Different Resolution Tables on harmony integration on patient origin and orig.ident-theta-0.5,0.5

1. load libraries

2. Load Seurat Object

#Load Seurat Object merged from cell lines and a control after filtration
load("CD4Tcells_harmony_integrated_0.5_theta_patientorigin_orig_ident.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)

Loading required package: ggraph

Attaching package: 'ggraph'

The following object is masked from 'package:sp':

    geometry

clustree(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
  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        0

table(All_samples_Merged$predicted.celltype.l2, All_samples_Merged$harmony_res_0.4)

                   
                        0     1     2     3     4     5     6     7     8     9    10
  B intermediate        1     0     0     1     1     0     4     0     0     0     0
  B memory             19    17     0     0    18     9   188     1     0     0     0
  CD14 Mono             0     0     0     0     0     0    11     0     0     1     0
  CD4 CTL               0     0     9     2     1     0     0     0     0     1     0
  CD4 Naive             3     0  1981     3     5    49     0     0     0     1     0
  CD4 Proliferating 10551  7841    23  2626  1288  1500  1030  2183  1968     0     1
  CD4 TCM            1711   342  5842    55  1799  1501  1508     8    11    53     0
  CD4 TEM               0     0    79     1     0     4     0     0     0     0     0
  CD8 Proliferating     0     0     0     0     0     0     2     0     0     0     0
  CD8 TCM              11     0     0     1     5     0     0     0     0     0     0
  CD8 TEM               1     0     0     0     4     4     6     0     0     0     0
  cDC1                  0     0     0     0     0     0     8     0     0     0     0
  cDC2                  0     3     0     0     0     0    46     1     0     2     1
  dnT                   1     1     0     0     0     8     5     0     0     0     0
  HSPC                 94  1021     0     4    46     7    34   599     0     0     0
  NK Proliferating     25   244     7  2717    45    87    21     8     7     0     0
  Treg                  0     0     0     0     2    40     3     0     0     0     0

table(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
  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        0

table(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
  B intermediate       0    0    0    0    2    1    0    0    0    4    0    0
  B memory            14   20    0    1  159   10    0    2    0   46    0    0
  CD14 Mono            0    0    0    0   11    0    0    0    0    0    1    0
  CD4 CTL              0    0    9    2    1    0    0    0    0    0    1    0
  CD4 Naive            0    0 1981    3    7   50    0    0    0    0    1    0
  CD4 Proliferating 7620 7910   23 2740  907 1898 2900 2105 2087  820    0    1
  CD4 TCM            317 1084 5840  154 3523 1523   92   17    9  218   53    0
  CD4 TEM              0    0   79    1    0    4    0    0    0    0    0    0
  CD8 Proliferating    0    1    0    0    1    0    0    0    0    0    0    0
  CD8 TCM              0    1    0    1   15    0    0    0    0    0    0    0
  CD8 TEM              0    0    0    0   11    4    0    0    0    0    0    0
  cDC1                 0    0    0    0    2    0    0    0    0    6    0    0
  cDC2                 3    0    0    0   43    0    0    0    0    4    2    1
  dnT                  1    1    0    0    5    8    0    0    0    0    0    0
  HSPC              1019   97    0   11   39    7    1  601    1   29    0    0
  NK Proliferating   251    3    7 2692    2  134   23    8   21   20    0    0
  Treg                 0    0    0    0    3   40    0    0    0    2    0    0

table(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
  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        0

table(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
  B intermediate       0    0    0    1    2    0    0    0    0    0    0    4    0    0
  B memory            15   14    0    2   22    0    3    0    5    0  141   50    0    0
  CD14 Mono            0    0    0    0    0    0    0    0    0    0   11    0    1    0
  CD4 CTL              0    0    8    2    1    0    0    0    0    1    0    0    1    0
  CD4 Naive            0    0 1169    4    9    0    0    0   46  813    0    0    1    0
  CD4 Proliferating 6651 6577   23 2720 1399 3800 2527 2749 1292    0  285  987    0    1
  CD4 TCM            289 1030 4703   65 2612  121   35   17 1226 1133 1291  255   53    0
  CD4 TEM              0    0   75    1    1    0    0    0    3    3    1    0    0    0
  CD8 Proliferating    0    0    0    0    0    0    0    0    0    0    1    1    0    0
  CD8 TCM              0    1    0    0   16    0    0    0    0    0    0    0    0    0
  CD8 TEM              0    0    0    0    5    0    0    0    3    0    6    1    0    0
  cDC1                 0    0    0    0    0    0    0    0    0    0    2    6    0    0
  cDC2                 2    0    0    0    1    0    1    0    0    0   42    4    2    1
  dnT                  1    0    0    0    0    0    0    0    8    0    5    1    0    0
  HSPC               990   89    0    4   51    1  629    1    4    0    5   31    0    0
  NK Proliferating   209    2    7 2712   35   23    7   59   81    0    1   25    0    0
  Treg                 0    0    0    0    2    0    0    0   40    0    1    2    0    0

table(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
  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        0

table(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    1    0    0    0    2    0    0    0    4    0    0
  B memory             6    3    0    0    0    9    0   12    2    0  180   40    0    0
  CD14 Mono            0    0    0    0    0    0    0    0    0    0   11    0    1    0
  CD4 CTL              0    0    8    2    0    1    0    0    0    1    0    0    1    0
  CD4 Naive            0    0  794    3    0   46    0    8    0 1190    0    0    1    0
  CD4 Proliferating 6412 5827   22 2102 3882 1881 3574 1236 2411    0  687  976    0    1
  CD4 TCM            883  161 4309   67   97 1609   17 2112   24 1614 1669  215   53    0
  CD4 TEM              0    0   71    1    0    4    0    0    0    7    1    0    0    0
  CD8 Proliferating    0    0    0    0    0    0    0    0    0    0    2    0    0    0
  CD8 TCM              1    0    0    1    0    0    0   15    0    0    0    0    0    0
  CD8 TEM              0    0    0    1    0    4    0    4    0    0    6    0    0    0
  cDC1                 0    0    0    0    0    0    0    0    0    0    2    6    0    0
  cDC2                 0    1    0    0    0    0    0    0    1    0   44    4    2    1
  dnT                  0    0    0    0    0    8    0    0    0    0    7    0    0    0
  HSPC                88  997    0    3    1    7    4   47  614    0   15   29    0    0
  NK Proliferating     3  173    8 2654   23  130  124   14    8    0    2   22    0    0
  Treg                 0    0    0    0    0   40    0    2    0    0    1    2    0    0

table(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
  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        0

table(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    1    0    0    2    0    0    0    0    0    4    0    0    0
  B memory             1    0    0    0    2   17    0   14   10    2  158   48    0    0    0
  CD14 Mono            0    0    0    0    0    0    0    0    0    0   11    0    0    1    0
  CD4 CTL              0    8    2    0    0    1    0    0    0    0    0    0    1    1    0
  CD4 Naive            0 1411    3    0    1    8    0    0   48    0    0    0  570    1    0
  CD4 Proliferating 5392   23 2268 3953 3795 1494 3656 2631 1626 2165  933 1074    0    0    1
  CD4 TCM            129 5007   60  110  152 2341   10  811 1557   16 1495  254  835   53    0
  CD4 TEM              0   75    1    0    0    0    0    0    4    0    1    0    3    0    0
  CD8 Proliferating    0    0    0    0    0    0    0    0    0    0    1    1    0    0    0
  CD8 TCM              0    0    1    0    1   15    0    0    0    0    0    0    0    0    0
  CD8 TEM              0    0    0    0    0    5    0    0    4    0    6    0    0    0    0
  cDC1                 0    0    0    0    0    0    0    0    0    0    2    6    0    0    0
  cDC2                 2    0    0    0    0    0    0    0    0    0   44    4    0    2    1
  dnT                  0    0    0    0    0    0    0    0    8    0    7    0    0    0    0
  HSPC               990    0    3    1   66   60    7   19    7  596   24   32    0    0    0
  NK Proliferating   139    7 2677   23    5   29  144    0   96    8    6   27    0    0    0
  Treg                 0    0    0    0    0    2    0    0   40    0    1    2    0    0    0

table(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
  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        0

table(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
  B intermediate       0    0    0    0    0    0    0    1    2    0    0    0    4    0    0    0
  B memory             3    0    0    0    0   19    0   13   11    1  163    0   42    0    0    0
  CD14 Mono            0    0    0    0    0    0    0    0    0    0   11    0    0    0    1    0
  CD4 CTL              0    8    2    0    0    0    0    1    0    0    0    1    0    0    1    0
  CD4 Naive            0 1397    4    0    0    0    0   41    7    0    0  584    0    8    1    0
  CD4 Proliferating 5409   22 2662 3748 3719 2873 3611 1745 1129 2185  903    0  997    7    0    1
  CD4 TCM            147 4994   86   70  104  889   13 1700 2096    7 1525  841  216   89   53    0
  CD4 TEM              0   75    1    0    0    0    0    4    0    0    1    3    0    0    0    0
  CD8 Proliferating    0    0    0    0    0    0    0    0    0    0    1    0    1    0    0    0
  CD8 TCM              0    0    1    0    0    0    0    0   16    0    0    0    0    0    0    0
  CD8 TEM              0    0    0    0    0    0    0    1    5    0    6    0    0    3    0    0
  cDC1                 0    0    0    0    0    0    0    0    0    0    2    0    6    0    0    0
  cDC2                 1    0    0    0    0    0    0    0    0    0   45    0    4    0    2    1
  dnT                  0    0    0    0    0    0    0    6    0    0    7    0    0    2    0    0
  HSPC               988    0    5   65    1   24    8    9   55  597   23    0   30    0    0    0
  NK Proliferating   135    7 2701    3   23    0  139  103    9    8    8    0   24    1    0    0
  Treg                 0    0    0    0    0    0    0   38    2    0    1    0    2    2    0    0

table(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
#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        0

table(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
  B intermediate       1    0    0    0    2    2    0    0    0    0    0    0    0    0    0    2    0    0
  B memory             2    0    0   29   11   10    0    0    3  160    0    0    1    0   22   14    0    0
  CD14 Mono            0    0    0    0    0    0    0    0    0   10    0    0    0    1    0    0    1    0
  CD4 CTL              2    8    0    0    1    0    0    0    0    0    1    0    0    0    0    0    1    0
  CD4 Naive            3  881    0    0    8   49    0    0    0    0 1100    0    0    0    0    0    1    0
  CD4 Proliferating 2502   23 3232 2991 1495 1342 2986 2628 2301 1171    0 2659 2275 1781  958  666    0    1
  CD4 TCM             63 4102   78  983 2145 1730   87    1   32 1521 1733   32   71    8  100   91   53    0
  CD4 TEM              1   66    0    0    0    4    0    0    0    1   12    0    0    0    0    0    0    0
  CD8 Proliferating    0    0    0    1    0    0    0    0    0    1    0    0    0    0    0    0    0    0
  CD8 TCM              0    0    0    1   15    0    0    0    0    0    0    1    0    0    0    0    0    0
  CD8 TEM              0    0    0    0    5    4    0    0    0    6    0    0    0    0    0    0    0    0
  cDC1                 0    0    0    0    0    0    0    0    0    2    0    0    0    0    3    3    0    0
  cDC2                 0    0    0    0    0    0    0    0    1   45    0    0    0    0    2    2    2    1
  dnT                  0    0    0    1    0    8    0    0    0    5    0    0    0    1    0    0    0    0
  HSPC                 4    0  752   23   54    6    1  176  622   35    0   65    6    0   33   28    0    0
  NK Proliferating  2649    9    7    1   82   80   24  225    8    6    0    2    0    5   50   13    0    0
  Treg                 0    0    0    0    2   40    0    0    0    1    0    0    0    0    0    2    0    0

table(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    0