Getting Started With SEraster (original) (raw)
Rasterized cell-type labels can be used to analyze pair-wise cell-type co-enrichment To do so, we binarize the rasterized cell-type labels using a relative enrichment metric and a previously developed tool called CooccurrenceAffinity. Please refer to our paper for more details about the methodology and CooccurrenceAffinityfor more details about the package.
# extract cell-type labels
ct_labels <- as.factor(colData(merfish_mousePOA)$celltype)
# compute relative enrichment (RE) metric
mat <- assay(rastCt, "pixelval")
mat_re <- do.call(rbind, lapply(rownames(rastCt), function(ct_label) {
mat[ct_label,] / (sum(mat[ct_label,]) / sum(mat) * colSums(mat))
}))
rownames(mat_re) <- rownames(mat)
# binarize
mat_bin <- ifelse(mat_re >= 1, 1, 0)
# add RE and binarized layers to SpatialExperiment object
assays(rastCt) <- list(pixelval = assay(rastCt, "pixelval"), re = mat_re, bin = mat_bin)ct_interest <- "Ependymal"
# plot pixel value for a cell-type of interest
plotRaster(rastCt, assay_name = "pixelval", feature_name = ct_interest, name = "cell-type counts", option = "inferno")# plot RE value for a cell-type of interest
plotRaster(rastCt, assay_name = "re", feature_name = ct_interest, name = "RE", option = "inferno")# plot binarized value for a cell-type of interest
plotRaster(rastCt, assay_name = "bin", feature_name = ct_interest, factor_levels = c(0,1), name = "binarized", option = "inferno")# run CooccurrenceAffinity
ct_coocc <- CooccurrenceAffinity::affinity(data = mat_bin, row.or.col = "row", squarematrix = c("all"))
#>
#> ------ as expected, the data ready for analysis has only 1 and 0... 1 = present, 0 = absent used for the interpretation ------
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AcceptAffCI(x, marg, lev, Int2): NAs introduced by coercion
#> Warning in AcceptAffCI(x, marg, lev, Int2): NAs introduced by coercion
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = Infty is capped, along with upper confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = Infty is capped, along with upper confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> Warning in AlphInts(x, marg, lev = lev, scal = scal, pvalType = pvalType): MLE = -Infty is capped, along with lower confidence limits
#> ~~~~~~~~~~ printing head of all elements of the output list ~~~~~~~~~~
#> $all
#> entity_1 entity_2 entity_1_count_mA entity_2_count_mB obs_cooccur_X
#> 1 Ambiguous Astrocyte 561 557 232
#> 2 Ambiguous Endothelial 1 561 308 136
#> 3 Ambiguous Endothelial 2 561 20 9
#> 4 Ambiguous Endothelial 3 561 102 49
#> 5 Ambiguous Ependymal 561 47 4
#> 6 Ambiguous Excitatory 561 504 192
#> total_N p_value exp_cooccur alpha_mle alpha_medianInt conf_level
#> 1 1301 0.3657 240.182 -0.105 [-0.111, -0.098] 0.95
#> 2 1301 0.693 132.812 0.055 [0.047, 0.064] 0.95
#> 3 1301 1 8.624 0.077 [-0.021, 0.181] 0.95
#> 4 1301 0.2998 43.983 0.215 [0.194, 0.237] 0.95
#> 5 1301 2.1435e-07 20.267 -2.150 [-2.252, -1.986] 0.95
#> 6 1301 0.0041 217.328 -0.337 [-0.343, -0.33] 0.95
#> ci_blaker ci_cp ci_midQ ci_midP jaccard
#> 1 [-0.331, 0.119] [-0.333, 0.123] [-0.327, 0.117] [-0.327, 0.117] 0.262
#> 2 [-0.208, 0.313] [-0.212, 0.321] [-0.203, 0.312] [-0.203, 0.313] 0.186
#> 3 [-0.894, 1.04] [-0.934, 1.061] [-0.823, 0.959] [-0.846, 0.98] 0.016
#> 4 [-0.201, 0.625] [-0.212, 0.641] [-0.19, 0.62] [-0.192, 0.622] 0.080
#> 5 [-3.27, -1.164] [-3.5, -1.128] [-3.291, -1.223] [-3.341, -1.2] 0.007
#> 6 [-0.569, -0.104] [-0.571, -0.104] [-0.565, -0.11] [-0.565, -0.11] 0.220
#> sorensen simpson errornote
#> 1 0.415 0.417 NA
#> 2 0.313 0.442 NA
#> 3 0.031 0.450 NA
#> 4 0.148 0.480 NA
#> 5 0.013 0.085 NA
#> 6 0.361 0.381 NA
#>
#> $occur_mat
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3 Ependymal
#> pixel23 1 0 0 0 0 0
#> pixel24 0 0 1 0 0 0
#> pixel25 0 1 0 0 0 0
#> pixel26 0 0 0 0 0 0
#> pixel27 1 0 1 0 0 0
#> pixel28 0 1 0 0 0 0
#> Excitatory Inhibitory Microglia OD Immature 1 OD Immature 2 OD Mature 1
#> pixel23 0 1 0 0 0 0
#> pixel24 0 1 0 0 0 0
#> pixel25 0 0 0 1 0 0
#> pixel26 1 0 0 0 0 0
#> pixel27 0 0 0 0 0 0
#> pixel28 1 0 0 0 0 0
#> OD Mature 2 OD Mature 3 OD Mature 4 Pericytes
#> pixel23 0 0 0 0
#> pixel24 0 0 0 0
#> pixel25 0 0 0 0
#> pixel26 0 0 0 0
#> pixel27 0 0 0 0
#> pixel28 0 0 0 0
#>
#> $alpha_mle
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte -0.105 NA NA NA NA
#> Endothelial 1 0.055 -0.015 NA NA NA
#> Endothelial 2 0.077 -0.118 0.779 NA NA
#> Endothelial 3 0.215 -0.029 0.322 1.902 NA
#> Ependymal -2.150 -0.807 -0.143 0.345 -0.667
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $alpha_mle_sig
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA 1.902 NA
#> Ependymal -2.15 -0.807 NA NA NA
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $p_value
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous <NA> <NA> <NA> <NA> NA
#> Astrocyte 0.3657 <NA> <NA> <NA> NA
#> Endothelial 1 0.693 0.9475 <NA> <NA> NA
#> Endothelial 2 1 0.825 0.1079 <NA> NA
#> Endothelial 3 0.2998 0.9173 0.1813 5e-04 NA
#> Ependymal 2.1435e-07 0.0159 0.7323 1 0.4274
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous <NA> <NA> <NA> NA NA
#> Astrocyte <NA> <NA> <NA> NA NA
#> Endothelial 1 <NA> <NA> <NA> NA NA
#> Endothelial 2 <NA> <NA> <NA> NA NA
#> Endothelial 3 <NA> <NA> <NA> NA NA
#> Ependymal <NA> <NA> <NA> NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $cooccur.null
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte 240.182 NA NA NA NA
#> Endothelial 1 132.812 131.865 NA NA NA
#> Endothelial 2 8.624 8.563 4.735 NA NA
#> Endothelial 3 43.983 43.669 24.148 1.568 NA
#> Ependymal 20.267 20.122 11.127 0.723 3.685
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $cooccur.obs
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte 232 NA NA NA NA
#> Endothelial 1 136 131 NA NA NA
#> Endothelial 2 9 8 8 NA NA
#> Endothelial 3 49 43 30 7 NA
#> Ependymal 4 12 10 1 2
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $jaccard
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte 0.262 NA NA NA NA
#> Endothelial 1 0.186 0.178 NA NA NA
#> Endothelial 2 0.016 0.014 0.025 NA NA
#> Endothelial 3 0.080 0.070 0.079 0.061 NA
#> Ependymal 0.007 0.020 0.029 0.015 0.014
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $jaccard_sig
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA 0.061 NA
#> Ependymal 0.007 0.02 NA NA NA
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $sorensen
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte 0.415 NA NA NA NA
#> Endothelial 1 0.313 0.303 NA NA NA
#> Endothelial 2 0.031 0.028 0.049 NA NA
#> Endothelial 3 0.148 0.131 0.146 0.115 NA
#> Ependymal 0.013 0.040 0.056 0.030 0.027
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $sorensen_sig
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA 0.115 NA
#> Ependymal 0.013 0.04 NA NA NA
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $simpson
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte 0.417 NA NA NA NA
#> Endothelial 1 0.442 0.425 NA NA NA
#> Endothelial 2 0.450 0.400 0.400 NA NA
#> Endothelial 3 0.480 0.422 0.294 0.35 NA
#> Ependymal 0.085 0.255 0.213 0.05 0.043
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#>
#> $simpson_sig
#> Ambiguous Astrocyte Endothelial 1 Endothelial 2 Endothelial 3
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA 0.35 NA
#> Ependymal 0.085 0.255 NA NA NA
#> Ependymal Excitatory Inhibitory Microglia OD Immature 1
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> OD Immature 2 OD Mature 1 OD Mature 2 OD Mature 3 OD Mature 4
#> Ambiguous NA NA NA NA NA
#> Astrocyte NA NA NA NA NA
#> Endothelial 1 NA NA NA NA NA
#> Endothelial 2 NA NA NA NA NA
#> Endothelial 3 NA NA NA NA NA
#> Ependymal NA NA NA NA NA
#> Pericytes
#> Ambiguous NA
#> Astrocyte NA
#> Endothelial 1 NA
#> Endothelial 2 NA
#> Endothelial 3 NA
#> Ependymal NA
#> ~~~~~~~~~~ COMPLETED: printing head of all elements of the output list ~~~~~~~~~~
# plot maximum likelihood estimates of affinity metric (alpha MLE)
CooccurrenceAffinity::plotgg(data = ct_coocc, variable = "alpha_mle", legendlimit = "datarange")
#> you can hide the printed values with show.value=F
#> use the argument value.digit to change number of digits and text.size to adjust the text size