Different Resolution Tables on harmony integration
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 0 0
B memory 0 0 2 9 1 2 4 0 0
B naive 0 1 9 36 7 4 8 0 0
CD16 Mono 0 0 1 0 0 0 0 0 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 0 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 0table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_0.4)
0 1 2 3 4 5 6 7 8 9
ASDC 33 0 0 0 3 0 0 13 0 2
B intermediate 2 0 0 1 5 0 5 3 0 0
B memory 0 0 0 0 17 0 1 0 0 0
B naive 0 0 0 3 37 0 23 2 0 0
CD16 Mono 0 0 0 0 0 0 0 1 0 0
CD4 CTL 0 0 7 2 1 0 0 2 0 0
CD4 Naive 0 0 1820 1 1 0 43 1 0 0
CD4 Proliferating 10078 7623 13 2665 866 2423 1628 548 1647 470
CD4 TCM 943 72 5980 98 2355 6 1407 1160 19 33
CD4 TEM 0 0 79 1 0 0 5 0 0 0
CD8 Proliferating 0 0 0 1 0 0 0 0 0 0
CD8 TCM 0 0 0 0 20 0 9 2 0 0
CD8 TEM 2 0 0 7 44 0 1 1 0 0
cDC2 281 460 0 8 141 86 16 646 4 86
HSPC 189 1258 0 4 41 746 13 1 0 42
NK Proliferating 22 158 7 2749 12 2 74 5 11 9table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_0.4)
0 1 2 3 4 5 6 7 8 9
L1 180 21 8 319 2205 1 2193 474 423 1
L2 26 14 7 5090 551 0 74 11 159 3
L3 5916 2 0 10 215 6 93 35 41 110
L4 5164 5 1 10 104 0 27 591 22 83
L5 68 1914 0 28 159 3201 28 172 169 283
L6 93 3815 0 20 103 7 150 401 445 114
L7 99 3799 1 43 165 48 55 657 421 43
PBMC 4 0 4570 20 35 0 453 19 0 5
PBMC_10x 0 1 3319 0 6 0 152 25 1 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 0 0
B memory 0 0 2 9 1 2 4 0 0
B naive 0 1 9 36 7 4 8 0 0
CD16 Mono 0 0 1 0 0 0 0 0 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 0 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 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 29 0 0 0 1 1 4 0 3 8 4 1
B intermediate 2 0 1 1 0 6 5 0 0 1 0 0
B memory 0 0 0 0 0 1 17 0 0 0 0 0
B naive 1 0 0 2 0 26 36 0 0 0 0 0
CD16 Mono 0 0 0 0 0 1 0 0 0 0 0 0
CD4 CTL 0 7 0 2 0 1 1 0 0 1 0 0
CD4 Naive 0 1820 0 1 0 44 1 0 0 0 0 0
CD4 Proliferating 7550 13 5939 2213 3151 1940 1061 2713 2494 174 505 208
CD4 TCM 900 5985 95 70 52 1706 2152 19 65 989 33 7
CD4 TEM 0 79 0 1 0 5 0 0 0 0 0 0
CD8 Proliferating 0 0 0 1 0 0 0 0 0 0 0 0
CD8 TCM 0 0 0 0 0 17 14 0 0 0 0 0
CD8 TEM 2 0 0 7 0 1 44 0 0 1 0 0
cDC2 291 0 551 6 157 32 131 4 6 457 89 4
HSPC 198 0 1146 2 831 13 43 9 1 1 50 0
NK Proliferating 0 7 124 2694 2 93 45 50 23 2 9 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 196 8 3 50 1 2694 2018 453 0 400 1 1
L2 24 7 2 4884 1 110 767 124 0 13 3 0
L3 5901 0 3 4 4 122 181 38 34 19 122 0
L4 2536 1 3 4 120 33 108 24 2556 343 87 192
L5 77 0 1511 12 3512 37 213 224 0 133 297 6
L6 100 0 3348 5 29 168 105 1106 0 149 122 16
L7 138 1 2985 22 527 87 129 825 0 562 53 2
PBMC 1 4574 0 19 0 462 28 0 2 12 5 3
PBMC_10x 0 3320 1 0 0 174 5 1 0 3 0 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 0 0
B memory 0 0 2 9 1 2 4 0 0
B naive 0 1 9 36 7 4 8 0 0
CD16 Mono 0 0 1 0 0 0 0 0 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 0 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 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
ASDC 27 0 0 0 0 5 0 0 3 12 0 4
B intermediate 2 0 1 0 0 5 5 0 0 3 0 0
B memory 0 0 0 0 0 17 1 0 0 0 0 0
B naive 1 0 0 0 0 39 23 0 0 2 0 0
CD16 Mono 0 0 0 0 0 0 0 0 0 1 0 0
CD4 CTL 0 0 2 0 0 1 0 7 0 2 0 0
CD4 Naive 0 0 1 1813 0 1 44 6 0 1 0 0
CD4 Proliferating 7267 6081 1974 1 3089 1380 1836 13 2719 726 2369 506
CD4 TCM 822 53 51 2753 18 2272 1581 3196 86 1178 29 34
CD4 TEM 0 0 1 5 0 0 5 74 0 0 0 0
CD8 Proliferating 0 0 1 0 0 0 0 0 0 0 0 0
CD8 TCM 0 0 0 0 0 15 14 0 0 2 0 0
CD8 TEM 2 0 5 0 0 46 1 0 0 1 0 0
cDC2 236 355 1 0 146 183 24 0 12 672 8 91
HSPC 189 1138 2 0 850 45 13 0 1 3 2 51
NK Proliferating 0 145 2659 0 2 79 89 9 23 9 25 9table(All_samples_Merged$cell_line, All_samples_Merged$harmony_res_0.6)
0 1 2 3 4 5 6 7 8 9 10 11
L1 160 13 37 0 1 2086 2486 9 0 561 471 1
L2 17 10 4621 0 1 1017 107 9 0 9 141 3
L3 5803 2 4 0 4 263 106 0 44 34 45 123
L4 2341 0 1 1 5 143 28 0 2790 575 31 92
L5 63 1480 7 0 3523 209 38 0 6 150 248 298
L6 70 3245 4 0 29 135 145 0 0 600 798 122
L7 91 3021 5 0 542 200 82 1 2 638 698 51
PBMC 1 0 19 2280 0 30 489 2260 2 20 0 5
PBMC_10x 0 1 0 2291 0 5 155 1026 0 25 1 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 0 0
B memory 0 0 2 9 1 2 4 0 0
B naive 0 1 9 36 7 4 8 0 0
CD16 Mono 0 0 1 0 0 0 0 0 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 0 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 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 0 0 28 0 2 3 0 1 0 6 0 8 2 1
B intermediate 0 0 2 0 0 6 5 0 0 0 0 3 0 0
B memory 0 0 0 0 0 17 1 0 0 0 0 0 0 0
B naive 0 1 0 0 0 39 23 0 0 0 0 1 0 1
CD16 Mono 0 0 0 0 0 0 0 0 0 0 0 1 0 0
CD4 CTL 0 2 0 0 0 1 0 0 7 0 0 2 0 0
CD4 Naive 0 1 0 1788 0 1 44 0 31 0 0 1 0 0
CD4 Proliferating 5691 2003 3541 1 3160 1406 1897 3406 12 3153 2438 549 495 209
CD4 TCM 59 52 806 2628 54 2169 1666 60 3338 90 14 1096 33 8
CD4 TEM 0 1 0 5 0 0 5 0 74 0 0 0 0 0
CD8 Proliferating 0 1 0 0 0 0 0 0 0 0 0 0 0 0
CD8 TCM 0 0 0 0 0 14 15 0 0 0 0 2 0 0
CD8 TEM 0 0 1 0 0 51 1 1 0 0 0 1 0 0
cDC2 327 3 263 0 167 137 27 20 0 8 4 679 89 4
HSPC 1129 2 38 0 859 39 13 152 0 2 9 4 47 0
NK Proliferating 118 2655 0 0 2 81 93 0 9 23 46 13 9 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 8 31 108 0 1 2037 2638 64 8 0 443 484 1 2
L2 3 4646 18 0 0 1035 115 6 9 0 89 11 3 0
L3 4 3 2767 0 3 212 101 3091 0 67 22 37 121 0
L4 0 2 1573 1 54 119 30 393 0 3206 20 330 86 193
L5 1469 7 43 0 3565 223 40 27 0 5 206 142 289 6
L6 2981 3 70 0 35 135 153 31 0 2 950 651 120 17
L7 2858 10 100 0 586 170 86 27 1 0 780 661 50 2
PBMC 0 19 0 2137 0 28 472 1 2420 2 0 19 5 3
PBMC_10x 1 0 0 2284 0 5 155 0 1033 0 1 25 0 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 0 0
B memory 0 0 2 9 1 2 4 0 0
B naive 0 1 9 36 7 4 8 0 0
CD16 Mono 0 0 1 0 0 0 0 0 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 0 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 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
ASDC 0 0 27 0 0 0 1 0 6 3 0 10 2 2
B intermediate 0 1 2 0 0 5 0 0 0 5 0 1 2 0
B memory 0 0 0 0 0 1 0 0 0 17 0 0 0 0
B naive 0 2 0 0 0 23 0 0 0 38 0 0 2 0
CD16 Mono 0 0 0 0 0 0 0 0 0 0 0 0 1 0
CD4 CTL 0 2 0 1 0 0 0 0 0 1 6 1 1 0
CD4 Naive 0 1 0 1803 0 44 0 0 0 1 16 0 1 0
CD4 Proliferating 5133 2435 3577 1 3068 1831 3335 3282 3163 739 12 154 720 511
CD4 TCM 64 98 767 2850 15 1591 39 29 114 2225 3096 1027 125 33
CD4 TEM 0 1 0 6 0 5 0 0 0 0 73 0 0 0
CD8 Proliferating 0 1 0 0 0 0 0 0 0 0 0 0 0 0
CD8 TCM 0 0 0 0 0 14 0 0 0 15 0 0 2 0
CD8 TEM 0 7 1 0 0 1 1 0 0 44 0 1 0 0
cDC2 379 7 246 0 144 19 19 6 29 145 0 478 170 86
HSPC 1130 4 43 0 857 13 142 11 3 35 0 1 5 50
NK Proliferating 83 2716 0 0 2 87 0 81 23 5 9 2 32 9table(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
L1 7 91 101 0 1 2514 44 518 0 2052 8 406 82 1
L2 2 5113 13 0 1 99 7 189 0 487 9 8 4 3
L3 2 8 2809 0 3 101 3029 52 80 184 0 19 19 122
L4 1 5 1548 1 3 27 389 29 3241 109 0 366 201 87
L5 1417 16 39 0 3536 33 24 322 10 144 0 147 40 294
L6 2741 7 68 0 27 142 24 1260 2 106 0 153 494 124
L7 2618 16 85 0 515 70 20 1038 3 156 1 559 195 55
PBMC 0 19 0 2362 0 493 0 0 2 30 2175 14 6 5
PBMC_10x 1 0 0 2298 0 155 0 1 0 5 1019 3 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 0 0
B memory 0 0 2 9 1 2 4 0 0
B naive 0 1 9 36 7 4 8 0 0
CD16 Mono 0 0 1 0 0 0 0 0 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 0 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 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 16
ASDC 0 0 28 0 0 1 4 3 0 0 0 9 2 0 4 0 0
B intermediate 0 1 2 0 5 0 0 5 0 0 0 2 0 0 0 1 0
B memory 0 0 0 0 1 0 0 17 0 0 0 0 0 0 0 0 0
B naive 0 2 0 0 24 0 0 37 0 0 0 2 0 0 0 0 0
CD16 Mono 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
CD4 CTL 0 2 0 0 0 0 0 1 7 0 0 2 0 0 0 0 0
CD4 Naive 0 1 0 0 39 0 0 1 5 1249 0 1 0 566 0 0 4
CD4 Proliferating 4284 2368 3535 3944 1908 3303 3323 831 12 1 2096 379 1169 0 511 297 0
CD4 TCM 66 89 849 18 1425 25 84 2171 3144 1933 5 1048 113 877 33 30 163
CD4 TEM 0 1 0 0 5 0 0 0 74 2 0 0 0 3 0 0 0
CD8 Proliferating 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CD8 TCM 0 0 1 0 15 0 0 13 0 0 0 2 0 0 0 0 0
CD8 TEM 0 0 1 0 1 0 0 52 0 0 0 1 0 0 0 0 0
cDC2 392 8 274 4 18 18 6 133 0 0 34 447 150 0 87 157 0
HSPC 1104 2 47 25 13 145 1 38 0 0 693 1 171 0 52 2 0
NK Proliferating 18 2713 0 159 91 0 23 14 9 0 2 2 0 0 9 9 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 16
L1 7 75 151 450 2566 31 1 2022 8 0 1 512 0 0 1 0 0
L2 3 5044 44 135 112 5 0 570 9 0 1 9 0 0 3 0 0
L3 1 7 2886 24 105 3008 62 172 0 0 4 34 1 0 121 2 1
L4 1 5 1348 21 28 370 3373 107 0 1 0 476 187 0 87 3 0
L5 1401 16 70 268 35 23 1 171 0 0 2792 132 803 0 302 8 0
L6 1900 8 116 2117 146 34 2 93 0 0 6 173 28 0 124 401 0
L7 2550 14 122 1134 81 21 0 147 1 0 26 514 586 0 53 82 0
PBMC 0 19 0 0 321 0 2 29 2205 1800 0 22 0 540 5 0 163
PBMC_10x 1 0 0 1 151 0 0 5 1028 1384 0 25 0 906 0 0 3#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 0 0
B memory 0 0 2 9 1 2 4 0 0
B naive 0 1 9 36 7 4 8 0 0
CD16 Mono 0 0 1 0 0 0 0 0 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 0 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 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
ASDC 0 0 24 3 0 0 4 3 0 0 0 11 2 0 2 2 0
B intermediate 0 1 2 0 5 0 0 5 0 0 0 1 0 0 2 0 0
B memory 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 1
B naive 0 3 0 0 24 0 0 36 0 0 0 0 0 0 1 0 1
CD16 Mono 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
CD4 CTL 0 2 0 0 1 0 0 0 7 0 0 1 0 0 1 0 0
CD4 Naive 0 1 0 0 29 0 0 1 32 1224 0 0 0 564 1 0 14
CD4 Proliferating 5012 2094 3095 3762 1796 3432 3233 1012 12 0 2058 162 1085 0 527 529 152
CD4 TCM 56 72 741 114 1656 22 62 1973 3127 1991 6 1010 50 857 124 36 176
CD4 TEM 0 1 0 0 5 0 0 0 74 2 0 0 0 3 0 0 0
CD8 Proliferating 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CD8 TCM 0 0 0 0 18 0 0 12 0 0 0 0 0 0 1 0 0
CD8 TEM 0 7 1 0 1 0 1 44 0 0 0 1 0 0 0 0 0
cDC2 360 6 237 17 29 4 25 126 0 0 29 487 143 0 171 92 2
HSPC 1113 2 54 1 0 15 141 40 0 0 682 1 178 0 3 51 13
NK Proliferating 78 2682 0 22 77 103 1 37 9 0 2 2 0 0 8 9 19table(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
L1 3 36 99 0 2827 470 68 1804 7 0 1 406 0 0 80 1 23
L2 1 4776 10 0 105 267 9 729 9 0 2 9 0 0 2 3 13
L3 0 5 2875 87 28 42 2939 192 0 0 4 26 0 0 19 126 85
L4 0 7 956 3818 15 28 373 108 1 0 0 342 51 0 199 92 17
L5 1434 11 48 7 29 274 24 194 0 0 2741 131 799 0 12 308 10
L6 2577 5 67 3 63 1439 35 109 0 0 6 182 26 0 419 127 90
L7 2603 13 99 2 70 1055 18 139 1 0 23 563 582 0 83 57 23
PBMC 0 19 0 2 421 0 1 26 2201 1820 0 14 0 546 6 5 45
PBMC_10x 1 0 0 0 83 1 0 5 1042 1397 0 3 0 878 22 0 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