Spatial Cell-Cell communication scores based on spatial expression of interacting cells at spots resolution
spatCellCellcomSpots(
gobject,
spat_unit = NULL,
feat_type = NULL,
ave_celltype_exp,
spatial_network_name = "Delaunay_network",
cluster_column = "cell_ID",
random_iter = 1000,
feature_set_1,
feature_set_2,
min_observations = 2,
expression_values = c("normalized", "scaled", "custom"),
detailed = FALSE,
adjust_method = c("fdr", "bonferroni", "BH", "holm", "hochberg", "hommel", "BY",
"none"),
adjust_target = c("features", "cells"),
do_parallel = TRUE,
cores = NA,
set_seed = TRUE,
seed_number = 1234,
verbose = c("a little", "a lot", "none")
)
giotto object to use
spatial unit (e.g. 'cell')
feature type (e.g. 'rna')
Matrix with average expression per cell type
spatial network to use for identifying interacting cells
cluster column with cell type information
number of iterations
first specific feature set from feature pairs
second specific feature set from feature pairs
minimum number of interactions needed to be considered
(e.g. 'normalized', 'scaled', 'custom')
provide more detailed information (random variance and z-score)
which method to adjust p-values
adjust multiple hypotheses at the cell or feature level
run calculations in parallel with mclapply
number of cores to use if do_parallel = TRUE
set a seed for reproducibility
seed number
verbose (e.g. 'a little', 'a lot', 'none')
Cell-Cell communication scores for feature pairs based on spatial interaction
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 in cells that are spatially in proximity to each other.
* LR_comb:Pair of ligand and receptor * lig_cell_type: cell type to assess expression level of ligand * lig_expr: average expression residual(observed - DWLS_predicted) of ligand in lig_cell_type * ligand: ligand name * rec_cell_type: cell type to assess expression level of receptor * rec_expr: average expression residual(observed - DWLS_predicted) of receptor in rec_cell_type * receptor: receptor name * LR_expr: combined average ligand and receptor expression residual * lig_nr: total number of cells from lig_cell_type that spatially interact with cells from rec_cell_type * rec_nr: total number of cells from rec_cell_type that spatially interact with cells from lig_cell_type * rand_expr: average combined ligand and receptor expression residual from random spatial permutations * av_diff: average difference between LR_expr and rand_expr over all random spatial permutations * sd_diff: (optional) standard deviation of the difference between LR_expr and rand_expr over all random spatial permutations * z_score: (optional) z-score * log2fc: LR_expr - rand_expr * pvalue: p-value * LR_cell_comb: cell type pair combination * p.adj: adjusted p-value * PI: significanc score: log2fc \* -log10(p.adj)