776244173, 3.73712390195578, 3.32298003757993, 2.70389301739633,
9.40504621323198, 5.22653986488779, 6.91535883117467, 4.01246708252778,
6.83368936007222, 5.52582112283756, 9.52527065730343, 5.19140504300594,
8.41044230709473, 6.70183763448149, 6.82530618272722, 9.10367484707385,
14.269079283004, 4.7895190725103, 6.59831102186193, 5.62791180796921,
6.17603897117078, 7.14836313854903, 5.96534776215752, 6.33691875052949,
4.8933652261893, 13.8731955783442, 17.7908931604276, 13.79737106661,
12.8477370319888, 1.87629146464169, 19.782149810344, 19.4288346171379,
18.9387338103106, 18.204667886657, 1.15545298295716, 19.7008843562255,
17.4563148757443, 14.7906976851945, 17.3621598140026, 1.16834398824722,
1.00026320200414, 15.0063681416214, 3.00477131232619, 5.1401701791212,
0.385864693671465, 4.36085817695906, 8.55562331421922, 5.70195167902857,
5.37442221703629, 4.73609448876232, 3.56490389804045, 5.62534291626265,
1.87125703754524, 4.91213823029151, 5.71994946518292, 5.81859005757918,
4.93084813430905, 8.53895935813586, 8.24653955462078, 5.77503573757907,
8.75251863257339, 6.42709499839693, 6.27165456948181, 6.44690599292517,
16.0425839032357, 5.03840921912342, 5.87823822697004, 4.41305622781316,
5.94650622780124, 5.56597112355133, 1.1121899643292, 5.33032094594091,
5.42635044082999, 6.6131685036545, 11.4281271025538, 6.12669843180726,
14.5658381014441, 18.4343010187149, 10.0486588804051, 19.8108604625488,
19.3252983829007, 9.68507033698261, 7.62796785042932, 14.9589012558262,
0.670023332349956, 11.1040308237076, 17.0357564882065, 1.06506975100686,
0.740390195945899), .Dim = c(96L, 7L), .Dimnames = list(NULL,
c("jd", "k1", "k2", "b1", "b2", "p1", "p2")))
和代码：
library(ggbiplot)
Param.pca <- prcomp(Param.clean,scale=TRUE)
groups <- factor(c(rep("Cercis L",16),rep("Cornus L",16),rep("Ginkgo L",16),rep("Cercis R",16),rep("Cornus R",16),rep("Ginkgo R",16)))
g <- ggbiplot(Param.pca, choices=c(1,2), obs.scale = 1, var.scale = 1, ellipse.prob=0.95,
groups = groups, ellipse = TRUE, alpha=0, varname.size=6,labels.size = 10)
g <- g + geom_point(aes(shape=groups,col=groups))
g <- g + theme(legend.direction = 'vertical',
legend.position = 'right',
axis.text=element_text(size=14),axis.title=element_text(size=14),
legend.text=element_text(size=14),legend.title=element_text(size=14))
plot(g)
根据@RichardTelford 的评论，您可以通过在控制台中键入 ggbiplot 来获取 ggbiplot 的代码。然后将其复制并粘贴到脚本文件中，并为其指定一个新名称，例如 my_ggbiplot。然后将函数中的最后一个 if 语句更改为：
if (var.axes) {
g <- g + geom_text(data = df.v,
aes(label = varname, x = xvar, y = yvar,
angle = angle, hjust = hjust),
color = "darkred", size = varname.size)
}
对此：
if (var.axes) {
df.v$varname = paste0(substr(df.v$varname,1,1),"[",substr(df.v$varname,2,2),"]")
g <- g + geom_text(data = df.v,
aes(label = varname, x = xvar, y = yvar,
angle = angle, hjust = hjust),
color = "darkred", size = varname.size, parse=TRUE)
}
注意添加创建新文本标签的行，然后添加 parse=TRUE 到 geom_text。这会对标签进行硬编码以专门针对您的情况，但如果您要经常这样做，则可以使该功能更通用。
到 运行 函数（一旦你将它加载到你的环境中）：
my_ggbiplot(Param.pca, choices=c(1,2), obs.scale = 1, var.scale = 1, ellipse.prob=0.95,
groups = groups, ellipse = TRUE, alpha=0, varname.size=6, labels.size = 10) +
geom_point(aes(shape=groups, col=groups)) +
theme(axis.text=element_text(size=14),
axis.title=element_text(size=14),
legend.text=element_text(size=14),
legend.title=element_text(size=14))
结果如下：
我有以下包含 7 个变量的 PCA 图（请参阅下面的数据和代码），我希望将变量名称放在下标中。
因此我尝试使用
在我的实际列名中创建下标c(expression("j"["d"]),expression("k"["1"]), etc.)
这只会导致变量名称在 PCA 图上变成 "j"["d"]、"k"["1"]。
这个问题有解决办法吗？例如让第二个字符变小或类似的东西？
该图是使用以下数据生成的：
Param.clean <- structure(c(0.314689287410068, 0.279479887056815, 0.448790689537864,
0.25336455455925, 0.289008161177184, 0.314501392595033, 0.291144087910652,
0.30630205659933, 0.283940162753961, 0.293902791758693, 0.384490609026053,
0.287376099118374, 0.308181312257512, 0.295516976083076, 0.299962079750977,
0.377418190053724, 0.577708482228635, 0.548861542714413, 0.445100820783724,
0.454234613160057, 0.509303280474031, 0.485557486397235, 0.512794671011103,
0.438809386918853, 0.584488774396788, 0.485077847448695, 0.54242611837146,
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0.670023332349956, 11.1040308237076, 17.0357564882065, 1.06506975100686,
0.740390195945899), .Dim = c(96L, 7L), .Dimnames = list(NULL,
c("jd", "k1", "k2", "b1", "b2", "p1", "p2")))
和代码：
library(ggbiplot)
Param.pca <- prcomp(Param.clean,scale=TRUE)
groups <- factor(c(rep("Cercis L",16),rep("Cornus L",16),rep("Ginkgo L",16),rep("Cercis R",16),rep("Cornus R",16),rep("Ginkgo R",16)))
g <- ggbiplot(Param.pca, choices=c(1,2), obs.scale = 1, var.scale = 1, ellipse.prob=0.95,
groups = groups, ellipse = TRUE, alpha=0, varname.size=6,labels.size = 10)
g <- g + geom_point(aes(shape=groups,col=groups))
g <- g + theme(legend.direction = 'vertical',
legend.position = 'right',
axis.text=element_text(size=14),axis.title=element_text(size=14),
legend.text=element_text(size=14),legend.title=element_text(size=14))
plot(g)
根据@RichardTelford 的评论，您可以通过在控制台中键入 ggbiplot 来获取 ggbiplot 的代码。然后将其复制并粘贴到脚本文件中，并为其指定一个新名称，例如 my_ggbiplot。然后将函数中的最后一个 if 语句更改为：
if (var.axes) {
g <- g + geom_text(data = df.v,
aes(label = varname, x = xvar, y = yvar,
angle = angle, hjust = hjust),
color = "darkred", size = varname.size)
}
对此：
if (var.axes) {
df.v$varname = paste0(substr(df.v$varname,1,1),"[",substr(df.v$varname,2,2),"]")
g <- g + geom_text(data = df.v,
aes(label = varname, x = xvar, y = yvar,
angle = angle, hjust = hjust),
color = "darkred", size = varname.size, parse=TRUE)
}
注意添加创建新文本标签的行，然后添加 parse=TRUE 到 geom_text。这会对标签进行硬编码以专门针对您的情况，但如果您要经常这样做，则可以使该功能更通用。
到 运行 函数（一旦你将它加载到你的环境中）：
my_ggbiplot(Param.pca, choices=c(1,2), obs.scale = 1, var.scale = 1, ellipse.prob=0.95,
groups = groups, ellipse = TRUE, alpha=0, varname.size=6, labels.size = 10) +
geom_point(aes(shape=groups, col=groups)) +
theme(axis.text=element_text(size=14),
axis.title=element_text(size=14),
legend.text=element_text(size=14),
legend.title=element_text(size=14))
结果如下：