Given a Seurat seurat and a data frame where the rows correspond to cells, in the same order as in the Seurat seurat, add two columns giving coordinates in a dimensionality reduced space.
addEmbedding(seurat, df, reduction = "tsne", dim1 = 1, dim2 = 2)
| seurat | Seurat object, where dimensionality reduction has been applied, i.e. (after applying Seurat::RunPCA() or Seurat::RunTSNE() to the object). |
|---|---|
| df | Data frame with at least one column, "Cell", giving the cell ID |
| reduction | String specifying the dimensionality reduction to use, retrieves t-SNE by default. This should match the names of the elements of the list seurat@dr, so it will typically be one of "pca" or "tsne". Default: "tsne" |
df <- data.frame(Cell = rownames(pbmc@meta.data), Cluster = pbmc@meta.data$res.1) addEmbedding(pbmc, df, reduction = "tsne")#> Cell Cluster tSNE_1 tSNE_2 #> 1 ATGCCAGAACGACT 0 14.421908279 8.3360216 #> 2 CATGGCCTGTGCAT 0 16.723770814 11.2549069 #> 3 GAACCTGATGAACC 0 0.908030298 21.2748866 #> 4 TGACTGGATTCTCA 0 -12.271303667 8.6030550 #> 5 AGTCAGACTGCACA 0 16.201709739 11.9711820 #> 6 TCTGATACACGTGT 0 -1.503498217 26.5058488 #> 7 TGGTATCTAAACAG 0 3.196139126 26.8241782 #> 8 GCAGCTCTGTTTCT 0 3.041964808 25.6720057 #> 9 GATATAACACGCAT 0 -0.332479188 26.7644197 #> 10 AATGTTGACAGTCA 0 1.243669881 22.3781207 #> 11 AGGTCATGAGTGTC 0 -13.680731501 31.5102633 #> 12 AGAGATGATCTCGC 0 -6.293455087 28.1804780 #> 13 GGGTAACTCTAGTG 0 -12.790928570 32.0014392 #> 14 CATGAGACACGGGA 0 -4.331897062 26.7160161 #> 15 TACGCCACTCCGAA 1 -11.759544327 29.8174179 #> 16 CTAAACCTGTGCAT 1 -12.733136620 29.2751380 #> 17 GTAAGCACTCATTC 0 -8.248354895 29.6684085 #> 18 TTGGTACTGAATCC 0 -9.498695771 33.2646927 #> 19 CATCATACGGAGCA 1 -0.123897970 7.3137891 #> 20 TACATCACGCTAAC 0 -8.761689191 31.8784827 #> 21 TTACCATGAATCGC 1 11.267524801 -7.7502193 #> 22 ATAGGAGAAACAGA 1 10.830642792 -1.6648856 #> 23 GCGCACGACTTTAC 1 12.126009055 -4.1942573 #> 24 ACTCGCACGAAAGT 1 10.518837726 -2.8920338 #> 25 ATTACCTGCCTTAT 1 10.812888644 -5.3162386 #> 26 CCCAACTGCAATCG 1 11.641561769 -11.7115868 #> 27 AAATTCGAATCACG 1 11.029848830 -10.7859849 #> 28 CCATCCGATTCGCC 1 0.524525437 2.6680775 #> 29 TCCACTCTGAGCTT 1 2.842385660 -6.7659340 #> 30 CATCAGGATGCACA 0 1.765949332 13.7652065 #> 31 CTAAACCTCTGACA 2 -13.769229712 -0.9654148 #> 32 GATAGAGAAGGGTG 1 0.291315721 -1.4997801 #> 33 CTAACGGAACCGAT 2 -19.823177661 -7.6726257 #> 34 AGATATACCCGTAA 2 -16.412599106 -2.9953991 #> 35 TACTCTGAATCGAC 2 -21.290385096 -12.0934748 #> 36 GCGCATCTTGCTCC 2 -16.366509204 -1.5806007 #> 37 GTTGACGATATCGG 2 -19.154132197 -9.1918960 #> 38 ACAGGTACTGGTGT 2 -18.668051691 -10.6042361 #> 39 GGCATATGCTTATC 2 -19.815841785 -11.0518872 #> 40 CATTACACCAACTG 2 -19.525030175 -13.4461417 #> 41 TAGGGACTGAACTC 1 19.818541617 -0.7697982 #> 42 GCTCCATGAGAAGT 0 -3.227278554 17.5278759 #> 43 TACAATGATGCTAG 0 -1.563300862 17.8771146 #> 44 CTTCATGACCGAAT 0 -13.838199504 6.7204449 #> 45 CTGCCAACAGGAGC 0 -12.983243619 7.2517782 #> 46 TTGCATTGAGCTAC 0 2.966270149 13.5316278 #> 47 AAGCAAGAGCTTAG 2 -15.264921694 -2.2315300 #> 48 CGGCACGAACTCAG 0 -2.511786042 18.7598190 #> 49 GGTGGAGATTACTC 2 -13.718933190 4.5965815 #> 50 GGCCGATGTACTCT 0 1.611568997 27.1503153 #> 51 CGTAGCCTGTATGC 1 12.325827568 -9.9448526 #> 52 TGAGCTGAATGCTG 0 -0.003217834 15.5313851 #> 53 CCTATAACGAGACG 1 0.480240876 1.6813063 #> 54 ATAAGTTGGTACGT 1 0.516931555 4.9550165 #> 55 AAGCGACTTTGACG 0 -0.022527847 8.8484629 #> 56 ACCAGTGAATACCG 1 10.488968602 0.1365850 #> 57 ATTGCACTTGCTTT 2 -11.983627401 -0.6092689 #> 58 CTAGGTGATGGTTG 1 11.333136132 1.9259971 #> 59 GCACTAGACCTTTA 0 13.198956232 7.0309165 #> 60 CATGCGCTAGTCAC 1 4.133553319 2.7933328 #> 61 TTGAGGACTACGCA 1 2.220542569 -2.0733281 #> 62 ATACCACTCTAAGC 0 3.383287311 12.3017264 #> 63 CATATAGACTAAGC 1 4.004630434 0.7702884 #> 64 TTTAGCTGTACTCT 1 11.760652564 4.6291459 #> 65 GACATTCTCCACCT 1 3.443966235 -3.5010797 #> 66 ACGTGATGCCATGA 1 3.129281479 -0.1206174 #> 67 ATTGTAGATTCCCG 1 3.066266235 -4.8967971 #> 68 GATAGAGATCACGA 1 13.595787604 -1.5966398 #> 69 AATGCGTGGACGGA 1 18.760765827 -1.2000304 #> 70 GCGTAAACACGGTT 1 12.328389051 5.5517228 #> 71 ATTCAGCTCATTGG 3 6.441959517 -51.6852111 #> 72 GGCATATGGGGAGT 3 2.479364626 -50.9310316 #> 73 ATCATCTGACACCA 3 4.957757342 -54.9005134 #> 74 GTCATACTTCGCCT 3 5.936833536 -50.5698921 #> 75 TTACGTACGTTCAG 3 4.199273262 -50.3082081 #> 76 GAGTTGTGGTAGCT 3 6.349423075 -55.7263336 #> 77 GACGCTCTCTCTCG 3 6.577643443 -48.6447265 #> 78 AGTCTTACTTCGGA 3 3.468797905 -53.1112770 #> 79 GGAACACTTCAGAC 3 5.095322092 -52.2787746 #> 80 CTTGATTGATCTTC 3 4.808983374 -47.9329706