Cell-Cell communication scores based on expression only
exprCellCellcom(
gobject,
feat_type = NULL,
spat_unit = NULL,
cluster_column = "cell_types",
random_iter = 1000,
feat_set_1,
feat_set_2,
log2FC_addendum = 0.1,
detailed = FALSE,
adjust_method = c("fdr", "bonferroni", "BH", "holm", "hochberg", "hommel", "BY",
"none"),
adjust_target = c("feats", "cells"),
set_seed = TRUE,
seed_number = 1234,
verbose = TRUE
)giotto object to use
feature type
spatial unit
cluster column with cell type information
number of iterations
first specific feature set from feature pairs
second specific feature set from feature pairs
addendum to add when calculating log2FC
provide more detailed information (random variance and z-score)
which method to adjust p-values
adjust multiple hypotheses at the cell or feature level
set seed for random simulations (default = TRUE)
seed number
verbose
Cell-Cell communication scores for feature pairs based on expression only
Statistical framework to identify if pairs of features (such as ligand-receptor combinations) are expressed at higher levels than expected based on a reshuffled null distribution of feature expression values, without considering the spatial position of cells. More details will follow soon.
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"
exprCellCellcom(g, cluster_column = "leiden_clus",
feat_set_1 = "Gm19935", feat_set_2 = "9630013A20Rik")
#> Key: <LR_comb>
#> LR_comb lig_cell_type lig_expr ligand rec_cell_type
#> <char> <fctr> <num> <char> <fctr>
#> 1: Gm19935-9630013A20Rik 6 0.4293181 Gm19935 4
#> 2: Gm19935-9630013A20Rik 6 0.4293181 Gm19935 5
#> 3: Gm19935-9630013A20Rik 6 0.4293181 Gm19935 1
#> 4: Gm19935-9630013A20Rik 6 0.4293181 Gm19935 3
#> 5: Gm19935-9630013A20Rik 2 0.3574502 Gm19935 4
#> 6: Gm19935-9630013A20Rik 2 0.3574502 Gm19935 5
#> 7: Gm19935-9630013A20Rik 2 0.3574502 Gm19935 1
#> 8: Gm19935-9630013A20Rik 2 0.3574502 Gm19935 3
#> 9: Gm19935-9630013A20Rik 5 0.2922187 Gm19935 4
#> 10: Gm19935-9630013A20Rik 6 0.4293181 Gm19935 2
#> 11: Gm19935-9630013A20Rik 5 0.2922187 Gm19935 5
#> 12: Gm19935-9630013A20Rik 5 0.2922187 Gm19935 1
#> 13: Gm19935-9630013A20Rik 4 0.2495580 Gm19935 4
#> 14: Gm19935-9630013A20Rik 1 0.2326362 Gm19935 4
#> 15: Gm19935-9630013A20Rik 5 0.2922187 Gm19935 3
#> 16: Gm19935-9630013A20Rik 3 0.2197897 Gm19935 4
#> 17: Gm19935-9630013A20Rik 4 0.2495580 Gm19935 5
#> 18: Gm19935-9630013A20Rik 4 0.2495580 Gm19935 1
#> 19: Gm19935-9630013A20Rik 2 0.3574502 Gm19935 2
#> 20: Gm19935-9630013A20Rik 6 0.4293181 Gm19935 6
#> 21: Gm19935-9630013A20Rik 1 0.2326362 Gm19935 5
#> 22: Gm19935-9630013A20Rik 1 0.2326362 Gm19935 1
#> 23: Gm19935-9630013A20Rik 4 0.2495580 Gm19935 3
#> 24: Gm19935-9630013A20Rik 3 0.2197897 Gm19935 5
#> 25: Gm19935-9630013A20Rik 3 0.2197897 Gm19935 1
#> 26: Gm19935-9630013A20Rik 1 0.2326362 Gm19935 3
#> 27: Gm19935-9630013A20Rik 3 0.2197897 Gm19935 3
#> 28: Gm19935-9630013A20Rik 5 0.2922187 Gm19935 2
#> 29: Gm19935-9630013A20Rik 2 0.3574502 Gm19935 6
#> 30: Gm19935-9630013A20Rik 6 0.4293181 Gm19935 7
#> 31: Gm19935-9630013A20Rik 4 0.2495580 Gm19935 2
#> 32: Gm19935-9630013A20Rik 1 0.2326362 Gm19935 2
#> 33: Gm19935-9630013A20Rik 3 0.2197897 Gm19935 2
#> 34: Gm19935-9630013A20Rik 5 0.2922187 Gm19935 6
#> 35: Gm19935-9630013A20Rik 2 0.3574502 Gm19935 7
#> 36: Gm19935-9630013A20Rik 4 0.2495580 Gm19935 6
#> 37: Gm19935-9630013A20Rik 1 0.2326362 Gm19935 6
#> 38: Gm19935-9630013A20Rik 7 0.0000000 Gm19935 4
#> 39: Gm19935-9630013A20Rik 3 0.2197897 Gm19935 6
#> 40: Gm19935-9630013A20Rik 7 0.0000000 Gm19935 5
#> 41: Gm19935-9630013A20Rik 5 0.2922187 Gm19935 7
#> 42: Gm19935-9630013A20Rik 7 0.0000000 Gm19935 1
#> 43: Gm19935-9630013A20Rik 7 0.0000000 Gm19935 3
#> 44: Gm19935-9630013A20Rik 4 0.2495580 Gm19935 7
#> 45: Gm19935-9630013A20Rik 1 0.2326362 Gm19935 7
#> 46: Gm19935-9630013A20Rik 3 0.2197897 Gm19935 7
#> 47: Gm19935-9630013A20Rik 7 0.0000000 Gm19935 2
#> 48: Gm19935-9630013A20Rik 7 0.0000000 Gm19935 6
#> 49: Gm19935-9630013A20Rik 7 0.0000000 Gm19935 7
#> LR_comb lig_cell_type lig_expr ligand rec_cell_type
#> rec_expr receptor LR_expr lig_nr rec_nr rand_expr av_diff
#> <num> <char> <num> <int> <int> <num> <num>
#> 1: 0.33023852 9630013A20Rik 0.75955660 10 108 0.5247843 0.234772341
#> 2: 0.29575033 9630013A20Rik 0.72506842 10 45 0.5262755 0.198792953
#> 3: 0.28874834 9630013A20Rik 0.71806642 10 122 0.5237300 0.194336461
#> 4: 0.26833691 9630013A20Rik 0.69765500 10 162 0.5254247 0.172230266
#> 5: 0.33023852 9630013A20Rik 0.68768868 84 108 0.5266116 0.161077071
#> 6: 0.29575033 9630013A20Rik 0.65320049 84 45 0.5281028 0.125097683
#> 7: 0.28874834 9630013A20Rik 0.64619850 84 122 0.5255573 0.120641191
#> 8: 0.26833691 9630013A20Rik 0.62578707 84 162 0.5272521 0.098534996
#> 9: 0.33023852 9630013A20Rik 0.62245718 45 108 0.5329486 0.089508532
#> 10: 0.17597264 9630013A20Rik 0.60529072 10 84 0.5246925 0.080598186
#> 11: 0.29575033 9630013A20Rik 0.58796899 45 45 0.5344398 0.053529145
#> 12: 0.28874834 9630013A20Rik 0.58096700 45 122 0.5318943 0.049072652
#> 13: 0.33023852 9630013A20Rik 0.57979653 108 108 0.5281585 0.051637977
#> 14: 0.33023852 9630013A20Rik 0.56287473 122 108 0.5279882 0.034886510
#> 15: 0.26833691 9630013A20Rik 0.56055557 45 162 0.5335891 0.026966457
#> 16: 0.33023852 9630013A20Rik 0.55002826 162 108 0.5269931 0.023035131
#> 17: 0.29575033 9630013A20Rik 0.54530835 108 45 0.5296498 0.015658590
#> 18: 0.28874834 9630013A20Rik 0.53830635 108 122 0.5271043 0.011202097
#> 19: 0.17597264 9630013A20Rik 0.53342280 84 84 0.5265199 0.006902916
#> 20: 0.09952757 9630013A20Rik 0.52884565 10 10 0.5209773 0.007868373
#> 21: 0.29575033 9630013A20Rik 0.52838655 122 45 0.5294794 -0.001092878
#> 22: 0.28874834 9630013A20Rik 0.52138455 122 122 0.5269339 -0.005549370
#> 23: 0.26833691 9630013A20Rik 0.51789492 108 162 0.5287990 -0.010904098
#> 24: 0.29575033 9630013A20Rik 0.51554007 162 45 0.5284843 -0.012944257
#> 25: 0.28874834 9630013A20Rik 0.50853808 162 122 0.5259388 -0.017400749
#> 26: 0.26833691 9630013A20Rik 0.50097313 122 162 0.5286287 -0.027655565
#> 27: 0.26833691 9630013A20Rik 0.48812665 162 162 0.5276336 -0.039506944
#> 28: 0.17597264 9630013A20Rik 0.46819130 45 84 0.5328569 -0.064665622
#> 29: 0.09952757 9630013A20Rik 0.45697772 84 10 0.5228046 -0.065826897
#> 30: 0.00000000 9630013A20Rik 0.42931808 10 93 0.5204358 -0.091117732
#> 31: 0.17597264 9630013A20Rik 0.42553065 108 84 0.5280668 -0.102536177
#> 32: 0.17597264 9630013A20Rik 0.40860885 122 84 0.5278965 -0.119287645
#> 33: 0.17597264 9630013A20Rik 0.39576238 162 84 0.5269014 -0.131139024
#> 34: 0.09952757 9630013A20Rik 0.39174622 45 10 0.5291417 -0.137395436
#> 35: 0.00000000 9630013A20Rik 0.35745016 84 93 0.5222632 -0.164813002
#> 36: 0.09952757 9630013A20Rik 0.34908558 108 10 0.5243516 -0.175265991
#> 37: 0.09952757 9630013A20Rik 0.33216378 122 10 0.5241812 -0.192017458
#> 38: 0.33023852 9630013A20Rik 0.33023852 93 108 0.5372749 -0.207036394
#> 39: 0.09952757 9630013A20Rik 0.31931730 162 10 0.5231861 -0.203868837
#> 40: 0.29575033 9630013A20Rik 0.29575033 93 45 0.5387661 -0.243015781
#> 41: 0.00000000 9630013A20Rik 0.29221866 45 93 0.5286002 -0.236381541
#> 42: 0.28874834 9630013A20Rik 0.28874834 93 122 0.5362206 -0.247472274
#> 43: 0.26833691 9630013A20Rik 0.26833691 93 162 0.5379154 -0.269578469
#> 44: 0.00000000 9630013A20Rik 0.24955801 108 93 0.5238101 -0.274252096
#> 45: 0.00000000 9630013A20Rik 0.23263621 122 93 0.5236398 -0.291003563
#> 46: 0.00000000 9630013A20Rik 0.21978974 162 93 0.5226447 -0.302854942
#> 47: 0.17597264 9630013A20Rik 0.17597264 93 84 0.5371832 -0.361210548
#> 48: 0.09952757 9630013A20Rik 0.09952757 93 10 0.5334679 -0.433940362
#> 49: 0.00000000 9630013A20Rik 0.00000000 93 93 0.5329265 -0.532926467
#> rec_expr receptor LR_expr lig_nr rec_nr rand_expr av_diff
#> log2fc pvalue LR_cell_comb p.adj PI
#> <num> <num> <char> <num> <num>
#> 1: 0.460234536 0.150 6--4 0.150 3.791913e-01
#> 2: 0.397716399 0.236 6--5 0.236 2.494032e-01
#> 3: 0.391296425 0.192 6--1 0.192 2.804417e-01
#> 4: 0.350928616 0.270 6--3 0.270 1.995507e-01
#> 5: 0.330054046 0.162 2--4 0.162 2.609028e-01
#> 6: 0.262033221 0.304 2--5 0.304 1.355043e-01
#> 7: 0.254417400 0.184 2--1 0.184 1.870431e-01
#> 8: 0.210501018 0.364 2--3 0.364 9.238861e-02
#> 9: 0.190823627 0.468 5--4 0.468 6.292488e-02
#> 10: 0.175071769 0.606 6--2 0.606 3.808290e-02
#> 11: 0.116860156 0.696 5--5 0.696 1.839271e-02
#> 12: 0.107901525 0.644 5--1 0.644 2.062151e-02
#> 13: 0.113974244 0.676 4--4 0.676 1.938170e-02
#> 14: 0.077998759 0.698 1--4 0.698 1.217908e-02
#> 15: 0.060132389 0.810 5--3 0.810 5.503014e-03
#> 16: 0.052052807 0.814 3--4 0.814 4.652251e-03
#> 17: 0.035439134 0.888 4--5 0.888 1.828200e-03
#> 18: 0.025543697 0.904 4--1 0.904 1.119620e-03
#> 19: 0.015808501 0.926 2--2 0.926 5.278303e-04
#> 20: 0.018165474 0.942 6--6 0.942 4.713776e-04
#> 21: -0.002506928 0.960 1--5 0.960 -4.444474e-05
#> 22: -0.012827017 0.948 1--1 0.948 -2.974799e-04
#> 23: -0.025237452 0.950 4--3 0.950 -5.621994e-04
#> 24: -0.030023992 0.944 3--5 0.944 -7.514406e-04
#> 25: -0.040674131 0.888 3--1 0.888 -2.098258e-03
#> 26: -0.064907641 0.792 1--3 0.792 -6.573510e-03
#> 27: -0.093795710 0.784 3--3 0.784 -9.912700e-03
#> 28: -0.155502627 0.658 5--2 0.658 -2.826635e-02
#> 29: -0.161160019 0.700 2--6 0.700 -2.496400e-02
#> 30: -0.229147029 0.894 6--7 0.894 -1.115086e-02
#> 31: -0.257143164 0.396 4--2 0.396 -1.034499e-01
#> 32: -0.303970191 0.188 1--2 0.188 -2.206344e-01
#> 33: -0.338589761 0.214 3--2 0.214 -2.267150e-01
#> 34: -0.355470921 0.380 5--6 0.380 -1.493747e-01
#> 35: -0.443910274 0.758 2--7 0.758 -5.341608e-02
#> 36: -0.475368241 0.286 4--6 0.286 -2.584263e-01
#> 37: -0.530386832 0.166 1--6 0.166 -4.136444e-01
#> 38: -0.566779176 0.642 7--4 0.642 -1.090851e-01
#> 39: -0.571620783 0.148 3--6 0.148 -4.742956e-01
#> 40: -0.690697215 0.532 7--5 0.532 -1.893121e-01
#> 41: -0.680484559 0.500 5--7 0.500 -2.048463e-01
#> 42: -0.710690600 0.522 7--1 0.522 -2.006489e-01
#> 43: -0.792339080 0.442 7--3 0.442 -2.809458e-01
#> 44: -0.835575030 0.356 4--7 0.356 -3.747972e-01
#> 45: -0.906767711 0.214 1--7 0.214 -6.071592e-01
#> 46: -0.961285460 0.216 3--7 0.216 -6.397799e-01
#> 47: -1.207182952 0.118 7--2 0.118 -1.120408e+00
#> 48: -1.666683505 0.082 7--6 0.082 -1.810329e+00
#> 49: -2.662037898 0.166 7--7 0.166 -2.076102e+00
#> log2fc pvalue LR_cell_comb p.adj PI