tests/testthat/_snaps/pca.md
In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses
can prepare pca
Code
prepare_pca(df = test_count_matrix[3:6])
Output
$data
Standard deviations (1, .., p=4):
[1] 218.22860 81.12065 33.51049 25.88166
Rotation (n x k) = (4 x 4):
PC1 PC2 PC3 PC4
T0_- -0.8423279 -0.5387762 0.013514466 -0.004613692
T3_A -0.3503926 0.5671455 0.641227641 -0.379997505
T3_B -0.2739171 0.4206085 -0.009173189 0.864854762
T3_C -0.3044309 0.4595157 -0.767176854 -0.328034833
$variance_explained
PC variance_explained
1 PC1 85.046773
2 PC2 11.751608
3 PC3 2.005378
4 PC4 1.196241
can prepare pca with scaling
Code
prepare_pca(df = test_count_matrix[3:6], scaled = T)
Output
$data
Standard deviations (1, .., p=4):
[1] 1.8290114 0.6218325 0.3945069 0.3352696
Rotation (n x k) = (4 x 4):
PC1 PC2 PC3 PC4
T0_- -0.4553397 -0.8900893 -0.01886846 -0.007123416
T3_A -0.5140102 0.2700273 -0.55776245 0.593110301
T3_B -0.5171755 0.2754655 -0.21950875 -0.780041125
T3_C -0.5108706 0.2427860 0.80022556 0.199261814
$variance_explained
PC variance_explained
1 PC1 83.632072
2 PC2 9.666893
3 PC3 3.890893
4 PC4 2.810142
can prepare pca with transform
Code
prepare_pca(df = test_count_matrix[3:6], transform = T)
Output
$data
Standard deviations (1, .., p=4):
[1] 2.732481e+03 4.775840e+02 3.689677e+02 3.439720e-13
Rotation (n x k) = (498 x 4):
PC1 PC2 PC3 PC4
[1,] -6.312612e-02 1.828884e-02 4.732036e-02 8.825290e-01
[2,] -1.540520e-02 -7.086642e-02 4.699002e-02 3.068933e-01
[3,] -3.957768e-02 -1.183371e-01 4.188281e-02 2.233352e-01
[4,] -3.214614e-02 -4.537490e-02 7.243763e-02 -6.400365e-03
[5,] -6.938214e-03 -6.560316e-02 -1.288658e-02 9.446512e-03
[6,] -1.777424e-02 5.330689e-02 3.921640e-02 -1.110433e-02
[7,] -8.951885e-02 -1.950371e-02 -8.877509e-02 9.225551e-03
[8,] -4.482429e-02 7.258838e-02 4.431838e-02 1.093555e-02
[9,] -3.309397e-02 2.029137e-02 1.392982e-02 -1.031638e-02
[10,] -8.556100e-02 3.284823e-02 -1.565225e-02 3.534297e-03
[11,] -1.748502e-02 -7.665229e-02 -8.047520e-04 -9.135440e-04
[12,] -2.080069e-04 -7.202347e-02 -4.836932e-02 1.850834e-03
[13,] -3.420846e-02 -4.093458e-03 4.581830e-02 -1.593698e-02
[14,] 2.624416e-03 -3.390809e-02 -3.994736e-02 4.259657e-03
[15,] -3.112586e-02 -7.814918e-03 2.415454e-02 -9.658904e-03
[16,] -2.309372e-02 -3.034630e-02 -1.857048e-02 1.085345e-02
[17,] -5.865665e-02 -5.299706e-02 2.744350e-02 -1.459890e-02
[18,] -3.543211e-02 -7.708076e-02 -5.326167e-02 -1.347050e-03
[19,] -4.038980e-02 6.248892e-02 -1.141207e-02 -1.193103e-02
[20,] -4.891850e-02 -6.726534e-02 9.025462e-02 -2.297290e-02
[21,] 5.664776e-05 -1.260434e-01 1.028370e-01 -2.422920e-02
[22,] -3.089657e-02 1.676419e-02 -5.640369e-02 5.716813e-03
[23,] -6.833143e-03 3.733575e-03 1.206621e-03 -2.488551e-03
[24,] -4.784317e-02 -5.853481e-02 5.602155e-03 2.021375e-03
[25,] -1.630722e-03 -7.585054e-02 3.283900e-02 -8.197578e-03
[26,] -1.597661e-02 -1.618607e-02 6.710222e-06 1.341768e-03
[27,] -2.560882e-02 1.743351e-02 2.400182e-02 -1.109032e-02
[28,] -3.734785e-02 -5.266493e-02 -1.997084e-02 -2.313047e-02
[29,] -7.059994e-03 -6.624292e-02 1.754160e-02 -1.186180e-03
[30,] -1.104333e-01 1.068366e-01 7.377178e-02 -2.483492e-03
[31,] -2.667432e-02 2.975190e-02 -2.176578e-02 -1.087562e-02
[32,] -7.055934e-02 -1.391863e-02 -6.516461e-02 -1.846219e-02
[33,] -1.643311e-02 -1.256770e-02 -1.443025e-02 4.987450e-03
[34,] -1.494780e-02 -8.794791e-03 1.336786e-02 -1.012285e-03
[35,] -5.693646e-02 5.807056e-02 1.839586e-02 -4.223290e-03
[36,] -3.541844e-02 -2.393489e-02 4.072977e-02 -3.876576e-03
[37,] -1.056079e-02 -2.670732e-02 4.021422e-02 -1.677647e-03
[38,] -5.741585e-03 -2.366006e-02 -4.769311e-03 -1.127072e-03
[39,] -2.590281e-02 4.046387e-02 6.492245e-02 3.254225e-03
[40,] -2.075440e-02 -2.044729e-02 -7.897870e-04 6.520001e-03
[41,] -5.214033e-02 1.209627e-02 -6.894807e-03 -1.462630e-02
[42,] -2.749920e-02 7.114683e-03 9.845494e-03 -8.986598e-03
[43,] -4.864495e-02 8.965257e-03 -2.516807e-02 -1.678366e-02
[44,] -3.781367e-02 1.153702e-02 2.200027e-02 -1.038102e-02
[45,] -4.890342e-02 2.666947e-02 5.695231e-03 1.741934e-02
[46,] -6.040728e-02 5.688180e-02 1.072743e-01 3.131736e-03
[47,] -3.047595e-02 -6.591744e-02 4.832229e-02 1.040586e-02
[48,] -5.635674e-02 -7.901073e-02 8.121881e-03 5.289951e-03
[49,] -9.763905e-02 -2.631455e-02 -4.303934e-02 3.776157e-02
[50,] -3.179084e-02 -4.217708e-02 -8.541190e-02 2.706215e-03
[51,] -1.543858e-02 1.109722e-03 3.686443e-02 -4.562293e-03
[52,] -3.113861e-02 1.093086e-02 4.476826e-02 -7.199986e-03
[53,] -5.696627e-03 -2.690888e-02 3.415335e-02 6.721439e-04
[54,] -2.864619e-02 -2.725329e-02 -3.024180e-02 -2.252121e-03
[55,] -6.502069e-03 -2.150499e-02 -1.674955e-02 4.296213e-03
[56,] -1.641802e-02 -2.663657e-02 1.448872e-02 7.544101e-04
[57,] -7.237063e-02 4.207408e-02 7.323077e-03 -2.029387e-02
[58,] -2.297522e-02 -1.211669e-03 1.330126e-02 -5.757474e-03
[59,] -4.792596e-02 2.612459e-02 1.178491e-02 -1.918985e-03
[60,] -2.044904e-02 1.266306e-02 -4.545472e-03 -6.060721e-03
[61,] -2.363222e-02 -1.359915e-02 -1.021883e-01 4.245837e-03
[62,] -4.502862e-03 -4.387247e-03 -4.039799e-03 2.900829e-04
[63,] -1.491981e-02 -3.250619e-03 -1.479585e-02 7.921967e-04
[64,] -2.685595e-03 -1.078122e-01 -5.604804e-02 1.067741e-02
[65,] -6.262641e-02 3.683284e-02 3.333741e-02 2.101961e-03
[66,] 1.067225e-03 2.915837e-02 4.232044e-02 -2.839610e-03
[67,] -4.844707e-02 2.580802e-02 1.391249e-02 -6.990143e-03
[68,] -7.442851e-03 -7.225809e-03 -2.582764e-02 1.669868e-03
[69,] -3.841762e-02 -2.599724e-02 -1.158152e-02 1.867376e-02
[70,] -1.452113e-02 -4.900542e-02 4.590220e-02 -1.211060e-03
[71,] -1.393558e-02 2.489095e-02 -4.979933e-02 2.863988e-03
[72,] -1.222015e-02 -4.414236e-03 -2.255263e-02 -1.852338e-03
[73,] -1.586680e-02 4.758438e-03 6.703153e-03 -4.447361e-04
[74,] -1.386712e-02 6.092282e-02 1.580476e-01 -9.449121e-03
[75,] -3.479929e-02 -9.428059e-03 -5.321405e-02 3.588147e-03
[76,] -9.781339e-02 7.835485e-02 1.427098e-03 1.093746e-02
[77,] 8.546662e-03 -4.598640e-02 -4.833527e-03 -4.959006e-04
[78,] -2.966412e-02 1.442336e-02 -1.050950e-02 -4.341713e-03
[79,] -3.118120e-02 2.652836e-02 4.808451e-02 -4.154429e-03
[80,] -1.459305e-02 1.163231e-02 -6.696172e-03 -1.775277e-03
[81,] -1.426710e-02 1.728451e-02 -7.813605e-03 -4.282879e-03
[82,] -9.683183e-03 2.069149e-03 4.997030e-02 -1.233796e-03
[83,] -1.489966e-02 -6.355378e-02 1.187196e-02 -9.106478e-04
[84,] -4.880931e-02 -9.520976e-03 4.397121e-02 -8.838806e-03
[85,] -1.874924e-02 -5.843354e-02 3.969319e-02 -1.008458e-02
[86,] -8.898412e-03 -3.086572e-02 -1.444690e-02 4.370363e-03
[87,] -2.041227e-02 -2.514705e-02 4.866825e-02 -7.203582e-03
[88,] -5.566186e-02 8.757350e-03 -8.495471e-02 1.702433e-02
[89,] -5.637458e-02 -2.170242e-02 3.828055e-02 -2.285379e-03
[90,] -1.971857e-02 2.444846e-03 -8.788620e-03 -9.582356e-03
[91,] -2.194073e-02 -2.294826e-03 -6.923952e-04 3.388832e-03
[92,] -1.214884e-02 -6.169609e-02 1.246075e-02 -3.751012e-03
[93,] -2.971130e-02 4.221220e-02 4.181805e-02 4.818582e-03
[94,] -3.035320e-02 -1.768813e-02 -9.357736e-03 7.485960e-03
[95,] -2.192053e-02 -1.381048e-02 -2.400702e-02 2.140439e-03
[96,] -1.193357e-02 -2.700296e-02 -6.806616e-02 3.746697e-03
[97,] -2.241590e-02 8.285377e-03 4.850086e-02 1.723588e-03
[98,] -3.136043e-02 3.469761e-02 7.993695e-02 -9.034507e-03
[99,] -1.947151e-03 -2.296614e-02 2.566020e-02 -1.907733e-03
[100,] -1.111037e-01 4.966286e-02 3.210062e-02 -1.881561e-02
[101,] -2.569543e-03 1.637901e-04 4.652086e-03 -1.526052e-03
[102,] -2.323466e-02 -1.041866e-01 -2.045816e-02 6.218260e-04
[103,] -2.307241e-02 -7.158902e-02 1.516625e-02 2.128100e-03
[104,] -6.080119e-02 6.191613e-02 3.188570e-02 -1.136081e-02
[105,] -3.023765e-02 -6.443423e-02 3.347982e-02 5.686602e-03
[106,] -9.372036e-02 1.038309e-02 -2.268048e-02 -2.682249e-02
[107,] -2.676843e-02 -4.206133e-02 5.343659e-02 -1.723435e-04
[108,] -7.244495e-02 8.122125e-02 8.973766e-02 -7.497122e-03
[109,] -1.305168e-03 -5.425584e-02 5.768695e-03 3.351603e-04
[110,] 5.587640e-03 -1.824887e-02 3.762176e-03 2.237617e-03
[111,] 1.154212e-03 -1.210426e-02 8.844292e-02 -6.014422e-03
[112,] -1.851503e-02 -1.107758e-01 -1.394103e-02 6.828945e-03
[113,] -5.997968e-02 1.694335e-02 -7.418846e-03 -8.179328e-03
[114,] -5.293605e-02 1.406366e-02 3.621677e-03 -1.455444e-02
[115,] -8.571378e-03 1.194735e-02 -2.930269e-02 -8.991941e-04
[116,] -5.696341e-03 -3.242270e-02 4.659274e-02 -3.269346e-03
[117,] -1.672725e-02 -6.134014e-02 9.835419e-02 -1.957479e-03
[118,] -8.124886e-02 3.313667e-02 -6.583330e-02 3.922675e-02
[119,] -3.558151e-02 -6.576321e-02 -4.111754e-03 -1.128614e-02
[120,] -5.216732e-02 -1.192798e-01 8.327059e-03 -8.365020e-03
[121,] -1.024293e-01 -9.672053e-03 -1.807651e-02 1.266986e-02
[122,] -3.287871e-02 -1.957521e-02 1.148641e-02 8.209290e-03
[123,] -8.437919e-02 -3.085894e-02 -7.320048e-02 -7.531646e-03
[124,] -1.279990e-02 -2.265401e-02 -1.877593e-02 -1.000213e-03
[125,] -4.901654e-03 -2.276348e-02 -1.678278e-04 4.808312e-04
[126,] -4.248618e-02 1.463944e-02 1.050126e-01 -1.450264e-02
[127,] -6.031026e-03 -2.049281e-02 -5.566195e-03 -2.615596e-04
[128,] -2.595227e-02 -3.528600e-02 3.943811e-03 -6.154860e-03
[129,] -4.759509e-02 -1.170059e-02 2.196627e-03 2.822998e-03
[130,] -5.055345e-02 2.802459e-02 1.378974e-02 -5.456092e-04
[131,] -1.866795e-02 1.678194e-02 -3.078759e-04 -1.378224e-03
[132,] -3.261158e-02 -3.676107e-02 1.309220e-02 -4.771305e-04
[133,] -5.439757e-02 -1.021215e-01 -2.656188e-02 -4.819435e-03
[134,] -2.356935e-02 -1.916713e-02 1.925748e-02 -5.308268e-03
[135,] -3.079070e-02 2.077196e-02 4.499012e-02 -6.710611e-03
[136,] -5.708655e-02 4.972869e-02 7.184215e-02 -2.231945e-02
[137,] -1.019425e-01 4.847508e-02 -3.847270e-02 4.258721e-03
[138,] -1.832155e-02 -2.267113e-03 -5.006751e-03 -5.631770e-03
[139,] -3.664292e-02 3.806276e-04 -1.108760e-02 -1.630553e-02
[140,] -8.094367e-03 -1.028729e-03 -3.303475e-02 -5.069801e-04
[141,] -6.594732e-02 3.907109e-02 6.984365e-02 -9.476470e-04
[142,] -6.668858e-02 5.668065e-02 -1.628287e-02 1.208773e-02
[143,] -4.206499e-03 -1.506893e-02 -2.721529e-03 1.077550e-04
[144,] -8.558673e-02 -2.300817e-02 -5.063769e-02 -3.403871e-02
[145,] -3.318418e-02 -4.225689e-02 1.728612e-03 7.763194e-03
[146,] -9.203687e-02 6.660068e-02 1.394894e-02 1.927595e-02
[147,] -1.070692e-01 2.789893e-02 -5.492786e-02 3.706702e-02
[148,] -2.749150e-02 1.159219e-03 2.687778e-02 -1.870916e-02
[149,] -5.926400e-02 -1.816379e-02 7.253285e-03 7.383675e-03
[150,] -3.697872e-02 -3.252213e-02 -4.221438e-02 -5.228358e-03
[151,] -1.227120e-02 -1.786422e-02 -1.738471e-02 7.018426e-04
[152,] -3.894960e-02 -2.292149e-03 4.932718e-02 1.636273e-04
[153,] -3.450812e-02 -4.562512e-03 -2.046947e-02 2.212597e-03
[154,] -6.529797e-02 3.311195e-02 2.644397e-02 -8.001824e-03
[155,] -5.712193e-03 -5.335677e-02 3.655773e-02 -4.777872e-03
[156,] -8.283663e-02 -8.192563e-02 -3.063881e-03 -8.565499e-04
[157,] -2.804421e-02 -1.801020e-02 -1.294603e-02 3.494853e-03
[158,] -9.783153e-02 2.697166e-02 -3.003954e-02 2.813617e-02
[159,] -3.583827e-02 2.686174e-02 -1.209046e-02 1.035043e-02
[160,] 2.394258e-03 -8.501765e-03 -3.210216e-02 3.065908e-03
[161,] -3.244973e-02 1.177902e-02 2.276373e-02 -1.923711e-02
[162,] -6.455655e-02 5.386121e-02 7.610154e-02 -1.030458e-02
[163,] -6.320660e-02 2.686380e-02 1.845503e-02 -8.238160e-04
[164,] -3.899459e-02 -6.715099e-03 1.769832e-02 6.902570e-04
[165,] -5.180516e-02 -6.585041e-02 -4.253894e-02 -2.525613e-04
[166,] 9.186178e-03 -3.955050e-02 4.679200e-02 -2.076545e-03
[167,] -4.558742e-03 -2.590427e-02 6.580111e-02 -5.199966e-03
[168,] -2.286590e-02 1.266004e-02 1.592620e-02 -3.315910e-03
[169,] -4.071682e-02 -1.376813e-02 3.883857e-02 -2.299513e-02
[170,] -5.164300e-02 9.138117e-02 2.875791e-02 -5.398733e-03
[171,] -6.014745e-03 -7.829477e-03 2.312790e-02 -3.919874e-03
[172,] -1.027898e-02 -8.575575e-03 9.391235e-03 2.915216e-04
[173,] -5.972204e-02 -5.110734e-02 -4.810614e-03 -1.357379e-03
[174,] -2.361763e-03 -5.460467e-02 1.220337e-02 -1.824380e-03
[175,] -1.109603e-02 -6.481199e-03 2.885963e-02 -9.391451e-03
[176,] -2.085691e-02 -3.140476e-02 -1.640682e-02 8.133497e-03
[177,] -3.198990e-02 -4.610643e-02 3.001831e-03 1.913660e-03
[178,] -6.797427e-02 -6.986600e-02 1.315622e-02 -3.223414e-02
[179,] -4.350937e-02 -1.509968e-02 -9.107386e-02 -6.658656e-03
[180,] -1.027952e-01 -3.253752e-02 -8.623396e-02 -2.995532e-02
[181,] 1.412810e-02 4.054313e-03 -4.857776e-02 5.333931e-03
[182,] -1.527361e-02 -1.720390e-02 2.070499e-02 1.015362e-03
[183,] -4.371945e-02 7.749547e-03 4.990130e-02 -1.593786e-02
[184,] 1.001995e-02 3.863466e-03 3.198814e-02 -4.416777e-04
[185,] -2.444499e-02 1.379155e-02 -9.607437e-03 3.918449e-03
[186,] -2.194199e-02 -1.189303e-01 9.220356e-02 -9.458558e-03
[187,] -3.934352e-02 -3.837355e-02 1.662724e-02 -8.024713e-03
[188,] -2.049071e-02 -4.602697e-02 -7.037320e-02 -9.062653e-03
[189,] -6.073740e-02 1.550460e-02 4.879270e-02 -1.864175e-02
[190,] -2.236704e-02 1.430154e-02 1.993675e-05 -1.306738e-03
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[398,] -7.134201e-02 4.904892e-03 -1.055111e-01 4.512171e-02
[399,] -2.884536e-02 5.380575e-02 -3.342506e-02 -3.246811e-03
[400,] -5.466651e-02 -1.778462e-03 1.095193e-02 -3.258524e-02
[401,] -2.901218e-02 -4.445882e-05 1.535670e-02 -1.368544e-03
[402,] -1.744394e-02 2.650936e-02 4.749336e-03 -8.914894e-03
[403,] -2.129297e-02 -1.904367e-02 -6.982008e-02 3.445991e-03
[404,] -4.625607e-02 4.453984e-02 -6.016468e-02 -9.374975e-03
[405,] -2.178641e-02 -9.053372e-02 -2.291831e-02 1.076606e-02
[406,] -7.720799e-02 2.108760e-02 -1.455489e-02 -6.505998e-03
[407,] -6.273839e-02 1.612627e-02 -2.396582e-02 -1.391460e-02
[408,] -2.232631e-02 -4.001581e-02 -6.068855e-03 -2.225132e-04
[409,] -3.936296e-02 4.158902e-02 -1.433695e-02 -1.656674e-02
[410,] -1.087366e-02 -8.239133e-02 6.125838e-02 1.817342e-04
[411,] -7.762519e-02 -3.512382e-03 7.268047e-02 1.107036e-03
[412,] -5.216486e-02 -5.047190e-02 -6.710261e-03 3.786038e-03
[413,] -1.688645e-02 4.958313e-03 2.988260e-02 -6.990672e-03
[414,] -2.849950e-02 -2.110360e-02 7.786997e-03 -1.178633e-02
[415,] -1.063276e-02 1.858688e-02 2.203427e-03 -4.298729e-03
[416,] -3.718529e-02 1.553457e-02 -1.459568e-02 -1.174422e-02
[417,] -6.680531e-02 -6.475310e-02 8.997765e-02 -8.699687e-03
[418,] -1.978828e-02 -3.601715e-02 -7.455370e-02 -7.606844e-04
[419,] -1.713474e-02 -5.446252e-02 4.165601e-02 -1.197809e-02
[420,] -2.179630e-02 -1.892249e-02 8.610978e-03 -2.063002e-03
[421,] -4.544582e-02 6.087251e-03 -3.124612e-02 -7.968048e-03
[422,] -6.083550e-02 6.053051e-02 7.711302e-02 -2.666618e-02
[423,] -3.268555e-02 1.368593e-02 -7.659948e-02 -1.717925e-03
[424,] -1.790135e-02 -2.118306e-03 2.976639e-03 2.606766e-03
[425,] -7.895966e-02 -5.056219e-03 1.524076e-02 -7.847702e-03
[426,] -7.702789e-03 -4.418395e-02 2.821600e-02 -3.741899e-03
[427,] -3.651183e-02 -2.758935e-02 3.663937e-02 1.597299e-03
[428,] 4.122708e-03 4.446700e-02 4.344992e-02 -5.686466e-03
[429,] -5.400188e-02 -5.033559e-02 3.079198e-02 9.057186e-04
[430,] -1.661446e-02 -2.993271e-02 -5.083537e-03 1.100905e-03
[431,] -2.338550e-02 -1.064157e-01 9.183444e-03 -7.699808e-05
[432,] -1.637521e-02 1.146829e-02 -3.988406e-02 8.082053e-04
[433,] 2.093227e-03 -4.208800e-02 7.286710e-02 1.932019e-04
[434,] -3.537604e-02 -1.100327e-02 3.092757e-03 2.387426e-03
[435,] -3.661580e-02 -1.864947e-02 -3.388084e-02 -7.180598e-03
[436,] -2.134794e-02 -8.314661e-03 -1.264344e-02 9.813677e-04
[437,] -5.878444e-02 6.068336e-02 -3.339747e-02 -7.472261e-04
[438,] -5.429675e-02 2.268021e-02 -1.000413e-03 -2.507479e-02
[439,] -2.720793e-02 3.499552e-02 2.070871e-02 5.497973e-04
[440,] -2.389663e-02 -4.879462e-02 1.438008e-02 -9.231296e-03
[441,] -4.328022e-02 -2.267775e-02 2.750114e-02 -2.996724e-03
[442,] -8.451624e-03 -6.449157e-02 -2.603447e-02 -3.857424e-03
[443,] -7.659991e-07 -3.500294e-02 1.888396e-02 -3.505380e-03
[444,] -2.690646e-02 2.539693e-02 1.397515e-01 6.187591e-03
[445,] -3.369152e-02 3.358770e-02 7.596626e-02 -1.352358e-02
[446,] -5.743780e-02 5.450906e-02 -2.145027e-02 -7.239489e-03
[447,] -3.008201e-02 1.127970e-02 3.833359e-02 -3.363307e-03
[448,] -2.418537e-02 -2.596796e-02 9.286824e-03 -3.190293e-03
[449,] -4.159206e-02 3.248049e-03 3.592653e-02 1.059751e-02
[450,] -8.844774e-02 5.089348e-02 7.049905e-04 2.929222e-03
[451,] -3.765697e-02 1.020651e-02 -3.607024e-02 4.602829e-03
[452,] -2.570730e-02 -2.813164e-02 -3.011045e-02 -1.494032e-03
[453,] -1.112428e-02 1.160217e-03 3.729016e-02 -2.126338e-03
[454,] -6.569410e-02 2.304070e-02 -8.496383e-02 1.019605e-02
[455,] -2.061535e-03 -6.516327e-02 1.033699e-01 -1.238998e-02
[456,] -6.885846e-02 2.523523e-02 5.721027e-02 8.301633e-03
[457,] -4.100282e-02 -7.369351e-04 -6.072719e-02 -9.496816e-03
[458,] -7.065030e-02 -7.035409e-02 -1.011705e-01 3.863118e-02
[459,] -5.830450e-02 7.912572e-03 7.267680e-02 -2.355054e-02
[460,] -2.456898e-02 -3.539776e-02 2.019639e-02 -6.569821e-03
[461,] -3.035927e-02 -2.671516e-02 2.743905e-02 -1.582992e-02
[462,] -3.027915e-02 -1.167586e-02 2.305771e-02 -1.117388e-02
[463,] -6.521135e-02 1.546358e-02 3.931978e-02 -7.679907e-03
[464,] -6.307924e-02 -3.986174e-03 -1.744659e-02 7.043012e-03
[465,] -3.171831e-02 4.147859e-02 -1.437467e-03 9.806475e-03
[466,] -8.282001e-02 -2.598861e-02 -1.191283e-02 -1.805805e-03
[467,] -3.296934e-02 -7.631440e-04 7.250069e-02 -9.621228e-04
[468,] -5.993873e-02 1.632836e-02 -6.456417e-02 -4.275273e-03
[469,] -2.012540e-02 -5.324960e-02 1.559411e-02 -1.150920e-02
[470,] -2.355414e-02 3.089503e-02 -1.639357e-02 6.620056e-03
[471,] -4.206828e-02 5.889884e-02 1.348085e-02 -2.513953e-02
[472,] -2.828940e-02 -3.775118e-02 2.947612e-02 -7.215256e-03
[473,] -3.565157e-02 -7.521361e-03 -1.124893e-02 -1.759576e-02
[474,] -9.532648e-03 -1.043933e-01 -4.129662e-02 -5.576737e-03
[475,] -5.130801e-02 -3.259609e-02 3.687652e-02 -1.471237e-02
[476,] -9.266476e-02 -3.413661e-03 -3.725817e-02 -3.018297e-02
[477,] -4.727947e-02 7.439780e-04 -7.792518e-02 -1.667112e-02
[478,] -1.350009e-02 2.355750e-02 -2.126486e-02 7.980522e-03
[479,] -6.179868e-02 -6.875776e-02 3.424548e-02 -1.908315e-02
[480,] -1.903872e-02 -1.374978e-01 1.242736e-01 -1.375474e-02
[481,] -4.517951e-02 -2.032934e-02 -3.885745e-02 -9.513343e-03
[482,] -3.696850e-02 -2.888583e-02 2.327650e-02 -3.132146e-03
[483,] -4.836677e-02 -6.077138e-02 -4.802265e-02 -2.017598e-02
[484,] -6.045000e-03 -3.615100e-02 2.256619e-02 -3.505473e-03
[485,] -1.492059e-02 -4.809589e-03 -3.130675e-02 -1.101080e-03
[486,] -1.606335e-02 -6.266873e-02 5.170091e-02 -7.687562e-03
[487,] -3.698408e-02 -2.188976e-02 -9.713973e-03 8.683240e-03
[488,] -2.629546e-02 -6.007535e-02 -3.906966e-02 7.632136e-03
[489,] -3.830816e-02 -1.488244e-02 -2.736894e-03 -1.726482e-03
[490,] -8.957217e-02 5.080250e-02 -5.585287e-02 -1.568902e-02
[491,] -5.733182e-03 -9.956114e-03 7.966596e-03 -2.692559e-03
[492,] -4.387702e-02 -1.402409e-02 -5.661580e-02 5.615252e-03
[493,] -5.462598e-02 4.552289e-02 6.241694e-02 -4.248524e-03
[494,] -3.193835e-02 -2.558365e-02 1.905417e-03 2.399014e-03
[495,] -3.339690e-02 4.831719e-02 9.941972e-03 -1.270186e-02
[496,] -7.985035e-03 -2.060099e-02 4.985037e-03 -2.938623e-03
[497,] -8.988853e-03 3.397693e-02 2.804638e-03 -6.084407e-03
[498,] -2.202186e-02 -3.915148e-02 2.839721e-03 -3.902339e-03
$variance_explained
PC variance_explained
1 PC1 9.534876e+01
2 PC2 2.912731e+00
3 PC3 1.738511e+00
4 PC4 1.510939e-30
can prepare pca with log transform
Code
prepare_pca(df = test_count_matrix[3:6], log_transform = T)
Output
$data
Standard deviations (1, .., p=4):
[1] 1.6429460 0.5557668 0.3476552 0.3018909
Rotation (n x k) = (4 x 4):
PC1 PC2 PC3 PC4
T0_- -0.4557836 -0.8892568 -0.03850871 -0.0008873807
T3_A -0.4798683 0.2626174 -0.40172521 0.7344218120
T3_B -0.5236962 0.2875918 -0.42714101 -0.6786632635
T3_C -0.5364048 0.2398863 0.80912576 0.0063237126
$variance_explained
PC variance_explained
1 PC1 83.824392
2 PC2 9.591995
3 PC3 3.753369
4 PC4 2.830244
can plot pca
Code
p$data
Output
PC1 PC2 PC3 PC4 PC5
T0_- -33.62613183 -6.439070 0.7232680 0.4286996 -3.5860350
T3_A -0.21900736 -9.401945 -0.4013321 -1.0314620 0.4772895
T3_B 14.57571048 -11.002677 -1.4252431 0.9706678 0.9382381
T3_C 9.69563648 -10.394493 -0.9529347 0.3893537 -1.1364381
T18_A -0.85395841 7.365705 1.0010557 17.8694881 2.1329670
T18_B 0.09028665 5.103602 -7.4847275 -2.9933557 13.2505468
T18_C -4.35851802 4.945270 -0.7934075 -6.3873665 5.8065618
T18_A_Starved 8.08879125 6.198627 -9.2802264 -0.2555649 -12.0908182
T18_B_Starved -0.43986752 10.177639 0.5057274 -6.5955674 -5.5316478
T18_C_Starved 7.04705828 3.447342 18.1078202 -2.3948928 -0.2606642
PC6 PC7 PC8 PC9 PC10
T0_- 2.2636988 -1.6046747 -1.6375648 2.10273388 1.125142e-14
T3_A -0.8727215 -1.1261056 8.0739865 -5.48778331 8.735200e-15
T3_B -2.4099736 -0.1187338 1.5396611 7.89418460 7.202572e-15
T3_C -3.0574301 0.9170718 -7.7374868 -4.59650194 1.505393e-14
T18_A -3.2147517 1.4402947 0.4969632 -0.46250920 1.333113e-14
T18_B 5.1641489 -7.7415508 -1.2311043 -0.15208017 1.286818e-14
T18_C -1.5394861 14.0452857 0.2371402 0.29894270 1.474515e-14
T18_A_Starved 9.4109694 1.4096994 0.4248301 -0.07558311 1.113692e-14
T18_B_Starved -12.7069309 -5.5116097 0.1887208 0.37825982 1.714601e-14
T18_C_Starved 6.9624769 -1.7096770 -0.3551460 0.10033674 1.421259e-14
Code
p$layers
Output
[[1]]
mapping: x = ~get(pc_x), y = ~get(pc_y)
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
can plot pca with color
Code
p$data
Output
PC1 PC2 PC3 PC4 PC5
T0_- -33.62613183 -6.439070 0.7232680 0.4286996 -3.5860350
T3_A -0.21900736 -9.401945 -0.4013321 -1.0314620 0.4772895
T3_B 14.57571048 -11.002677 -1.4252431 0.9706678 0.9382381
T3_C 9.69563648 -10.394493 -0.9529347 0.3893537 -1.1364381
T18_A -0.85395841 7.365705 1.0010557 17.8694881 2.1329670
T18_B 0.09028665 5.103602 -7.4847275 -2.9933557 13.2505468
T18_C -4.35851802 4.945270 -0.7934075 -6.3873665 5.8065618
T18_A_Starved 8.08879125 6.198627 -9.2802264 -0.2555649 -12.0908182
T18_B_Starved -0.43986752 10.177639 0.5057274 -6.5955674 -5.5316478
T18_C_Starved 7.04705828 3.447342 18.1078202 -2.3948928 -0.2606642
PC6 PC7 PC8 PC9 PC10
T0_- 2.2636988 -1.6046747 -1.6375648 2.10273388 1.125142e-14
T3_A -0.8727215 -1.1261056 8.0739865 -5.48778331 8.735200e-15
T3_B -2.4099736 -0.1187338 1.5396611 7.89418460 7.202572e-15
T3_C -3.0574301 0.9170718 -7.7374868 -4.59650194 1.505393e-14
T18_A -3.2147517 1.4402947 0.4969632 -0.46250920 1.333113e-14
T18_B 5.1641489 -7.7415508 -1.2311043 -0.15208017 1.286818e-14
T18_C -1.5394861 14.0452857 0.2371402 0.29894270 1.474515e-14
T18_A_Starved 9.4109694 1.4096994 0.4248301 -0.07558311 1.113692e-14
T18_B_Starved -12.7069309 -5.5116097 0.1887208 0.37825982 1.714601e-14
T18_C_Starved 6.9624769 -1.7096770 -0.3551460 0.10033674 1.421259e-14
color
T0_- T0
T3_A T3
T3_B T3
T3_C T3
T18_A T18
T18_B T18
T18_C T18
T18_A_Starved T18_Starved
T18_B_Starved T18_Starved
T18_C_Starved T18_Starved
Code
p$layers
Output
[[1]]
mapping: x = ~get(pc_x), y = ~get(pc_y), colour = ~color
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
can plot pca with shape
Code
p$data
Output
PC1 PC2 PC3 PC4 PC5
T0_- -33.62613183 -6.439070 0.7232680 0.4286996 -3.5860350
T3_A -0.21900736 -9.401945 -0.4013321 -1.0314620 0.4772895
T3_B 14.57571048 -11.002677 -1.4252431 0.9706678 0.9382381
T3_C 9.69563648 -10.394493 -0.9529347 0.3893537 -1.1364381
T18_A -0.85395841 7.365705 1.0010557 17.8694881 2.1329670
T18_B 0.09028665 5.103602 -7.4847275 -2.9933557 13.2505468
T18_C -4.35851802 4.945270 -0.7934075 -6.3873665 5.8065618
T18_A_Starved 8.08879125 6.198627 -9.2802264 -0.2555649 -12.0908182
T18_B_Starved -0.43986752 10.177639 0.5057274 -6.5955674 -5.5316478
T18_C_Starved 7.04705828 3.447342 18.1078202 -2.3948928 -0.2606642
PC6 PC7 PC8 PC9 PC10
T0_- 2.2636988 -1.6046747 -1.6375648 2.10273388 1.125142e-14
T3_A -0.8727215 -1.1261056 8.0739865 -5.48778331 8.735200e-15
T3_B -2.4099736 -0.1187338 1.5396611 7.89418460 7.202572e-15
T3_C -3.0574301 0.9170718 -7.7374868 -4.59650194 1.505393e-14
T18_A -3.2147517 1.4402947 0.4969632 -0.46250920 1.333113e-14
T18_B 5.1641489 -7.7415508 -1.2311043 -0.15208017 1.286818e-14
T18_C -1.5394861 14.0452857 0.2371402 0.29894270 1.474515e-14
T18_A_Starved 9.4109694 1.4096994 0.4248301 -0.07558311 1.113692e-14
T18_B_Starved -12.7069309 -5.5116097 0.1887208 0.37825982 1.714601e-14
T18_C_Starved 6.9624769 -1.7096770 -0.3551460 0.10033674 1.421259e-14
shape
T0_- T0
T3_A T3
T3_B T3
T3_C T3
T18_A T18
T18_B T18
T18_C T18
T18_A_Starved T18_Starved
T18_B_Starved T18_Starved
T18_C_Starved T18_Starved
Code
p$layers
Output
[[1]]
mapping: x = ~get(pc_x), y = ~get(pc_y), shape = ~shape
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
can plot pca with color and shape
Code
p$data
Output
PC1 PC2 PC3 PC4 PC5
T0_- -33.62613183 -6.439070 0.7232680 0.4286996 -3.5860350
T3_A -0.21900736 -9.401945 -0.4013321 -1.0314620 0.4772895
T3_B 14.57571048 -11.002677 -1.4252431 0.9706678 0.9382381
T3_C 9.69563648 -10.394493 -0.9529347 0.3893537 -1.1364381
T18_A -0.85395841 7.365705 1.0010557 17.8694881 2.1329670
T18_B 0.09028665 5.103602 -7.4847275 -2.9933557 13.2505468
T18_C -4.35851802 4.945270 -0.7934075 -6.3873665 5.8065618
T18_A_Starved 8.08879125 6.198627 -9.2802264 -0.2555649 -12.0908182
T18_B_Starved -0.43986752 10.177639 0.5057274 -6.5955674 -5.5316478
T18_C_Starved 7.04705828 3.447342 18.1078202 -2.3948928 -0.2606642
PC6 PC7 PC8 PC9 PC10
T0_- 2.2636988 -1.6046747 -1.6375648 2.10273388 1.125142e-14
T3_A -0.8727215 -1.1261056 8.0739865 -5.48778331 8.735200e-15
T3_B -2.4099736 -0.1187338 1.5396611 7.89418460 7.202572e-15
T3_C -3.0574301 0.9170718 -7.7374868 -4.59650194 1.505393e-14
T18_A -3.2147517 1.4402947 0.4969632 -0.46250920 1.333113e-14
T18_B 5.1641489 -7.7415508 -1.2311043 -0.15208017 1.286818e-14
T18_C -1.5394861 14.0452857 0.2371402 0.29894270 1.474515e-14
T18_A_Starved 9.4109694 1.4096994 0.4248301 -0.07558311 1.113692e-14
T18_B_Starved -12.7069309 -5.5116097 0.1887208 0.37825982 1.714601e-14
T18_C_Starved 6.9624769 -1.7096770 -0.3551460 0.10033674 1.421259e-14
color shape
T0_- T0 T0
T3_A T3 T3
T3_B T3 T3
T3_C T3 T3
T18_A T18 T18
T18_B T18 T18
T18_C T18 T18
T18_A_Starved T18_Starved T18
T18_B_Starved T18_Starved T18
T18_C_Starved T18_Starved T18
Code
p$layers
Output
[[1]]
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.
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can prepare pca
Code
prepare_pca(df = test_count_matrix[3:6])
Output
$data
Standard deviations (1, .., p=4):
[1] 218.22860 81.12065 33.51049 25.88166
Rotation (n x k) = (4 x 4):
PC1 PC2 PC3 PC4
T0_- -0.8423279 -0.5387762 0.013514466 -0.004613692
T3_A -0.3503926 0.5671455 0.641227641 -0.379997505
T3_B -0.2739171 0.4206085 -0.009173189 0.864854762
T3_C -0.3044309 0.4595157 -0.767176854 -0.328034833
$variance_explained
PC variance_explained
1 PC1 85.046773
2 PC2 11.751608
3 PC3 2.005378
4 PC4 1.196241
can prepare pca with scaling
Code
prepare_pca(df = test_count_matrix[3:6], scaled = T)
Output
$data
Standard deviations (1, .., p=4):
[1] 1.8290114 0.6218325 0.3945069 0.3352696
Rotation (n x k) = (4 x 4):
PC1 PC2 PC3 PC4
T0_- -0.4553397 -0.8900893 -0.01886846 -0.007123416
T3_A -0.5140102 0.2700273 -0.55776245 0.593110301
T3_B -0.5171755 0.2754655 -0.21950875 -0.780041125
T3_C -0.5108706 0.2427860 0.80022556 0.199261814
$variance_explained
PC variance_explained
1 PC1 83.632072
2 PC2 9.666893
3 PC3 3.890893
4 PC4 2.810142
can prepare pca with transform
Code
prepare_pca(df = test_count_matrix[3:6], transform = T)
Output
$data
Standard deviations (1, .., p=4):
[1] 2.732481e+03 4.775840e+02 3.689677e+02 3.439720e-13
Rotation (n x k) = (498 x 4):
PC1 PC2 PC3 PC4
[1,] -6.312612e-02 1.828884e-02 4.732036e-02 8.825290e-01
[2,] -1.540520e-02 -7.086642e-02 4.699002e-02 3.068933e-01
[3,] -3.957768e-02 -1.183371e-01 4.188281e-02 2.233352e-01
[4,] -3.214614e-02 -4.537490e-02 7.243763e-02 -6.400365e-03
[5,] -6.938214e-03 -6.560316e-02 -1.288658e-02 9.446512e-03
[6,] -1.777424e-02 5.330689e-02 3.921640e-02 -1.110433e-02
[7,] -8.951885e-02 -1.950371e-02 -8.877509e-02 9.225551e-03
[8,] -4.482429e-02 7.258838e-02 4.431838e-02 1.093555e-02
[9,] -3.309397e-02 2.029137e-02 1.392982e-02 -1.031638e-02
[10,] -8.556100e-02 3.284823e-02 -1.565225e-02 3.534297e-03
[11,] -1.748502e-02 -7.665229e-02 -8.047520e-04 -9.135440e-04
[12,] -2.080069e-04 -7.202347e-02 -4.836932e-02 1.850834e-03
[13,] -3.420846e-02 -4.093458e-03 4.581830e-02 -1.593698e-02
[14,] 2.624416e-03 -3.390809e-02 -3.994736e-02 4.259657e-03
[15,] -3.112586e-02 -7.814918e-03 2.415454e-02 -9.658904e-03
[16,] -2.309372e-02 -3.034630e-02 -1.857048e-02 1.085345e-02
[17,] -5.865665e-02 -5.299706e-02 2.744350e-02 -1.459890e-02
[18,] -3.543211e-02 -7.708076e-02 -5.326167e-02 -1.347050e-03
[19,] -4.038980e-02 6.248892e-02 -1.141207e-02 -1.193103e-02
[20,] -4.891850e-02 -6.726534e-02 9.025462e-02 -2.297290e-02
[21,] 5.664776e-05 -1.260434e-01 1.028370e-01 -2.422920e-02
[22,] -3.089657e-02 1.676419e-02 -5.640369e-02 5.716813e-03
[23,] -6.833143e-03 3.733575e-03 1.206621e-03 -2.488551e-03
[24,] -4.784317e-02 -5.853481e-02 5.602155e-03 2.021375e-03
[25,] -1.630722e-03 -7.585054e-02 3.283900e-02 -8.197578e-03
[26,] -1.597661e-02 -1.618607e-02 6.710222e-06 1.341768e-03
[27,] -2.560882e-02 1.743351e-02 2.400182e-02 -1.109032e-02
[28,] -3.734785e-02 -5.266493e-02 -1.997084e-02 -2.313047e-02
[29,] -7.059994e-03 -6.624292e-02 1.754160e-02 -1.186180e-03
[30,] -1.104333e-01 1.068366e-01 7.377178e-02 -2.483492e-03
[31,] -2.667432e-02 2.975190e-02 -2.176578e-02 -1.087562e-02
[32,] -7.055934e-02 -1.391863e-02 -6.516461e-02 -1.846219e-02
[33,] -1.643311e-02 -1.256770e-02 -1.443025e-02 4.987450e-03
[34,] -1.494780e-02 -8.794791e-03 1.336786e-02 -1.012285e-03
[35,] -5.693646e-02 5.807056e-02 1.839586e-02 -4.223290e-03
[36,] -3.541844e-02 -2.393489e-02 4.072977e-02 -3.876576e-03
[37,] -1.056079e-02 -2.670732e-02 4.021422e-02 -1.677647e-03
[38,] -5.741585e-03 -2.366006e-02 -4.769311e-03 -1.127072e-03
[39,] -2.590281e-02 4.046387e-02 6.492245e-02 3.254225e-03
[40,] -2.075440e-02 -2.044729e-02 -7.897870e-04 6.520001e-03
[41,] -5.214033e-02 1.209627e-02 -6.894807e-03 -1.462630e-02
[42,] -2.749920e-02 7.114683e-03 9.845494e-03 -8.986598e-03
[43,] -4.864495e-02 8.965257e-03 -2.516807e-02 -1.678366e-02
[44,] -3.781367e-02 1.153702e-02 2.200027e-02 -1.038102e-02
[45,] -4.890342e-02 2.666947e-02 5.695231e-03 1.741934e-02
[46,] -6.040728e-02 5.688180e-02 1.072743e-01 3.131736e-03
[47,] -3.047595e-02 -6.591744e-02 4.832229e-02 1.040586e-02
[48,] -5.635674e-02 -7.901073e-02 8.121881e-03 5.289951e-03
[49,] -9.763905e-02 -2.631455e-02 -4.303934e-02 3.776157e-02
[50,] -3.179084e-02 -4.217708e-02 -8.541190e-02 2.706215e-03
[51,] -1.543858e-02 1.109722e-03 3.686443e-02 -4.562293e-03
[52,] -3.113861e-02 1.093086e-02 4.476826e-02 -7.199986e-03
[53,] -5.696627e-03 -2.690888e-02 3.415335e-02 6.721439e-04
[54,] -2.864619e-02 -2.725329e-02 -3.024180e-02 -2.252121e-03
[55,] -6.502069e-03 -2.150499e-02 -1.674955e-02 4.296213e-03
[56,] -1.641802e-02 -2.663657e-02 1.448872e-02 7.544101e-04
[57,] -7.237063e-02 4.207408e-02 7.323077e-03 -2.029387e-02
[58,] -2.297522e-02 -1.211669e-03 1.330126e-02 -5.757474e-03
[59,] -4.792596e-02 2.612459e-02 1.178491e-02 -1.918985e-03
[60,] -2.044904e-02 1.266306e-02 -4.545472e-03 -6.060721e-03
[61,] -2.363222e-02 -1.359915e-02 -1.021883e-01 4.245837e-03
[62,] -4.502862e-03 -4.387247e-03 -4.039799e-03 2.900829e-04
[63,] -1.491981e-02 -3.250619e-03 -1.479585e-02 7.921967e-04
[64,] -2.685595e-03 -1.078122e-01 -5.604804e-02 1.067741e-02
[65,] -6.262641e-02 3.683284e-02 3.333741e-02 2.101961e-03
[66,] 1.067225e-03 2.915837e-02 4.232044e-02 -2.839610e-03
[67,] -4.844707e-02 2.580802e-02 1.391249e-02 -6.990143e-03
[68,] -7.442851e-03 -7.225809e-03 -2.582764e-02 1.669868e-03
[69,] -3.841762e-02 -2.599724e-02 -1.158152e-02 1.867376e-02
[70,] -1.452113e-02 -4.900542e-02 4.590220e-02 -1.211060e-03
[71,] -1.393558e-02 2.489095e-02 -4.979933e-02 2.863988e-03
[72,] -1.222015e-02 -4.414236e-03 -2.255263e-02 -1.852338e-03
[73,] -1.586680e-02 4.758438e-03 6.703153e-03 -4.447361e-04
[74,] -1.386712e-02 6.092282e-02 1.580476e-01 -9.449121e-03
[75,] -3.479929e-02 -9.428059e-03 -5.321405e-02 3.588147e-03
[76,] -9.781339e-02 7.835485e-02 1.427098e-03 1.093746e-02
[77,] 8.546662e-03 -4.598640e-02 -4.833527e-03 -4.959006e-04
[78,] -2.966412e-02 1.442336e-02 -1.050950e-02 -4.341713e-03
[79,] -3.118120e-02 2.652836e-02 4.808451e-02 -4.154429e-03
[80,] -1.459305e-02 1.163231e-02 -6.696172e-03 -1.775277e-03
[81,] -1.426710e-02 1.728451e-02 -7.813605e-03 -4.282879e-03
[82,] -9.683183e-03 2.069149e-03 4.997030e-02 -1.233796e-03
[83,] -1.489966e-02 -6.355378e-02 1.187196e-02 -9.106478e-04
[84,] -4.880931e-02 -9.520976e-03 4.397121e-02 -8.838806e-03
[85,] -1.874924e-02 -5.843354e-02 3.969319e-02 -1.008458e-02
[86,] -8.898412e-03 -3.086572e-02 -1.444690e-02 4.370363e-03
[87,] -2.041227e-02 -2.514705e-02 4.866825e-02 -7.203582e-03
[88,] -5.566186e-02 8.757350e-03 -8.495471e-02 1.702433e-02
[89,] -5.637458e-02 -2.170242e-02 3.828055e-02 -2.285379e-03
[90,] -1.971857e-02 2.444846e-03 -8.788620e-03 -9.582356e-03
[91,] -2.194073e-02 -2.294826e-03 -6.923952e-04 3.388832e-03
[92,] -1.214884e-02 -6.169609e-02 1.246075e-02 -3.751012e-03
[93,] -2.971130e-02 4.221220e-02 4.181805e-02 4.818582e-03
[94,] -3.035320e-02 -1.768813e-02 -9.357736e-03 7.485960e-03
[95,] -2.192053e-02 -1.381048e-02 -2.400702e-02 2.140439e-03
[96,] -1.193357e-02 -2.700296e-02 -6.806616e-02 3.746697e-03
[97,] -2.241590e-02 8.285377e-03 4.850086e-02 1.723588e-03
[98,] -3.136043e-02 3.469761e-02 7.993695e-02 -9.034507e-03
[99,] -1.947151e-03 -2.296614e-02 2.566020e-02 -1.907733e-03
[100,] -1.111037e-01 4.966286e-02 3.210062e-02 -1.881561e-02
[101,] -2.569543e-03 1.637901e-04 4.652086e-03 -1.526052e-03
[102,] -2.323466e-02 -1.041866e-01 -2.045816e-02 6.218260e-04
[103,] -2.307241e-02 -7.158902e-02 1.516625e-02 2.128100e-03
[104,] -6.080119e-02 6.191613e-02 3.188570e-02 -1.136081e-02
[105,] -3.023765e-02 -6.443423e-02 3.347982e-02 5.686602e-03
[106,] -9.372036e-02 1.038309e-02 -2.268048e-02 -2.682249e-02
[107,] -2.676843e-02 -4.206133e-02 5.343659e-02 -1.723435e-04
[108,] -7.244495e-02 8.122125e-02 8.973766e-02 -7.497122e-03
[109,] -1.305168e-03 -5.425584e-02 5.768695e-03 3.351603e-04
[110,] 5.587640e-03 -1.824887e-02 3.762176e-03 2.237617e-03
[111,] 1.154212e-03 -1.210426e-02 8.844292e-02 -6.014422e-03
[112,] -1.851503e-02 -1.107758e-01 -1.394103e-02 6.828945e-03
[113,] -5.997968e-02 1.694335e-02 -7.418846e-03 -8.179328e-03
[114,] -5.293605e-02 1.406366e-02 3.621677e-03 -1.455444e-02
[115,] -8.571378e-03 1.194735e-02 -2.930269e-02 -8.991941e-04
[116,] -5.696341e-03 -3.242270e-02 4.659274e-02 -3.269346e-03
[117,] -1.672725e-02 -6.134014e-02 9.835419e-02 -1.957479e-03
[118,] -8.124886e-02 3.313667e-02 -6.583330e-02 3.922675e-02
[119,] -3.558151e-02 -6.576321e-02 -4.111754e-03 -1.128614e-02
[120,] -5.216732e-02 -1.192798e-01 8.327059e-03 -8.365020e-03
[121,] -1.024293e-01 -9.672053e-03 -1.807651e-02 1.266986e-02
[122,] -3.287871e-02 -1.957521e-02 1.148641e-02 8.209290e-03
[123,] -8.437919e-02 -3.085894e-02 -7.320048e-02 -7.531646e-03
[124,] -1.279990e-02 -2.265401e-02 -1.877593e-02 -1.000213e-03
[125,] -4.901654e-03 -2.276348e-02 -1.678278e-04 4.808312e-04
[126,] -4.248618e-02 1.463944e-02 1.050126e-01 -1.450264e-02
[127,] -6.031026e-03 -2.049281e-02 -5.566195e-03 -2.615596e-04
[128,] -2.595227e-02 -3.528600e-02 3.943811e-03 -6.154860e-03
[129,] -4.759509e-02 -1.170059e-02 2.196627e-03 2.822998e-03
[130,] -5.055345e-02 2.802459e-02 1.378974e-02 -5.456092e-04
[131,] -1.866795e-02 1.678194e-02 -3.078759e-04 -1.378224e-03
[132,] -3.261158e-02 -3.676107e-02 1.309220e-02 -4.771305e-04
[133,] -5.439757e-02 -1.021215e-01 -2.656188e-02 -4.819435e-03
[134,] -2.356935e-02 -1.916713e-02 1.925748e-02 -5.308268e-03
[135,] -3.079070e-02 2.077196e-02 4.499012e-02 -6.710611e-03
[136,] -5.708655e-02 4.972869e-02 7.184215e-02 -2.231945e-02
[137,] -1.019425e-01 4.847508e-02 -3.847270e-02 4.258721e-03
[138,] -1.832155e-02 -2.267113e-03 -5.006751e-03 -5.631770e-03
[139,] -3.664292e-02 3.806276e-04 -1.108760e-02 -1.630553e-02
[140,] -8.094367e-03 -1.028729e-03 -3.303475e-02 -5.069801e-04
[141,] -6.594732e-02 3.907109e-02 6.984365e-02 -9.476470e-04
[142,] -6.668858e-02 5.668065e-02 -1.628287e-02 1.208773e-02
[143,] -4.206499e-03 -1.506893e-02 -2.721529e-03 1.077550e-04
[144,] -8.558673e-02 -2.300817e-02 -5.063769e-02 -3.403871e-02
[145,] -3.318418e-02 -4.225689e-02 1.728612e-03 7.763194e-03
[146,] -9.203687e-02 6.660068e-02 1.394894e-02 1.927595e-02
[147,] -1.070692e-01 2.789893e-02 -5.492786e-02 3.706702e-02
[148,] -2.749150e-02 1.159219e-03 2.687778e-02 -1.870916e-02
[149,] -5.926400e-02 -1.816379e-02 7.253285e-03 7.383675e-03
[150,] -3.697872e-02 -3.252213e-02 -4.221438e-02 -5.228358e-03
[151,] -1.227120e-02 -1.786422e-02 -1.738471e-02 7.018426e-04
[152,] -3.894960e-02 -2.292149e-03 4.932718e-02 1.636273e-04
[153,] -3.450812e-02 -4.562512e-03 -2.046947e-02 2.212597e-03
[154,] -6.529797e-02 3.311195e-02 2.644397e-02 -8.001824e-03
[155,] -5.712193e-03 -5.335677e-02 3.655773e-02 -4.777872e-03
[156,] -8.283663e-02 -8.192563e-02 -3.063881e-03 -8.565499e-04
[157,] -2.804421e-02 -1.801020e-02 -1.294603e-02 3.494853e-03
[158,] -9.783153e-02 2.697166e-02 -3.003954e-02 2.813617e-02
[159,] -3.583827e-02 2.686174e-02 -1.209046e-02 1.035043e-02
[160,] 2.394258e-03 -8.501765e-03 -3.210216e-02 3.065908e-03
[161,] -3.244973e-02 1.177902e-02 2.276373e-02 -1.923711e-02
[162,] -6.455655e-02 5.386121e-02 7.610154e-02 -1.030458e-02
[163,] -6.320660e-02 2.686380e-02 1.845503e-02 -8.238160e-04
[164,] -3.899459e-02 -6.715099e-03 1.769832e-02 6.902570e-04
[165,] -5.180516e-02 -6.585041e-02 -4.253894e-02 -2.525613e-04
[166,] 9.186178e-03 -3.955050e-02 4.679200e-02 -2.076545e-03
[167,] -4.558742e-03 -2.590427e-02 6.580111e-02 -5.199966e-03
[168,] -2.286590e-02 1.266004e-02 1.592620e-02 -3.315910e-03
[169,] -4.071682e-02 -1.376813e-02 3.883857e-02 -2.299513e-02
[170,] -5.164300e-02 9.138117e-02 2.875791e-02 -5.398733e-03
[171,] -6.014745e-03 -7.829477e-03 2.312790e-02 -3.919874e-03
[172,] -1.027898e-02 -8.575575e-03 9.391235e-03 2.915216e-04
[173,] -5.972204e-02 -5.110734e-02 -4.810614e-03 -1.357379e-03
[174,] -2.361763e-03 -5.460467e-02 1.220337e-02 -1.824380e-03
[175,] -1.109603e-02 -6.481199e-03 2.885963e-02 -9.391451e-03
[176,] -2.085691e-02 -3.140476e-02 -1.640682e-02 8.133497e-03
[177,] -3.198990e-02 -4.610643e-02 3.001831e-03 1.913660e-03
[178,] -6.797427e-02 -6.986600e-02 1.315622e-02 -3.223414e-02
[179,] -4.350937e-02 -1.509968e-02 -9.107386e-02 -6.658656e-03
[180,] -1.027952e-01 -3.253752e-02 -8.623396e-02 -2.995532e-02
[181,] 1.412810e-02 4.054313e-03 -4.857776e-02 5.333931e-03
[182,] -1.527361e-02 -1.720390e-02 2.070499e-02 1.015362e-03
[183,] -4.371945e-02 7.749547e-03 4.990130e-02 -1.593786e-02
[184,] 1.001995e-02 3.863466e-03 3.198814e-02 -4.416777e-04
[185,] -2.444499e-02 1.379155e-02 -9.607437e-03 3.918449e-03
[186,] -2.194199e-02 -1.189303e-01 9.220356e-02 -9.458558e-03
[187,] -3.934352e-02 -3.837355e-02 1.662724e-02 -8.024713e-03
[188,] -2.049071e-02 -4.602697e-02 -7.037320e-02 -9.062653e-03
[189,] -6.073740e-02 1.550460e-02 4.879270e-02 -1.864175e-02
[190,] -2.236704e-02 1.430154e-02 1.993675e-05 -1.306738e-03
[191,] -1.184641e-02 -6.335073e-02 -2.301777e-02 7.476655e-04
[192,] -1.497688e-02 -5.149985e-02 5.526993e-02 -7.508763e-03
[193,] -5.593903e-02 -4.733795e-02 -7.504198e-02 -1.586859e-02
[194,] -2.152160e-02 1.808834e-03 -2.165929e-02 6.128455e-03
[195,] -1.698890e-02 9.344372e-03 -3.220171e-04 -4.904276e-03
[196,] -5.595937e-02 4.002420e-02 3.392752e-02 4.874193e-03
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[404,] -4.625607e-02 4.453984e-02 -6.016468e-02 -9.374975e-03
[405,] -2.178641e-02 -9.053372e-02 -2.291831e-02 1.076606e-02
[406,] -7.720799e-02 2.108760e-02 -1.455489e-02 -6.505998e-03
[407,] -6.273839e-02 1.612627e-02 -2.396582e-02 -1.391460e-02
[408,] -2.232631e-02 -4.001581e-02 -6.068855e-03 -2.225132e-04
[409,] -3.936296e-02 4.158902e-02 -1.433695e-02 -1.656674e-02
[410,] -1.087366e-02 -8.239133e-02 6.125838e-02 1.817342e-04
[411,] -7.762519e-02 -3.512382e-03 7.268047e-02 1.107036e-03
[412,] -5.216486e-02 -5.047190e-02 -6.710261e-03 3.786038e-03
[413,] -1.688645e-02 4.958313e-03 2.988260e-02 -6.990672e-03
[414,] -2.849950e-02 -2.110360e-02 7.786997e-03 -1.178633e-02
[415,] -1.063276e-02 1.858688e-02 2.203427e-03 -4.298729e-03
[416,] -3.718529e-02 1.553457e-02 -1.459568e-02 -1.174422e-02
[417,] -6.680531e-02 -6.475310e-02 8.997765e-02 -8.699687e-03
[418,] -1.978828e-02 -3.601715e-02 -7.455370e-02 -7.606844e-04
[419,] -1.713474e-02 -5.446252e-02 4.165601e-02 -1.197809e-02
[420,] -2.179630e-02 -1.892249e-02 8.610978e-03 -2.063002e-03
[421,] -4.544582e-02 6.087251e-03 -3.124612e-02 -7.968048e-03
[422,] -6.083550e-02 6.053051e-02 7.711302e-02 -2.666618e-02
[423,] -3.268555e-02 1.368593e-02 -7.659948e-02 -1.717925e-03
[424,] -1.790135e-02 -2.118306e-03 2.976639e-03 2.606766e-03
[425,] -7.895966e-02 -5.056219e-03 1.524076e-02 -7.847702e-03
[426,] -7.702789e-03 -4.418395e-02 2.821600e-02 -3.741899e-03
[427,] -3.651183e-02 -2.758935e-02 3.663937e-02 1.597299e-03
[428,] 4.122708e-03 4.446700e-02 4.344992e-02 -5.686466e-03
[429,] -5.400188e-02 -5.033559e-02 3.079198e-02 9.057186e-04
[430,] -1.661446e-02 -2.993271e-02 -5.083537e-03 1.100905e-03
[431,] -2.338550e-02 -1.064157e-01 9.183444e-03 -7.699808e-05
[432,] -1.637521e-02 1.146829e-02 -3.988406e-02 8.082053e-04
[433,] 2.093227e-03 -4.208800e-02 7.286710e-02 1.932019e-04
[434,] -3.537604e-02 -1.100327e-02 3.092757e-03 2.387426e-03
[435,] -3.661580e-02 -1.864947e-02 -3.388084e-02 -7.180598e-03
[436,] -2.134794e-02 -8.314661e-03 -1.264344e-02 9.813677e-04
[437,] -5.878444e-02 6.068336e-02 -3.339747e-02 -7.472261e-04
[438,] -5.429675e-02 2.268021e-02 -1.000413e-03 -2.507479e-02
[439,] -2.720793e-02 3.499552e-02 2.070871e-02 5.497973e-04
[440,] -2.389663e-02 -4.879462e-02 1.438008e-02 -9.231296e-03
[441,] -4.328022e-02 -2.267775e-02 2.750114e-02 -2.996724e-03
[442,] -8.451624e-03 -6.449157e-02 -2.603447e-02 -3.857424e-03
[443,] -7.659991e-07 -3.500294e-02 1.888396e-02 -3.505380e-03
[444,] -2.690646e-02 2.539693e-02 1.397515e-01 6.187591e-03
[445,] -3.369152e-02 3.358770e-02 7.596626e-02 -1.352358e-02
[446,] -5.743780e-02 5.450906e-02 -2.145027e-02 -7.239489e-03
[447,] -3.008201e-02 1.127970e-02 3.833359e-02 -3.363307e-03
[448,] -2.418537e-02 -2.596796e-02 9.286824e-03 -3.190293e-03
[449,] -4.159206e-02 3.248049e-03 3.592653e-02 1.059751e-02
[450,] -8.844774e-02 5.089348e-02 7.049905e-04 2.929222e-03
[451,] -3.765697e-02 1.020651e-02 -3.607024e-02 4.602829e-03
[452,] -2.570730e-02 -2.813164e-02 -3.011045e-02 -1.494032e-03
[453,] -1.112428e-02 1.160217e-03 3.729016e-02 -2.126338e-03
[454,] -6.569410e-02 2.304070e-02 -8.496383e-02 1.019605e-02
[455,] -2.061535e-03 -6.516327e-02 1.033699e-01 -1.238998e-02
[456,] -6.885846e-02 2.523523e-02 5.721027e-02 8.301633e-03
[457,] -4.100282e-02 -7.369351e-04 -6.072719e-02 -9.496816e-03
[458,] -7.065030e-02 -7.035409e-02 -1.011705e-01 3.863118e-02
[459,] -5.830450e-02 7.912572e-03 7.267680e-02 -2.355054e-02
[460,] -2.456898e-02 -3.539776e-02 2.019639e-02 -6.569821e-03
[461,] -3.035927e-02 -2.671516e-02 2.743905e-02 -1.582992e-02
[462,] -3.027915e-02 -1.167586e-02 2.305771e-02 -1.117388e-02
[463,] -6.521135e-02 1.546358e-02 3.931978e-02 -7.679907e-03
[464,] -6.307924e-02 -3.986174e-03 -1.744659e-02 7.043012e-03
[465,] -3.171831e-02 4.147859e-02 -1.437467e-03 9.806475e-03
[466,] -8.282001e-02 -2.598861e-02 -1.191283e-02 -1.805805e-03
[467,] -3.296934e-02 -7.631440e-04 7.250069e-02 -9.621228e-04
[468,] -5.993873e-02 1.632836e-02 -6.456417e-02 -4.275273e-03
[469,] -2.012540e-02 -5.324960e-02 1.559411e-02 -1.150920e-02
[470,] -2.355414e-02 3.089503e-02 -1.639357e-02 6.620056e-03
[471,] -4.206828e-02 5.889884e-02 1.348085e-02 -2.513953e-02
[472,] -2.828940e-02 -3.775118e-02 2.947612e-02 -7.215256e-03
[473,] -3.565157e-02 -7.521361e-03 -1.124893e-02 -1.759576e-02
[474,] -9.532648e-03 -1.043933e-01 -4.129662e-02 -5.576737e-03
[475,] -5.130801e-02 -3.259609e-02 3.687652e-02 -1.471237e-02
[476,] -9.266476e-02 -3.413661e-03 -3.725817e-02 -3.018297e-02
[477,] -4.727947e-02 7.439780e-04 -7.792518e-02 -1.667112e-02
[478,] -1.350009e-02 2.355750e-02 -2.126486e-02 7.980522e-03
[479,] -6.179868e-02 -6.875776e-02 3.424548e-02 -1.908315e-02
[480,] -1.903872e-02 -1.374978e-01 1.242736e-01 -1.375474e-02
[481,] -4.517951e-02 -2.032934e-02 -3.885745e-02 -9.513343e-03
[482,] -3.696850e-02 -2.888583e-02 2.327650e-02 -3.132146e-03
[483,] -4.836677e-02 -6.077138e-02 -4.802265e-02 -2.017598e-02
[484,] -6.045000e-03 -3.615100e-02 2.256619e-02 -3.505473e-03
[485,] -1.492059e-02 -4.809589e-03 -3.130675e-02 -1.101080e-03
[486,] -1.606335e-02 -6.266873e-02 5.170091e-02 -7.687562e-03
[487,] -3.698408e-02 -2.188976e-02 -9.713973e-03 8.683240e-03
[488,] -2.629546e-02 -6.007535e-02 -3.906966e-02 7.632136e-03
[489,] -3.830816e-02 -1.488244e-02 -2.736894e-03 -1.726482e-03
[490,] -8.957217e-02 5.080250e-02 -5.585287e-02 -1.568902e-02
[491,] -5.733182e-03 -9.956114e-03 7.966596e-03 -2.692559e-03
[492,] -4.387702e-02 -1.402409e-02 -5.661580e-02 5.615252e-03
[493,] -5.462598e-02 4.552289e-02 6.241694e-02 -4.248524e-03
[494,] -3.193835e-02 -2.558365e-02 1.905417e-03 2.399014e-03
[495,] -3.339690e-02 4.831719e-02 9.941972e-03 -1.270186e-02
[496,] -7.985035e-03 -2.060099e-02 4.985037e-03 -2.938623e-03
[497,] -8.988853e-03 3.397693e-02 2.804638e-03 -6.084407e-03
[498,] -2.202186e-02 -3.915148e-02 2.839721e-03 -3.902339e-03
$variance_explained
PC variance_explained
1 PC1 9.534876e+01
2 PC2 2.912731e+00
3 PC3 1.738511e+00
4 PC4 1.510939e-30
can prepare pca with log transform
Code
prepare_pca(df = test_count_matrix[3:6], log_transform = T)
Output
$data
Standard deviations (1, .., p=4):
[1] 1.6429460 0.5557668 0.3476552 0.3018909
Rotation (n x k) = (4 x 4):
PC1 PC2 PC3 PC4
T0_- -0.4557836 -0.8892568 -0.03850871 -0.0008873807
T3_A -0.4798683 0.2626174 -0.40172521 0.7344218120
T3_B -0.5236962 0.2875918 -0.42714101 -0.6786632635
T3_C -0.5364048 0.2398863 0.80912576 0.0063237126
$variance_explained
PC variance_explained
1 PC1 83.824392
2 PC2 9.591995
3 PC3 3.753369
4 PC4 2.830244
can plot pca
Code
p$data
Output
PC1 PC2 PC3 PC4 PC5
T0_- -33.62613183 -6.439070 0.7232680 0.4286996 -3.5860350
T3_A -0.21900736 -9.401945 -0.4013321 -1.0314620 0.4772895
T3_B 14.57571048 -11.002677 -1.4252431 0.9706678 0.9382381
T3_C 9.69563648 -10.394493 -0.9529347 0.3893537 -1.1364381
T18_A -0.85395841 7.365705 1.0010557 17.8694881 2.1329670
T18_B 0.09028665 5.103602 -7.4847275 -2.9933557 13.2505468
T18_C -4.35851802 4.945270 -0.7934075 -6.3873665 5.8065618
T18_A_Starved 8.08879125 6.198627 -9.2802264 -0.2555649 -12.0908182
T18_B_Starved -0.43986752 10.177639 0.5057274 -6.5955674 -5.5316478
T18_C_Starved 7.04705828 3.447342 18.1078202 -2.3948928 -0.2606642
PC6 PC7 PC8 PC9 PC10
T0_- 2.2636988 -1.6046747 -1.6375648 2.10273388 1.125142e-14
T3_A -0.8727215 -1.1261056 8.0739865 -5.48778331 8.735200e-15
T3_B -2.4099736 -0.1187338 1.5396611 7.89418460 7.202572e-15
T3_C -3.0574301 0.9170718 -7.7374868 -4.59650194 1.505393e-14
T18_A -3.2147517 1.4402947 0.4969632 -0.46250920 1.333113e-14
T18_B 5.1641489 -7.7415508 -1.2311043 -0.15208017 1.286818e-14
T18_C -1.5394861 14.0452857 0.2371402 0.29894270 1.474515e-14
T18_A_Starved 9.4109694 1.4096994 0.4248301 -0.07558311 1.113692e-14
T18_B_Starved -12.7069309 -5.5116097 0.1887208 0.37825982 1.714601e-14
T18_C_Starved 6.9624769 -1.7096770 -0.3551460 0.10033674 1.421259e-14
Code
p$layers
Output
[[1]]
mapping: x = ~get(pc_x), y = ~get(pc_y)
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
can plot pca with color
Code
p$data
Output
PC1 PC2 PC3 PC4 PC5
T0_- -33.62613183 -6.439070 0.7232680 0.4286996 -3.5860350
T3_A -0.21900736 -9.401945 -0.4013321 -1.0314620 0.4772895
T3_B 14.57571048 -11.002677 -1.4252431 0.9706678 0.9382381
T3_C 9.69563648 -10.394493 -0.9529347 0.3893537 -1.1364381
T18_A -0.85395841 7.365705 1.0010557 17.8694881 2.1329670
T18_B 0.09028665 5.103602 -7.4847275 -2.9933557 13.2505468
T18_C -4.35851802 4.945270 -0.7934075 -6.3873665 5.8065618
T18_A_Starved 8.08879125 6.198627 -9.2802264 -0.2555649 -12.0908182
T18_B_Starved -0.43986752 10.177639 0.5057274 -6.5955674 -5.5316478
T18_C_Starved 7.04705828 3.447342 18.1078202 -2.3948928 -0.2606642
PC6 PC7 PC8 PC9 PC10
T0_- 2.2636988 -1.6046747 -1.6375648 2.10273388 1.125142e-14
T3_A -0.8727215 -1.1261056 8.0739865 -5.48778331 8.735200e-15
T3_B -2.4099736 -0.1187338 1.5396611 7.89418460 7.202572e-15
T3_C -3.0574301 0.9170718 -7.7374868 -4.59650194 1.505393e-14
T18_A -3.2147517 1.4402947 0.4969632 -0.46250920 1.333113e-14
T18_B 5.1641489 -7.7415508 -1.2311043 -0.15208017 1.286818e-14
T18_C -1.5394861 14.0452857 0.2371402 0.29894270 1.474515e-14
T18_A_Starved 9.4109694 1.4096994 0.4248301 -0.07558311 1.113692e-14
T18_B_Starved -12.7069309 -5.5116097 0.1887208 0.37825982 1.714601e-14
T18_C_Starved 6.9624769 -1.7096770 -0.3551460 0.10033674 1.421259e-14
color
T0_- T0
T3_A T3
T3_B T3
T3_C T3
T18_A T18
T18_B T18
T18_C T18
T18_A_Starved T18_Starved
T18_B_Starved T18_Starved
T18_C_Starved T18_Starved
Code
p$layers
Output
[[1]]
mapping: x = ~get(pc_x), y = ~get(pc_y), colour = ~color
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
can plot pca with shape
Code
p$data
Output
PC1 PC2 PC3 PC4 PC5
T0_- -33.62613183 -6.439070 0.7232680 0.4286996 -3.5860350
T3_A -0.21900736 -9.401945 -0.4013321 -1.0314620 0.4772895
T3_B 14.57571048 -11.002677 -1.4252431 0.9706678 0.9382381
T3_C 9.69563648 -10.394493 -0.9529347 0.3893537 -1.1364381
T18_A -0.85395841 7.365705 1.0010557 17.8694881 2.1329670
T18_B 0.09028665 5.103602 -7.4847275 -2.9933557 13.2505468
T18_C -4.35851802 4.945270 -0.7934075 -6.3873665 5.8065618
T18_A_Starved 8.08879125 6.198627 -9.2802264 -0.2555649 -12.0908182
T18_B_Starved -0.43986752 10.177639 0.5057274 -6.5955674 -5.5316478
T18_C_Starved 7.04705828 3.447342 18.1078202 -2.3948928 -0.2606642
PC6 PC7 PC8 PC9 PC10
T0_- 2.2636988 -1.6046747 -1.6375648 2.10273388 1.125142e-14
T3_A -0.8727215 -1.1261056 8.0739865 -5.48778331 8.735200e-15
T3_B -2.4099736 -0.1187338 1.5396611 7.89418460 7.202572e-15
T3_C -3.0574301 0.9170718 -7.7374868 -4.59650194 1.505393e-14
T18_A -3.2147517 1.4402947 0.4969632 -0.46250920 1.333113e-14
T18_B 5.1641489 -7.7415508 -1.2311043 -0.15208017 1.286818e-14
T18_C -1.5394861 14.0452857 0.2371402 0.29894270 1.474515e-14
T18_A_Starved 9.4109694 1.4096994 0.4248301 -0.07558311 1.113692e-14
T18_B_Starved -12.7069309 -5.5116097 0.1887208 0.37825982 1.714601e-14
T18_C_Starved 6.9624769 -1.7096770 -0.3551460 0.10033674 1.421259e-14
shape
T0_- T0
T3_A T3
T3_B T3
T3_C T3
T18_A T18
T18_B T18
T18_C T18
T18_A_Starved T18_Starved
T18_B_Starved T18_Starved
T18_C_Starved T18_Starved
Code
p$layers
Output
[[1]]
mapping: x = ~get(pc_x), y = ~get(pc_y), shape = ~shape
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
can plot pca with color and shape
Code
p$data
Output
PC1 PC2 PC3 PC4 PC5
T0_- -33.62613183 -6.439070 0.7232680 0.4286996 -3.5860350
T3_A -0.21900736 -9.401945 -0.4013321 -1.0314620 0.4772895
T3_B 14.57571048 -11.002677 -1.4252431 0.9706678 0.9382381
T3_C 9.69563648 -10.394493 -0.9529347 0.3893537 -1.1364381
T18_A -0.85395841 7.365705 1.0010557 17.8694881 2.1329670
T18_B 0.09028665 5.103602 -7.4847275 -2.9933557 13.2505468
T18_C -4.35851802 4.945270 -0.7934075 -6.3873665 5.8065618
T18_A_Starved 8.08879125 6.198627 -9.2802264 -0.2555649 -12.0908182
T18_B_Starved -0.43986752 10.177639 0.5057274 -6.5955674 -5.5316478
T18_C_Starved 7.04705828 3.447342 18.1078202 -2.3948928 -0.2606642
PC6 PC7 PC8 PC9 PC10
T0_- 2.2636988 -1.6046747 -1.6375648 2.10273388 1.125142e-14
T3_A -0.8727215 -1.1261056 8.0739865 -5.48778331 8.735200e-15
T3_B -2.4099736 -0.1187338 1.5396611 7.89418460 7.202572e-15
T3_C -3.0574301 0.9170718 -7.7374868 -4.59650194 1.505393e-14
T18_A -3.2147517 1.4402947 0.4969632 -0.46250920 1.333113e-14
T18_B 5.1641489 -7.7415508 -1.2311043 -0.15208017 1.286818e-14
T18_C -1.5394861 14.0452857 0.2371402 0.29894270 1.474515e-14
T18_A_Starved 9.4109694 1.4096994 0.4248301 -0.07558311 1.113692e-14
T18_B_Starved -12.7069309 -5.5116097 0.1887208 0.37825982 1.714601e-14
T18_C_Starved 6.9624769 -1.7096770 -0.3551460 0.10033674 1.421259e-14
color shape
T0_- T0 T0
T3_A T3 T3
T3_B T3 T3
T3_C T3 T3
T18_A T18 T18
T18_B T18 T18
T18_C T18 T18
T18_A_Starved T18_Starved T18
T18_B_Starved T18_Starved T18
T18_C_Starved T18_Starved T18
Code
p$layers
Output
[[1]]
geom_point: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
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