Combine spatial and expression based cell-cell communication data.tables
combCCcom(
spatialCC,
exprCC,
min_lig_nr = 3,
min_rec_nr = 3,
min_padj_value = 1,
min_log2fc = 0,
min_av_diff = 0,
detailed = FALSE
)spatial cell-cell communication scores
expression cell-cell communication scores
minimum number of ligand cells
minimum number of receptor cells
minimum adjusted p-value
minimum log2 fold-change
minimum average expression difference
detailed option used with spatCellCellcom
(default = FALSE)
combined data.table with spatial and expression communication data
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> cell_spatInfo_spatVector.shp
#> cell
#>
#> 3.2 read Giotto spatial centroid information
#> cell
#>
#> 3.3 read Giotto spatial overlap information
#> No overlaps were found, overlap loading will be
#> skipped
#>
#> 4. read Giotto image information
#> a giotto python environment was found
#> Using python path:
#> "/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw"
exprCC <- exprCellCellcom(g, cluster_column = "leiden_clus",
feat_set_1 = "Gm19935", feat_set_2 = "9630013A20Rik")
spatialCC <- spatCellCellcom(gobject = g, cluster_column = "leiden_clus",
feat_set_1 = "Gm19935", feat_set_2 = "9630013A20Rik", verbose = "a lot",
random_iter = 10)
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10 <- Inf returned
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10
#> simulations: 1 2 3 4 5 6 7 8 9 10 <- Inf returned
#> Warning: no adjusted p.values that are not zero; returning Inf
#> Warning: no adjusted p.values that are not zero; returning Inf
combCCcom(spatialCC = spatialCC, exprCC = exprCC)
#> Key: <LR_comb, LR_cell_comb, lig_cell_type, rec_cell_type, ligand, receptor>
#> LR_comb LR_cell_comb lig_cell_type rec_cell_type ligand
#> <char> <char> <fctr> <fctr> <char>
#> 1: Gm19935-9630013A20Rik 1--1 1 1 Gm19935
#> 2: Gm19935-9630013A20Rik 1--3 1 3 Gm19935
#> 3: Gm19935-9630013A20Rik 1--5 1 5 Gm19935
#> 4: Gm19935-9630013A20Rik 1--6 1 6 Gm19935
#> 5: Gm19935-9630013A20Rik 1--7 1 7 Gm19935
#> 6: Gm19935-9630013A20Rik 2--2 2 2 Gm19935
#> 7: Gm19935-9630013A20Rik 2--5 2 5 Gm19935
#> 8: Gm19935-9630013A20Rik 3--1 3 1 Gm19935
#> 9: Gm19935-9630013A20Rik 3--3 3 3 Gm19935
#> 10: Gm19935-9630013A20Rik 3--4 3 4 Gm19935
#> 11: Gm19935-9630013A20Rik 3--5 3 5 Gm19935
#> 12: Gm19935-9630013A20Rik 3--6 3 6 Gm19935
#> 13: Gm19935-9630013A20Rik 4--3 4 3 Gm19935
#> 14: Gm19935-9630013A20Rik 4--4 4 4 Gm19935
#> 15: Gm19935-9630013A20Rik 4--6 4 6 Gm19935
#> 16: Gm19935-9630013A20Rik 5--1 5 1 Gm19935
#> 17: Gm19935-9630013A20Rik 5--2 5 2 Gm19935
#> 18: Gm19935-9630013A20Rik 5--3 5 3 Gm19935
#> 19: Gm19935-9630013A20Rik 5--5 5 5 Gm19935
#> 20: Gm19935-9630013A20Rik 5--6 5 6 Gm19935
#> 21: Gm19935-9630013A20Rik 6--1 6 1 Gm19935
#> 22: Gm19935-9630013A20Rik 6--3 6 3 Gm19935
#> 23: Gm19935-9630013A20Rik 6--4 6 4 Gm19935
#> 24: Gm19935-9630013A20Rik 6--5 6 5 Gm19935
#> 25: Gm19935-9630013A20Rik 6--6 6 6 Gm19935
#> 26: Gm19935-9630013A20Rik 6--7 6 7 Gm19935
#> 27: Gm19935-9630013A20Rik 7--1 7 1 Gm19935
#> 28: Gm19935-9630013A20Rik 7--6 7 6 Gm19935
#> 29: Gm19935-9630013A20Rik 7--7 7 7 Gm19935
#> LR_comb LR_cell_comb lig_cell_type rec_cell_type ligand
#> receptor lig_expr_spat rec_expr_spat LR_expr_spat lig_nr_spat
#> <char> <num> <num> <num> <int>
#> 1: 9630013A20Rik 0.30914232 0.17530545 0.4844478 161
#> 2: 9630013A20Rik 0.20683620 0.09032721 0.2971634 102
#> 3: 9630013A20Rik 0.17850483 0.11224192 0.2907468 41
#> 4: 9630013A20Rik 1.26325380 0.32184532 1.5850991 17
#> 5: 9630013A20Rik 0.55560407 0.00000000 0.5556041 14
#> 6: 9630013A20Rik 0.11342034 0.23907794 0.3524983 121
#> 7: 9630013A20Rik 0.06646316 0.60181006 0.6682732 38
#> 8: 9630013A20Rik 0.29380142 0.12413060 0.4179320 89
#> 9: 9630013A20Rik 0.21449815 0.07000002 0.2844982 108
#> 10: 9630013A20Rik 0.33661638 0.00000000 0.3366164 6
#> 11: 9630013A20Rik 0.67646973 0.00000000 0.6764697 5
#> 12: 9630013A20Rik 0.00000000 0.00000000 0.0000000 9
#> 13: 9630013A20Rik 0.00000000 0.00000000 0.0000000 6
#> 14: 9630013A20Rik 0.09396233 0.10048837 0.1944507 93
#> 15: 9630013A20Rik 0.14061468 0.00000000 0.1406147 26
#> 16: 9630013A20Rik 0.13598163 0.31893557 0.4549172 57
#> 17: 9630013A20Rik 0.11024392 0.73487022 0.8451141 34
#> 18: 9630013A20Rik 0.00000000 0.00000000 0.0000000 6
#> 19: 9630013A20Rik 0.14614174 0.95582749 1.1019692 76
#> 20: 9630013A20Rik 1.78685038 0.98253548 2.7693859 23
#> 21: 9630013A20Rik 1.39370283 0.22070242 1.6144053 15
#> 22: 9630013A20Rik 0.59885919 0.17685852 0.7757177 4
#> 23: 9630013A20Rik 0.27008393 0.13080439 0.4008883 47
#> 24: 9630013A20Rik 1.25341386 0.86184960 2.1152635 16
#> 25: 9630013A20Rik 1.34521521 0.20155242 1.5467676 37
#> 26: 9630013A20Rik 0.60686608 0.00000000 0.6068661 9
#> 27: 9630013A20Rik 0.40437296 0.45406594 0.8584389 8
#> 28: 9630013A20Rik 0.00000000 0.00000000 0.0000000 5
#> 29: 9630013A20Rik 0.60289491 0.38773430 0.9906292 8
#> receptor lig_expr_spat rec_expr_spat LR_expr_spat lig_nr_spat
#> rec_nr_spat rand_expr_spat av_diff_spat log2fc_spat pvalue_spat
#> <int> <num> <num> <num> <num>
#> 1: 161 0.4844478 0.00000000 0.000000e+00 1.0
#> 2: 89 0.3646706 -0.06750721 -2.264757e-01 0.2
#> 3: 57 0.6479728 -0.35722602 -9.367519e-01 0.0
#> 4: 15 0.8177809 0.76731822 8.766118e-01 0.0
#> 5: 8 0.9235238 -0.36791974 -6.426480e-01 0.2
#> 6: 121 0.3467125 0.00578580 1.856575e-02 0.7
#> 7: 34 0.5744252 0.09384803 1.879610e-01 0.4
#> 8: 102 0.4373695 -0.01943749 -5.315170e-02 0.4
#> 9: 108 0.2844982 0.00000000 0.000000e+00 1.0
#> 10: 6 0.3119815 0.02463484 8.378658e-02 0.8
#> 11: 6 0.4740738 0.20239588 4.356933e-01 0.3
#> 12: 4 0.5237612 -0.52376116 -2.640994e+00 0.2
#> 13: 6 0.1706255 -0.17062548 -1.436298e+00 0.6
#> 14: 93 0.1944507 0.00000000 -3.203427e-16 1.0
#> 15: 47 0.5544684 -0.41385376 -1.443599e+00 0.0
#> 16: 41 0.6904034 -0.23548624 -5.103167e-01 0.4
#> 17: 38 0.5955208 0.24959330 4.423948e-01 0.0
#> 18: 5 0.3260308 -0.32603077 -2.090958e+00 0.5
#> 19: 76 0.9785259 0.12344334 1.563391e-01 0.1
#> 20: 16 1.2538033 1.51558255 1.083724e+00 0.0
#> 21: 17 1.1145144 0.49989085 4.973286e-01 0.2
#> 22: 9 0.9073401 -0.13162236 -2.020130e-01 0.6
#> 23: 26 0.8144591 -0.41357082 -8.684297e-01 0.0
#> 24: 23 1.0979788 1.01728464 8.868759e-01 0.0
#> 25: 37 1.4609677 0.08579996 7.719634e-02 0.8
#> 26: 5 1.4236741 -0.81680803 -1.108046e+00 0.2
#> 27: 14 0.6622601 0.19617876 3.304030e-01 0.4
#> 28: 9 1.5946353 -1.59463534 -4.082903e+00 0.0
#> 29: 8 1.2206012 -0.22997195 -2.760341e-01 0.3
#> rec_nr_spat rand_expr_spat av_diff_spat log2fc_spat pvalue_spat
#> p.adj_spat PI_spat lig_expr rec_expr LR_expr lig_nr rec_nr
#> <num> <num> <num> <num> <num> <int> <int>
#> 1: 1.0 0.000000000 0.2326362 0.28874834 0.52138455 122 122
#> 2: 0.2 -0.158299738 0.2326362 0.26833691 0.50097313 122 162
#> 3: 0.0 -0.372771048 0.2326362 0.29575033 0.52838655 122 45
#> 4: 0.0 0.612725328 0.2326362 0.09952757 0.33216378 122 10
#> 5: 0.2 -0.449191643 0.2326362 0.00000000 0.23263621 122 93
#> 6: 0.7 0.002875871 0.3574502 0.17597264 0.53342280 84 84
#> 7: 0.4 0.074797218 0.3574502 0.29575033 0.65320049 84 45
#> 8: 0.4 -0.021151189 0.2197897 0.28874834 0.50853808 162 122
#> 9: 1.0 0.000000000 0.2197897 0.26833691 0.48812665 162 162
#> 10: 0.8 0.008119758 0.2197897 0.33023852 0.55002826 162 108
#> 11: 0.3 0.227814790 0.2197897 0.29575033 0.51554007 162 45
#> 12: 0.2 -1.845975399 0.2197897 0.09952757 0.31931730 162 10
#> 13: 0.6 -0.318640847 0.2495580 0.26833691 0.51789492 108 162
#> 14: 1.0 0.000000000 0.2495580 0.33023852 0.57979653 108 108
#> 15: 0.0 Inf 0.2495580 0.09952757 0.34908558 108 10
#> 16: 0.4 -0.203075434 0.2922187 0.28874834 0.58096700 45 122
#> 17: 0.0 0.176046606 0.2922187 0.17597264 0.46819130 45 84
#> 18: 0.5 -0.629440967 0.2922187 0.26833691 0.56055557 45 162
#> 19: 0.1 0.156339149 0.2922187 0.29575033 0.58796899 45 45
#> 20: 0.0 -Inf 0.2922187 0.09952757 0.39174622 45 10
#> 21: 0.2 0.347617756 0.4293181 0.28874834 0.71806642 10 122
#> 22: 0.6 -0.044816333 0.4293181 0.26833691 0.69765500 10 162
#> 23: 0.0 Inf 0.4293181 0.33023852 0.75955660 10 108
#> 24: 0.0 -Inf 0.4293181 0.29575033 0.72506842 10 45
#> 25: 0.8 0.007481098 0.4293181 0.09952757 0.52884565 10 10
#> 26: 0.2 -0.774490595 0.4293181 0.00000000 0.42931808 10 93
#> 27: 0.4 0.131480586 0.0000000 0.28874834 0.28874834 93 122
#> 28: 0.0 -2.853826696 0.0000000 0.09952757 0.09952757 93 10
#> 29: 0.3 -0.144332371 0.0000000 0.00000000 0.00000000 93 93
#> p.adj_spat PI_spat lig_expr rec_expr LR_expr lig_nr rec_nr
#> rand_expr av_diff log2fc pvalue p.adj PI LR_expr_rnk
#> <num> <num> <num> <num> <num> <num> <num>
#> 1: 0.5269339 -0.005549370 -0.012827017 0.948 0.948 -2.974799e-04 14
#> 2: 0.5286287 -0.027655565 -0.064907641 0.792 0.792 -6.573510e-03 18
#> 3: 0.5294794 -0.001092878 -0.002506928 0.960 0.960 -4.444474e-05 13
#> 4: 0.5241812 -0.192017458 -0.530386832 0.166 0.166 -4.136444e-01 24
#> 5: 0.5236398 -0.291003563 -0.906767711 0.214 0.214 -6.071592e-01 27
#> 6: 0.5265199 0.006902916 0.015808501 0.926 0.926 5.278303e-04 11
#> 7: 0.5281028 0.125097683 0.262033221 0.304 0.304 1.355043e-01 5
#> 8: 0.5259388 -0.017400749 -0.040674131 0.888 0.888 -2.098258e-03 17
#> 9: 0.5276336 -0.039506944 -0.093795710 0.784 0.784 -9.912700e-03 19
#> 10: 0.5269931 0.023035131 0.052052807 0.814 0.814 4.652251e-03 10
#> 11: 0.5284843 -0.012944257 -0.030023992 0.944 0.944 -7.514406e-04 16
#> 12: 0.5231861 -0.203868837 -0.571620783 0.148 0.148 -4.742956e-01 25
#> 13: 0.5287990 -0.010904098 -0.025237452 0.950 0.950 -5.621994e-04 15
#> 14: 0.5281585 0.051637977 0.113974244 0.676 0.676 1.938170e-02 8
#> 15: 0.5243516 -0.175265991 -0.475368241 0.286 0.286 -2.584263e-01 23
#> 16: 0.5318943 0.049072652 0.107901525 0.644 0.644 2.062151e-02 7
#> 17: 0.5328569 -0.064665622 -0.155502627 0.658 0.658 -2.826635e-02 20
#> 18: 0.5335891 0.026966457 0.060132389 0.810 0.810 5.503014e-03 9
#> 19: 0.5344398 0.053529145 0.116860156 0.696 0.696 1.839271e-02 6
#> 20: 0.5291417 -0.137395436 -0.355470921 0.380 0.380 -1.493747e-01 22
#> 21: 0.5237300 0.194336461 0.391296425 0.192 0.192 2.804417e-01 3
#> 22: 0.5254247 0.172230266 0.350928616 0.270 0.270 1.995507e-01 4
#> 23: 0.5247843 0.234772341 0.460234536 0.150 0.150 3.791913e-01 1
#> 24: 0.5262755 0.198792953 0.397716399 0.236 0.236 2.494032e-01 2
#> 25: 0.5209773 0.007868373 0.018165474 0.942 0.942 4.713776e-04 12
#> 26: 0.5204358 -0.091117732 -0.229147029 0.894 0.894 -1.115086e-02 21
#> 27: 0.5362206 -0.247472274 -0.710690600 0.522 0.522 -2.006489e-01 26
#> 28: 0.5334679 -0.433940362 -1.666683505 0.082 0.082 -1.810329e+00 28
#> 29: 0.5329265 -0.532926467 -2.662037898 0.166 0.166 -2.076102e+00 29
#> rand_expr av_diff log2fc pvalue p.adj PI LR_expr_rnk
#> LR_spat_rnk exprPI_rnk spatPI_rnk
#> <num> <num> <num>
#> 1: 15.0 14 14.0
#> 2: 21.0 18 19.0
#> 3: 22.0 13 22.0
#> 4: 4.0 25 3.0
#> 5: 14.0 27 23.0
#> 6: 19.0 11 12.0
#> 7: 12.0 5 9.0
#> 8: 17.0 17 16.0
#> 9: 23.0 19 14.0
#> 10: 20.0 10 10.0
#> 11: 11.0 16 5.0
#> 12: 27.5 26 26.0
#> 13: 27.5 15 21.0
#> 14: 24.0 7 14.0
#> 15: 25.0 24 1.5
#> 16: 16.0 6 20.0
#> 17: 9.0 21 6.0
#> 18: 27.5 9 24.0
#> 19: 6.0 8 7.0
#> 20: 1.0 22 28.5
#> 21: 3.0 2 4.0
#> 22: 10.0 4 17.0
#> 23: 18.0 1 1.5
#> 24: 2.0 3 28.5
#> 25: 5.0 12 11.0
#> 26: 13.0 20 25.0
#> 27: 8.0 23 8.0
#> 28: 27.5 28 27.0
#> 29: 7.0 29 18.0
#> LR_spat_rnk exprPI_rnk spatPI_rnk