Hinzufügen von Indizes zu den Variablennamen einer PCA mit ggbiplot?

Question

Ich habe das folgende PCA-Diagramm mit 7 Variablen (siehe Daten und Code unten), wo ich die Variablennamen tiefgestellt werden soll. In ggbiplot() werden die Variablennamen jedoch automatisch aus den Spaltennamen der Matrix übernommen, die zum Generieren der PCA verwendet wurde, und (soweit ich weiß) sind keine Optionen verfügbar, um diese manuell hinzuzufügen.

Deshalb habe ich versucht, durch Verwendung von

c(expression("j"["d"]),expression("k"["1"]), etc.) 

tiefgestellten Indizes in meinen eigentlichen Spaltennamen zu schaffen, das nur in den Variablennamen ergibt Drehen in "j" [ "d"], "K" [ "1"] auf dem PCA-Plot.

Gibt es eine Problemumgehung für dieses Problem? z.B. den zweiten Charakter kleiner oder etwas Ähnliches machen?

Das Grundstück wurde mit den erzeugten Daten mit:

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., -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, 
-1.74987, -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"))) 

und Code:

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) 

Answer 1

Im Anschluss an @ RichardTelford Kommentar, können Sie den Code für ggbiplot erhalten, indem ggbiplot in der Konsole eingeben. Dann kopieren und fügen Sie diese in eine Skriptdatei ein und weisen Sie sie einem neuen Namen zu, z. B. my_ggbiplot. Ändern Sie dann die letzte if Anweisung in der Funktion von dieser:

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) 
} 

dazu:

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) 
} 

Notiere die Zugabe der Linie, die die neuen Beschriftungen und dann die Zugabe von parse=TRUE-geom_text schafft. Dies codiert die Beschriftungen so, dass sie speziell für Ihren Fall funktionieren. Sie können die Funktion jedoch allgemeiner gestalten, wenn Sie dies häufig tun.

die Funktion auszuführen (wenn Sie es in Ihrer Umgebung geladen haben):

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)) 

Und hier ist das Ergebnis: