Different evaluation test on harmony integration on patient origin and cell_line-theta-0.5 both
Nasir Mahmood Abbasi
2025-01-22
1. load libraries
2. Load Seurat Object
#Load Seurat Object merged from cell lines and a control after filtration
load("../0-R_Objects/CD4Tcells_harmony_integrated_0.5_theta_patientorigin_cell_line.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 = "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)
clustree(All_samples_Merged, prefix = "harmony_res_")
Visualize Harmony Integrated Data distribution
#0.6
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
B intermediate 0 0 2 1 2 2 0 0 0
B memory 0 0 11 1 38 82 120 0 0
CD14 Mono 0 0 1 0 5 0 6 0 0
CD4 CTL 0 0 0 0 0 0 0 12 1
CD4 Naive 0 0 0 7 0 0 0 523 1512
CD4 Proliferating 2461 2852 5452 5391 4732 4002 4115 0 6
CD4 TCM 3320 270 887 562 178 557 517 4576 1963
CD4 TEM 1 0 0 0 0 0 0 60 23
CD8 Proliferating 0 0 0 0 0 1 1 0 0
CD8 TCM 1 16 0 0 0 0 0 0 0
CD8 TEM 1 8 0 0 2 3 1 0 0
cDC1 0 0 0 0 2 6 0 0 0
cDC2 0 0 0 4 11 3 35 0 0
dnT 2 3 0 1 2 5 2 0 0
HSPC 0 0 60 7 1035 213 490 0 0
NK Proliferating 38 2785 6 24 11 259 38 0 0
Treg 1 1 9 9 4 15 6 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
B intermediate 0 0 0 1 0 2 1 0 0 0 3 0
B memory 15 0 3 11 0 10 21 3 0 135 54 0
CD14 Mono 0 0 0 0 0 0 0 0 0 11 0 1
CD4 CTL 0 7 0 0 2 0 1 0 0 2 0 1
CD4 Naive 0 1979 0 3 2 51 5 0 0 1 0 1
CD4 Proliferating 6752 25 6040 4605 1688 1851 1595 2583 2596 325 951 0
CD4 TCM 271 5845 116 1517 45 1626 1855 45 7 1254 197 52
CD4 TEM 0 79 0 0 1 4 0 0 0 0 0 0
CD8 Proliferating 0 0 0 0 0 0 0 0 0 1 1 0
CD8 TCM 0 0 1 10 1 0 5 0 0 0 0 0
CD8 TEM 0 0 0 1 0 4 4 0 0 6 0 0
cDC1 0 0 0 0 0 1 0 0 0 2 5 0
cDC2 3 0 0 0 0 0 1 1 0 42 4 2
dnT 1 0 0 0 0 8 0 0 0 5 1 0
HSPC 976 0 46 65 3 8 38 632 1 2 34 0
NK Proliferating 231 4 25 1 2579 117 88 7 89 2 18 0
Treg 0 0 1 0 0 41 3 0 0 0 0 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
L1 6 20 56 618 24 2641 1712 1 438 301 8 0
L2 5 4 2 102 4263 107 1100 0 343 6 3 0
L3 5 0 2970 3061 2 50 155 4 36 19 125 1
L4 0 1 3147 1834 2 35 90 7 51 567 271 2
L5 1711 0 14 257 4 39 234 3008 301 149 305 0
L6 3324 0 32 108 5 178 124 26 746 162 443 0
L7 3196 0 7 209 5 74 185 225 777 555 98 0
PBMC 1 4602 4 21 16 439 17 0 0 24 15 32
PBMC_10x 1 3312 0 4 0 160 0 0 1 5 0 22#0.7
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
B intermediate 0 0 2 1 2 2 0 0 0
B memory 0 0 11 1 38 82 120 0 0
CD14 Mono 0 0 1 0 5 0 6 0 0
CD4 CTL 0 0 0 0 0 0 0 12 1
CD4 Naive 0 0 0 7 0 0 0 523 1512
CD4 Proliferating 2461 2852 5452 5391 4732 4002 4115 0 6
CD4 TCM 3320 270 887 562 178 557 517 4576 1963
CD4 TEM 1 0 0 0 0 0 0 60 23
CD8 Proliferating 0 0 0 0 0 1 1 0 0
CD8 TCM 1 16 0 0 0 0 0 0 0
CD8 TEM 1 8 0 0 2 3 1 0 0
cDC1 0 0 0 0 2 6 0 0 0
cDC2 0 0 0 4 11 3 35 0 0
dnT 2 3 0 1 2 5 2 0 0
HSPC 0 0 60 7 1035 213 490 0 0
NK Proliferating 38 2785 6 24 11 259 38 0 0
Treg 1 1 9 9 4 15 6 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
B intermediate 0 0 0 0 0 0 2 1 0 0 0 2 2 0
B memory 14 0 5 0 0 3 12 8 3 0 0 194 13 0
CD14 Mono 0 0 0 0 0 0 0 0 0 0 0 11 0 1
CD4 CTL 0 0 0 0 2 0 1 0 0 7 0 2 0 1
CD4 Naive 0 1748 0 0 2 0 8 51 0 231 0 1 0 1
CD4 Proliferating 5690 3 3924 3942 1736 3912 1499 1847 2576 25 2669 732 456 0
CD4 TCM 261 3120 826 11 37 148 2168 1609 33 2730 92 1697 46 52
CD4 TEM 0 26 0 0 1 0 0 4 0 53 0 0 0 0
CD8 Proliferating 0 0 0 0 0 0 0 0 0 0 0 2 0 0
CD8 TCM 0 0 1 0 0 1 15 0 0 0 0 0 0 0
CD8 TEM 0 0 0 0 0 0 5 4 0 0 0 6 0 0
cDC1 0 0 0 0 0 0 0 1 0 0 0 5 2 0
cDC2 2 0 0 0 0 0 0 0 1 0 0 44 4 2
dnT 1 0 0 0 0 0 0 8 0 0 0 6 0 0
HSPC 987 0 29 9 1 59 37 8 633 0 1 10 31 0
NK Proliferating 132 0 0 318 2496 3 53 107 7 5 23 5 12 0
Treg 0 0 0 0 0 0 2 41 0 0 1 1 0 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 6 4 187 456 22 89 1926 2636 1 18 2 476 2 0
L2 3 0 22 537 4224 9 1016 101 1 5 0 14 3 0
L3 8 0 2624 28 2 3228 204 49 12 0 53 134 85 1
L4 0 0 1681 44 1 681 118 34 2 1 2720 641 82 2
L5 1721 0 98 416 2 29 232 34 3032 0 8 181 269 0
L6 2545 0 46 1557 2 60 110 175 31 0 0 547 75 0
L7 2802 0 127 1242 6 28 155 68 174 0 1 683 45 0
PBMC 1 2303 0 0 16 2 37 434 0 2302 2 37 5 32
PBMC_10x 1 2590 0 0 0 0 4 158 0 725 0 5 0 22#0.8
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
B intermediate 0 0 2 1 2 2 0 0 0
B memory 0 0 11 1 38 82 120 0 0
CD14 Mono 0 0 1 0 5 0 6 0 0
CD4 CTL 0 0 0 0 0 0 0 12 1
CD4 Naive 0 0 0 7 0 0 0 523 1512
CD4 Proliferating 2461 2852 5452 5391 4732 4002 4115 0 6
CD4 TCM 3320 270 887 562 178 557 517 4576 1963
CD4 TEM 1 0 0 0 0 0 0 60 23
CD8 Proliferating 0 0 0 0 0 1 1 0 0
CD8 TCM 1 16 0 0 0 0 0 0 0
CD8 TEM 1 8 0 0 2 3 1 0 0
cDC1 0 0 0 0 2 6 0 0 0
cDC2 0 0 0 4 11 3 35 0 0
dnT 2 3 0 1 2 5 2 0 0
HSPC 0 0 60 7 1035 213 490 0 0
NK Proliferating 38 2785 6 24 11 259 38 0 0
Treg 1 1 9 9 4 15 6 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 14
B intermediate 0 0 0 0 0 1 2 0 0 0 0 0 1 3 0
B memory 13 14 0 0 0 9 29 0 1 3 0 1 133 49 0
CD14 Mono 0 0 0 0 0 0 0 0 0 0 0 0 11 0 1
CD4 CTL 0 0 2 0 1 1 0 7 0 0 0 0 1 0 1
CD4 Naive 0 0 2 0 1687 51 8 292 0 0 0 0 1 0 1
CD4 Proliferating 4645 3634 1911 4012 1 1896 1257 26 3297 2341 2854 1960 241 936 0
CD4 TCM 252 903 56 6 2532 1680 2401 3307 71 37 97 47 1217 172 52
CD4 TEM 0 0 1 0 12 4 0 67 0 0 0 0 0 0 0
CD8 Proliferating 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
CD8 TCM 0 1 1 0 0 0 14 0 0 0 1 0 0 0 0
CD8 TEM 0 0 0 0 0 4 5 0 0 0 0 0 6 0 0
cDC1 0 0 0 0 0 1 0 0 0 0 0 0 2 5 0
cDC2 2 0 0 0 0 0 2 0 0 1 0 0 41 5 2
dnT 1 1 0 0 0 8 0 0 0 0 0 0 5 0 0
HSPC 968 39 2 15 0 9 42 0 52 626 1 14 2 35 0
NK Proliferating 136 0 2438 374 0 111 41 5 5 7 23 0 2 19 0
Treg 0 0 0 0 0 41 3 0 0 0 1 0 0 0 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 4 148 30 447 1 2706 1983 20 71 1 4 38 364 8 0
L2 1 16 4355 575 0 136 732 5 11 1 1 93 6 3 0
L3 8 2702 3 24 0 49 225 0 2810 4 77 404 19 102 1
L4 0 1514 2 47 0 34 165 1 429 1 2885 260 397 270 2
L5 1399 72 2 442 0 37 230 0 21 2800 7 565 148 299 0
L6 2304 69 2 1493 0 176 185 0 49 27 0 268 151 424 0
L7 2299 71 3 1379 0 74 245 0 33 181 1 394 547 104 0
PBMC 1 0 16 0 1941 444 35 2656 2 0 2 0 27 15 32
PBMC_10x 1 0 0 0 2291 160 4 1022 0 0 0 0 5 0 22#0.9
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
B intermediate 0 0 2 1 2 2 0 0 0
B memory 0 0 11 1 38 82 120 0 0
CD14 Mono 0 0 1 0 5 0 6 0 0
CD4 CTL 0 0 0 0 0 0 0 12 1
CD4 Naive 0 0 0 7 0 0 0 523 1512
CD4 Proliferating 2461 2852 5452 5391 4732 4002 4115 0 6
CD4 TCM 3320 270 887 562 178 557 517 4576 1963
CD4 TEM 1 0 0 0 0 0 0 60 23
CD8 Proliferating 0 0 0 0 0 1 1 0 0
CD8 TCM 1 16 0 0 0 0 0 0 0
CD8 TEM 1 8 0 0 2 3 1 0 0
cDC1 0 0 0 0 2 6 0 0 0
cDC2 0 0 0 4 11 3 35 0 0
dnT 2 3 0 1 2 5 2 0 0
HSPC 0 0 60 7 1035 213 490 0 0
NK Proliferating 38 2785 6 24 11 259 38 0 0
Treg 1 1 9 9 4 15 6 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
B intermediate 0 0 0 0 1 0 0 1 0 1 0 1 0 3 0
B memory 14 5 0 0 6 0 0 8 0 20 3 141 0 55 0
CD14 Mono 0 0 0 0 0 0 0 0 0 0 0 11 0 0 1
CD4 CTL 0 0 2 0 0 0 7 0 0 1 0 2 0 0 1
CD4 Naive 0 0 2 1769 3 0 210 51 0 5 0 1 0 0 1
CD4 Proliferating 4478 4470 1855 1 3129 3612 25 1821 3221 1295 2532 248 1337 987 0
CD4 TCM 253 361 49 2593 1187 116 3310 1508 8 1846 29 1306 4 208 52
CD4 TEM 0 0 1 13 0 0 65 4 0 0 0 1 0 0 0
CD8 Proliferating 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0
CD8 TCM 0 1 1 0 11 0 0 0 0 4 0 0 0 0 0
CD8 TEM 0 0 0 0 1 0 0 4 0 4 0 6 0 0 0
cDC1 0 0 0 0 0 0 0 0 0 0 0 2 0 6 0
cDC2 3 0 0 0 0 0 0 0 0 0 1 43 0 4 2
dnT 0 0 0 0 0 0 0 8 0 0 0 6 0 1 0
HSPC 976 66 2 0 33 2 0 7 5 33 626 3 14 38 0
NK Proliferating 135 4 2561 0 0 22 4 101 177 78 7 2 47 23 0
Treg 0 0 0 0 0 1 0 41 0 3 0 0 0 0 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
L1 4 100 30 1 565 1 20 2587 444 1686 1 376 2 8 0
L2 1 10 4409 0 133 0 4 97 381 885 2 7 3 3 0
L3 2 3923 3 0 1974 141 0 48 31 165 10 21 0 109 1
L4 0 722 4 0 782 3605 1 34 70 110 0 404 0 273 2
L5 1344 32 1 0 326 2 0 32 332 167 3063 152 271 300 0
L6 2298 75 3 0 242 2 0 150 1197 100 25 187 365 504 0
L7 2208 43 7 0 325 0 0 68 955 160 97 593 761 114 0
PBMC 1 2 16 1986 20 2 2671 381 0 17 0 28 0 15 32
PBMC_10x 1 0 0 2389 4 0 925 157 1 0 0 6 0 0 22#1
#0.9
table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$cell_line)
L1 L2 L3 L4 L5 L6 L7 PBMC PBMC_10x
B intermediate 0 0 2 1 2 2 0 0 0
B memory 0 0 11 1 38 82 120 0 0
CD14 Mono 0 0 1 0 5 0 6 0 0
CD4 CTL 0 0 0 0 0 0 0 12 1
CD4 Naive 0 0 0 7 0 0 0 523 1512
CD4 Proliferating 2461 2852 5452 5391 4732 4002 4115 0 6
CD4 TCM 3320 270 887 562 178 557 517 4576 1963
CD4 TEM 1 0 0 0 0 0 0 60 23
CD8 Proliferating 0 0 0 0 0 1 1 0 0
CD8 TCM 1 16 0 0 0 0 0 0 0
CD8 TEM 1 8 0 0 2 3 1 0 0
cDC1 0 0 0 0 2 6 0 0 0
cDC2 0 0 0 4 11 3 35 0 0
dnT 2 3 0 1 2 5 2 0 0
HSPC 0 0 60 7 1035 213 490 0 0
NK Proliferating 38 2785 6 24 11 259 38 0 0
Treg 1 1 9 9 4 15 6 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
B intermediate 0 0 0 0 1 0 0 2 0 0 0 0 1 3 0 0 0
B memory 14 0 0 1 16 0 2 13 1 5 3 0 136 61 0 0 0
CD14 Mono 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0 1
CD4 CTL 0 2 0 0 1 7 0 0 0 0 0 0 2 0 0 0 1
CD4 Naive 0 3 1698 0 38 281 0 7 0 0 0 0 1 0 5 8 1
CD4 Proliferating 4757 1788 1 3837 1921 26 3629 1431 2820 2730 2523 2163 227 1152 6 0 0
CD4 TCM 286 66 2413 84 1745 3446 148 2050 6 689 26 11 1259 258 211 80 52
CD4 TEM 0 1 11 0 3 67 0 0 0 0 0 0 2 0 0 0 0
CD8 Proliferating 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0
CD8 TCM 0 1 0 1 0 0 0 15 0 0 0 0 0 0 0 0 0
CD8 TEM 0 0 0 0 5 0 0 3 0 0 0 0 6 0 0 1 0
cDC1 0 0 0 0 0 0 0 0 0 0 0 0 2 6 0 0 0
cDC2 3 0 0 0 0 0 0 0 0 0 1 0 42 5 0 0 2
dnT 1 0 0 0 8 0 0 0 0 0 0 0 5 1 0 0 0
HSPC 886 3 0 64 13 0 1 55 97 16 632 0 1 37 0 0 0
NK Proliferating 25 2372 0 3 104 4 23 21 535 0 7 21 2 43 1 0 0
Treg 0 0 0 0 41 0 0 2 0 0 0 0 1 1 0 0 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
L1 2 32 1 73 3011 21 1 1660 179 110 1 340 378 8 8 0 0
L2 2 4175 0 8 165 4 0 678 606 11 0 274 7 3 1 1 0
L3 7 3 0 3219 57 0 136 446 15 2322 5 38 14 164 1 0 1
L4 0 2 0 592 42 1 3654 158 28 833 6 27 368 293 1 0 2
L5 1612 3 0 28 48 0 9 313 285 58 2983 207 147 329 0 0 0
L6 1734 2 0 40 177 0 0 110 1569 35 22 709 175 575 0 0 0
L7 2613 3 0 28 109 0 1 200 777 71 175 599 574 181 0 0 0
PBMC 1 16 1862 2 192 2752 2 30 0 0 0 0 30 15 206 31 32
PBMC_10x 1 0 2260 0 95 1053 0 4 0 0 0 1 6 0 6 57 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