Different Resolution Tables on harmony integration on patient origin and orig.ident-theta-0.5,0.5_Annotated_again
Nasir Mahmood Abbasi
2025-01-29
1. load libraries
2. Load Seurat Object
#Load Seurat Object merged from cell lines and a control after filtration
load("0-robj/CD4_T_cells_Harmony_integrated_0.5_Theta_Patient_origin_and_orig_ident_Annotated_again.robj")
3. Harmony Visualization
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "cell_line",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "predicted.celltype.l2",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.1",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.2",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.3",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.4",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.5",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.6",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.7",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.8",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_0.9",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_1",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "harmony_res_1.2",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "predicted.celltype.l1",
label = TRUE,
label.box = TRUE) 
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "predicted.celltype.l2",
label = TRUE,
label.box = TRUE)
DimPlot(All_samples_Merged,
reduction = "umap",
group.by = "predicted.celltype.l3",
label = TRUE,
label.box = TRUE)
4. clusTree
library(clustree)Loading required package: ggraph
Attaching package: 'ggraph'
The following object is masked from 'package:sp':
geometryclustree(All_samples_Merged, prefix = "harmony_res_")
Visualize Harmony Integrated Data distribution
#0.4
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
ASDC 0 0 32 15 0 1 3 0 0
B intermediate 0 0 7 2 1 5 1 5 0
B memory 0 0 2 9 1 2 4 7 0
B naive 0 1 9 36 7 4 8 24 1
CD16 Mono 0 0 1 0 0 0 0 23 0
CD4 CTL 0 0 0 0 0 0 0 11 1
CD4 Naive 0 0 0 0 0 0 0 428 1438
CD4 Proliferating 2393 2809 5218 5349 4431 3872 3884 0 5
CD4 TCM 3372 259 732 519 111 146 290 4603 2041
CD4 TEM 2 0 0 0 0 0 0 64 19
CD8 Proliferating 0 0 0 0 0 1 0 0 0
CD8 TCM 30 1 0 0 0 0 0 0 0
CD8 TEM 0 55 0 0 0 0 0 1 0
cDC2 0 0 257 41 265 697 468 0 0
HSPC 0 0 167 12 1203 259 653 0 0
NK Proliferating 28 2810 3 24 3 161 20 0 0
Platelet 0 0 0 0 0 0 0 5 0table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_0.4)
0 1 2 3 4 5 6 7 8 9 10
ASDC 35 0 0 0 1 0 15 0 0 0 0
B intermediate 6 0 0 1 3 5 6 0 0 0 0
B memory 9 1 6 0 7 1 1 0 0 0 0
B naive 14 3 15 0 24 28 4 0 0 2 0
CD16 Mono 0 0 1 0 0 0 0 0 0 23 0
CD4 CTL 0 0 8 2 1 0 0 0 0 1 0
CD4 Naive 1 0 1819 2 0 43 0 0 0 1 0
CD4 Proliferating 10252 7459 22 2601 1199 1473 938 2072 1944 0 1
CD4 TCM 1511 82 5983 53 1719 1536 1136 4 25 24 0
CD4 TEM 0 0 79 1 0 5 0 0 0 0 0
CD8 Proliferating 0 0 0 0 0 1 0 0 0 0 0
CD8 TCM 2 0 0 0 13 14 2 0 0 0 0
CD8 TEM 18 0 1 8 28 1 0 0 0 0 0
cDC2 333 496 0 1 132 19 710 27 7 2 1
HSPC 214 1277 0 6 51 13 38 695 0 0 0
NK Proliferating 22 151 7 2735 36 70 16 2 10 0 0
Platelet 0 0 0 0 0 0 0 0 0 5 0table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_0.4)
0 1 2 3 4 5 6 7 8 9 10
L1 642 24 17 459 1661 2137 464 1 420 0 0
L2 96 12 7 4686 860 86 11 0 177 0 0
L3 5990 13 0 14 142 106 118 3 41 1 0
L4 5186 10 1 9 75 30 662 0 32 2 0
L5 180 2144 0 51 253 31 414 2742 205 0 2
L6 133 3643 0 62 80 152 510 10 558 0 0
L7 161 3621 0 109 126 64 654 44 552 0 0
PBMC 24 1 4595 19 17 451 31 0 0 33 0
PBMC_10x 5 1 3321 1 0 152 2 0 1 22 0#0.5
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
ASDC 0 0 32 15 0 1 3 0 0
B intermediate 0 0 7 2 1 5 1 5 0
B memory 0 0 2 9 1 2 4 7 0
B naive 0 1 9 36 7 4 8 24 1
CD16 Mono 0 0 1 0 0 0 0 23 0
CD4 CTL 0 0 0 0 0 0 0 11 1
CD4 Naive 0 0 0 0 0 0 0 428 1438
CD4 Proliferating 2393 2809 5218 5349 4431 3872 3884 0 5
CD4 TCM 3372 259 732 519 111 146 290 4603 2041
CD4 TEM 2 0 0 0 0 0 0 64 19
CD8 Proliferating 0 0 0 0 0 1 0 0 0
CD8 TCM 30 1 0 0 0 0 0 0 0
CD8 TEM 0 55 0 0 0 0 0 1 0
cDC2 0 0 257 41 265 697 468 0 0
HSPC 0 0 167 12 1203 259 653 0 0
NK Proliferating 28 2810 3 24 3 161 20 0 0
Platelet 0 0 0 0 0 0 0 5 0table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_0.5)
0 1 2 3 4 5 6 7 8 9 10 11
ASDC 0 30 0 0 13 0 3 0 0 5 0 0
B intermediate 0 3 0 0 8 6 0 0 0 4 0 0
B memory 0 0 6 0 17 1 0 0 0 1 0 0
B naive 0 2 15 6 33 28 0 0 0 4 2 0
CD16 Mono 0 0 1 0 0 0 0 0 0 0 23 0
CD4 CTL 0 0 8 2 1 0 0 0 0 0 1 0
CD4 Naive 0 0 1819 1 1 44 0 0 0 0 1 0
CD4 Proliferating 7248 7630 22 2687 785 1876 2888 1986 2061 777 0 1
CD4 TCM 81 933 5981 160 3096 1559 90 4 27 118 24 0
CD4 TEM 0 0 79 1 0 5 0 0 0 0 0 0
CD8 Proliferating 0 0 0 0 0 1 0 0 0 0 0 0
CD8 TCM 0 1 0 1 14 14 0 0 0 1 0 0
CD8 TEM 0 1 1 8 45 1 0 0 0 0 0 0
cDC2 465 308 0 10 673 22 12 42 8 185 2 1
HSPC 1278 208 0 11 43 13 1 699 2 39 0 0
NK Proliferating 153 1 7 2718 2 109 22 2 20 15 0 0
Platelet 0 0 0 0 0 0 0 0 0 0 5 0table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_0.5)
0 1 2 3 4 5 6 7 8 9 10 11
L1 13 259 17 316 2241 2481 1 1 412 84 0 0
L2 12 63 7 5129 369 159 0 0 190 6 0 0
L3 14 5933 0 17 187 111 51 0 16 98 1 0
L4 4 2205 1 11 488 33 2956 0 35 272 2 0
L5 2058 330 0 47 322 43 4 2687 259 270 0 2
L6 3583 166 0 27 279 163 1 9 596 324 0 0
L7 3538 159 0 36 791 83 0 36 610 78 0 0
PBMC 2 2 4593 22 47 452 3 0 0 17 33 0
PBMC_10x 1 0 3321 0 7 154 0 0 0 0 22 0#0.6
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
ASDC 0 0 32 15 0 1 3 0 0
B intermediate 0 0 7 2 1 5 1 5 0
B memory 0 0 2 9 1 2 4 7 0
B naive 0 1 9 36 7 4 8 24 1
CD16 Mono 0 0 1 0 0 0 0 23 0
CD4 CTL 0 0 0 0 0 0 0 11 1
CD4 Naive 0 0 0 0 0 0 0 428 1438
CD4 Proliferating 2393 2809 5218 5349 4431 3872 3884 0 5
CD4 TCM 3372 259 732 519 111 146 290 4603 2041
CD4 TEM 2 0 0 0 0 0 0 64 19
CD8 Proliferating 0 0 0 0 0 1 0 0 0
CD8 TCM 30 1 0 0 0 0 0 0 0
CD8 TEM 0 55 0 0 0 0 0 1 0
cDC2 0 0 257 41 265 697 468 0 0
HSPC 0 0 167 12 1203 259 653 0 0
NK Proliferating 28 2810 3 24 3 161 20 0 0
Platelet 0 0 0 0 0 0 0 5 0table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_0.6)
0 1 2 3 4 5 6 7 8 9 10 11 12 13
ASDC 0 29 0 0 3 3 0 0 0 0 11 5 0 0
B intermediate 0 2 0 1 7 0 0 0 5 0 2 4 0 0
B memory 0 0 5 0 17 0 0 0 1 1 0 1 0 0
B naive 0 1 14 1 41 0 0 0 25 1 0 5 2 0
CD16 Mono 0 0 1 0 0 0 0 0 0 0 0 0 23 0
CD4 CTL 0 0 7 2 1 0 0 0 0 1 0 0 1 0
CD4 Naive 0 0 1050 3 2 0 0 0 40 770 0 0 1 0
CD4 Proliferating 6303 6307 22 2682 1302 3782 2370 2746 1276 0 234 936 0 1
CD4 TCM 74 903 4802 72 2453 116 7 34 1261 1174 1031 122 24 0
CD4 TEM 0 0 76 1 1 0 0 0 4 3 0 0 0 0
CD8 Proliferating 0 0 0 0 0 0 0 0 1 0 0 0 0 0
CD8 TCM 0 1 0 0 21 0 0 0 8 0 0 1 0 0
CD8 TEM 0 1 1 0 53 0 0 0 0 0 0 1 0 0
cDC2 416 264 0 4 174 21 82 9 10 0 511 234 2 1
HSPC 1233 205 0 4 53 1 742 2 13 0 2 39 0 0
NK Proliferating 131 0 7 2741 28 22 1 35 64 0 1 19 0 0
Platelet 0 0 0 0 0 0 0 0 0 0 0 0 5 0table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_0.6)
0 1 2 3 4 5 6 7 8 9 10 11 12 13
L1 5 265 17 619 2304 1 1 432 1719 0 380 82 0 0
L2 1 24 7 4744 937 0 1 148 62 0 4 7 0 0
L3 6 5795 0 11 213 107 8 62 98 0 21 106 1 0
L4 2 1299 1 8 115 3824 0 54 24 0 406 272 2 0
L5 1838 117 0 25 244 5 3006 324 27 0 164 270 0 2
L6 3074 87 0 23 107 5 22 999 140 0 182 509 0 0
L7 3229 124 0 48 189 0 164 807 51 0 615 104 0 0
PBMC 1 2 3817 31 41 3 0 0 436 773 17 17 33 0
PBMC_10x 1 0 2143 2 6 0 0 0 151 1177 3 0 22 0#0.7
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
ASDC 0 0 32 15 0 1 3 0 0
B intermediate 0 0 7 2 1 5 1 5 0
B memory 0 0 2 9 1 2 4 7 0
B naive 0 1 9 36 7 4 8 24 1
CD16 Mono 0 0 1 0 0 0 0 23 0
CD4 CTL 0 0 0 0 0 0 0 11 1
CD4 Naive 0 0 0 0 0 0 0 428 1438
CD4 Proliferating 2393 2809 5218 5349 4431 3872 3884 0 5
CD4 TCM 3372 259 732 519 111 146 290 4603 2041
CD4 TEM 2 0 0 0 0 0 0 64 19
CD8 Proliferating 0 0 0 0 0 1 0 0 0
CD8 TCM 30 1 0 0 0 0 0 0 0
CD8 TEM 0 55 0 0 0 0 0 1 0
cDC2 0 0 257 41 265 697 468 0 0
HSPC 0 0 167 12 1203 259 653 0 0
NK Proliferating 28 2810 3 24 3 161 20 0 0
Platelet 0 0 0 0 0 0 0 5 0table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_0.7)
0 1 2 3 4 5 6 7 8 9 10 11 12 13
ASDC 21 0 0 0 3 0 0 2 0 0 20 5 0 0
B intermediate 3 0 0 1 0 5 0 6 0 0 2 4 0 0
B memory 0 0 5 0 0 1 0 17 0 1 0 1 0 0
B naive 1 0 14 1 0 28 0 39 0 1 0 4 2 0
CD16 Mono 0 0 1 0 0 0 0 0 0 0 0 0 23 0
CD4 CTL 0 0 7 2 0 1 0 0 0 1 0 0 1 0
CD4 Naive 0 0 705 2 0 41 0 1 0 1116 0 0 1 0
CD4 Proliferating 6158 5504 22 2059 3868 1856 3574 1143 2272 0 575 929 0 1
CD4 TCM 802 43 4379 65 99 1633 34 1992 7 1685 1194 116 24 0
CD4 TEM 0 0 71 1 0 5 0 0 0 8 0 0 0 0
CD8 Proliferating 0 0 0 0 0 1 0 0 0 0 0 0 0 0
CD8 TCM 0 0 0 0 0 18 0 12 0 0 0 1 0 0
CD8 TEM 2 0 1 9 0 1 0 42 0 0 1 0 0 0
cDC2 208 263 0 1 10 31 11 132 59 0 826 184 2 1
HSPC 197 1243 0 4 1 13 13 56 720 0 8 39 0 0
NK Proliferating 1 109 7 2690 22 105 87 10 2 0 1 15 0 0
Platelet 0 0 0 0 0 0 0 0 0 0 0 0 5 0table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_0.7)
0 1 2 3 4 5 6 7 8 9 10 11 12 13
L1 214 6 16 108 1 2619 512 1818 1 0 444 86 0 0
L2 30 1 8 4668 0 155 307 746 0 0 14 6 0 0
L3 5711 9 0 5 103 115 63 233 7 0 85 96 1 0
L4 1178 0 1 5 3891 34 46 123 0 0 461 266 2 0
L5 108 1780 0 10 4 39 390 246 2964 0 210 269 0 2
L6 62 2430 0 6 1 169 1361 95 16 0 553 455 0 0
L7 88 2935 0 12 0 86 1039 156 72 0 840 103 0 0
PBMC 2 0 3443 20 3 376 0 31 0 1229 17 17 33 0
PBMC_10x 0 1 1744 1 0 146 1 4 0 1583 3 0 22 0#0.8
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
ASDC 0 0 32 15 0 1 3 0 0
B intermediate 0 0 7 2 1 5 1 5 0
B memory 0 0 2 9 1 2 4 7 0
B naive 0 1 9 36 7 4 8 24 1
CD16 Mono 0 0 1 0 0 0 0 23 0
CD4 CTL 0 0 0 0 0 0 0 11 1
CD4 Naive 0 0 0 0 0 0 0 428 1438
CD4 Proliferating 2393 2809 5218 5349 4431 3872 3884 0 5
CD4 TCM 3372 259 732 519 111 146 290 4603 2041
CD4 TEM 2 0 0 0 0 0 0 64 19
CD8 Proliferating 0 0 0 0 0 1 0 0 0
CD8 TCM 30 1 0 0 0 0 0 0 0
CD8 TEM 0 55 0 0 0 0 0 1 0
cDC2 0 0 257 41 265 697 468 0 0
HSPC 0 0 167 12 1203 259 653 0 0
NK Proliferating 28 2810 3 24 3 161 20 0 0
Platelet 0 0 0 0 0 0 0 5 0table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_0.8)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
ASDC 0 0 0 3 11 3 0 16 0 0 13 5 0 0 0
B intermediate 0 0 1 0 0 6 0 3 5 0 2 4 0 0 0
B memory 0 5 0 0 0 17 0 0 1 0 0 1 1 0 0
B naive 0 14 0 0 0 40 0 1 29 0 0 3 1 2 0
CD16 Mono 0 1 0 0 0 0 0 0 0 0 0 0 0 23 0
CD4 CTL 0 7 2 0 0 1 0 0 0 0 0 0 1 1 0
CD4 Naive 0 1275 2 0 1 1 0 0 42 0 0 0 544 1 0
CD4 Proliferating 5079 22 2226 3937 3690 1378 3675 2478 1600 2052 805 1018 0 0 1
CD4 TCM 34 5123 59 106 113 2201 25 726 1587 5 1097 114 859 24 0
CD4 TEM 0 76 1 0 0 0 0 0 5 0 0 0 3 0 0
CD8 Proliferating 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
CD8 TCM 0 0 0 0 0 14 0 0 16 0 0 1 0 0 0
CD8 TEM 0 1 8 0 1 44 0 1 1 0 0 0 0 0 0
cDC2 220 0 1 17 45 170 6 217 25 37 744 243 0 2 1
HSPC 1231 0 4 2 159 76 16 33 13 691 25 44 0 0 0
NK Proliferating 89 7 2712 22 2 23 95 0 75 2 3 19 0 0 0
Platelet 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_0.8)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
L1 3 17 275 0 82 2022 466 142 2352 1 393 72 0 0 0
L2 0 7 4656 0 8 865 251 20 108 2 12 6 0 0 0
L3 7 0 9 131 3390 268 55 2379 54 1 26 107 0 1 0
L4 0 1 5 3945 453 124 47 715 29 0 414 272 0 2 0
L5 1866 0 15 5 35 354 420 84 36 2724 209 272 0 0 2
L6 2000 0 16 3 27 118 1481 63 146 15 693 586 0 0 0
L7 2776 0 18 0 26 186 1096 71 73 44 922 119 0 0 0
PBMC 0 4049 21 3 0 33 0 1 451 0 17 18 545 33 0
PBMC_10x 1 2457 1 0 1 4 1 0 151 0 3 0 864 22 0#0.9
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
ASDC 0 0 32 15 0 1 3 0 0
B intermediate 0 0 7 2 1 5 1 5 0
B memory 0 0 2 9 1 2 4 7 0
B naive 0 1 9 36 7 4 8 24 1
CD16 Mono 0 0 1 0 0 0 0 23 0
CD4 CTL 0 0 0 0 0 0 0 11 1
CD4 Naive 0 0 0 0 0 0 0 428 1438
CD4 Proliferating 2393 2809 5218 5349 4431 3872 3884 0 5
CD4 TCM 3372 259 732 519 111 146 290 4603 2041
CD4 TEM 2 0 0 0 0 0 0 64 19
CD8 Proliferating 0 0 0 0 0 1 0 0 0
CD8 TCM 30 1 0 0 0 0 0 0 0
CD8 TEM 0 55 0 0 0 0 0 1 0
cDC2 0 0 257 41 265 697 468 0 0
HSPC 0 0 167 12 1203 259 653 0 0
NK Proliferating 28 2810 3 24 3 161 20 0 0
Platelet 0 0 0 0 0 0 0 5 0table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_0.9)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
ASDC 0 0 0 1 2 26 0 0 3 0 14 0 5 0 0 0
B intermediate 0 0 0 0 0 3 0 6 6 0 2 0 4 0 0 0
B memory 0 5 0 0 0 0 0 1 17 0 0 1 1 0 0 0
B naive 0 14 3 0 0 1 0 29 37 0 0 1 3 0 2 0
CD16 Mono 0 1 0 0 0 0 0 0 0 0 0 0 0 0 23 0
CD4 CTL 0 7 2 0 0 0 0 1 0 0 0 1 0 0 1 0
CD4 Naive 0 1260 2 0 0 0 0 35 1 0 0 559 0 8 1 0
CD4 Proliferating 5085 21 2615 3654 3699 2710 3622 1714 1016 2077 790 0 950 7 0 1
CD4 TCM 37 5111 92 57 103 770 29 1713 1950 3 1115 864 109 96 24 0
CD4 TEM 0 76 1 0 0 0 0 5 0 0 0 3 0 0 0 0
CD8 Proliferating 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
CD8 TCM 0 0 0 0 0 0 0 19 11 0 0 0 1 0 0 0
CD8 TEM 0 1 8 0 0 1 0 1 45 0 0 0 0 0 0 0
cDC2 245 0 4 20 16 253 10 42 162 25 751 0 197 0 2 1
HSPC 1237 0 4 153 4 41 16 13 77 691 19 0 39 0 0 0
NK Proliferating 79 7 2731 1 23 0 94 82 7 2 5 0 17 1 0 0
Platelet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_0.9)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
L1 3 16 300 66 2 157 473 2579 1739 1 404 0 74 11 0 0
L2 0 7 5057 7 0 17 213 122 489 1 8 0 6 8 0 0
L3 7 0 11 3119 111 2610 59 111 273 1 29 0 96 0 1 0
L4 2 1 9 604 3722 765 38 35 128 0 432 0 269 0 2 0
L5 1841 0 21 34 6 92 395 43 361 2741 217 0 269 0 0 2
L6 2075 0 13 29 3 82 1481 166 122 13 677 0 486 1 0 0
L7 2754 0 31 26 0 81 1111 83 187 41 908 0 109 0 0 0
PBMC 0 4036 19 1 3 1 0 428 29 0 18 551 17 35 33 0
PBMC_10x 1 2443 1 0 0 0 1 95 4 0 3 878 0 57 22 0#1
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
ASDC 0 0 32 15 0 1 3 0 0
B intermediate 0 0 7 2 1 5 1 5 0
B memory 0 0 2 9 1 2 4 7 0
B naive 0 1 9 36 7 4 8 24 1
CD16 Mono 0 0 1 0 0 0 0 23 0
CD4 CTL 0 0 0 0 0 0 0 11 1
CD4 Naive 0 0 0 0 0 0 0 428 1438
CD4 Proliferating 2393 2809 5218 5349 4431 3872 3884 0 5
CD4 TCM 3372 259 732 519 111 146 290 4603 2041
CD4 TEM 2 0 0 0 0 0 0 64 19
CD8 Proliferating 0 0 0 0 0 1 0 0 0
CD8 TCM 30 1 0 0 0 0 0 0 0
CD8 TEM 0 55 0 0 0 0 0 1 0
cDC2 0 0 257 41 265 697 468 0 0
HSPC 0 0 167 12 1203 259 653 0 0
NK Proliferating 28 2810 3 24 3 161 20 0 0
Platelet 0 0 0 0 0 0 0 5 0table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_1)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
ASDC 0 0 0 30 2 0 3 0 0 11 0 0 0 0 1 4 0 0
B intermediate 1 0 0 2 6 6 0 0 0 2 0 0 1 0 2 1 0 0
B memory 0 5 0 0 17 1 0 0 0 0 1 0 0 0 1 0 0 0
B naive 1 14 0 0 40 28 0 0 0 0 1 0 1 0 0 3 2 0
CD16 Mono 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 0
CD4 CTL 2 7 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0
CD4 Naive 2 787 0 0 1 43 0 0 0 0 1032 0 0 0 0 0 1 0
CD4 Proliferating 2459 22 2943 2829 1403 1312 2975 2695 2152 1018 0 2573 2250 1755 938 636 0 1
CD4 TCM 72 4176 27 818 2024 1750 87 1 5 1081 1799 33 68 23 24 61 24 0
CD4 TEM 1 67 0 0 0 5 0 0 0 0 12 0 0 0 0 0 0 0
CD8 Proliferating 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
CD8 TCM 0 0 0 1 12 18 0 0 0 0 0 0 0 0 0 0 0 0
CD8 TEM 0 1 0 1 52 1 0 0 0 0 0 1 0 0 0 0 0 0
cDC2 4 0 138 302 124 33 10 1 76 809 0 4 23 7 125 69 2 1
HSPC 3 0 958 47 68 13 1 196 732 41 0 147 10 0 41 37 0 0
NK Proliferating 2682 9 3 0 70 64 22 137 2 2 0 1 0 11 36 10 0 0
Platelet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_1)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
L1 594 17 4 175 1901 2173 2 35 1 379 0 50 47 403 1 43 0 0
L2 4523 9 1 11 1039 84 0 48 1 13 0 8 54 138 2 4 0 0
L3 10 0 12 2449 204 115 54 6 2 21 0 2106 1345 13 3 87 1 0
L4 7 1 0 1189 120 34 3029 7 1 395 0 515 413 24 3 267 2 0
L5 19 0 1504 58 265 39 9 265 2786 233 0 32 276 190 80 264 0 2
L6 8 0 699 97 93 153 1 1788 20 880 0 23 110 530 649 97 0 0
L7 40 0 1849 50 160 68 0 880 156 1022 0 24 108 497 428 49 0 0
PBMC 25 3430 0 1 33 457 3 0 0 18 1158 1 0 0 2 10 33 0
PBMC_10x 1 1632 0 0 5 152 0 1 0 3 1688 0 0 1 0 0 22 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