Skip to content

Commit

Permalink
update prioritization weights
Browse files Browse the repository at this point in the history
  • Loading branch information
@csangara
csangara committed Aug 30, 2024
1 parent f072b81 commit 395e1c7
Show file tree
Hide file tree
Showing 7 changed files with 37 additions and 36 deletions.
10 changes: 5 additions & 5 deletions R/prioritization.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -584,15 +584,15 @@ generate_prioritization_tables = function(sender_receiver_info, sender_receiver_


# have a weighted average the final score (no product!!)
sum_prioritization_weights = weights["de_ligand"] + weights["de_receptor"] + weights["activity_scaled"] + weights["exprs_ligand"] + weights["exprs_receptor"] + weights["ligand_condition_specificity"] + weights["receptor_condition_specificity"]
sum_prioritization_weights = 0.5*weights["de_ligand"] + 0.5*weights["de_receptor"] + weights["activity_scaled"] + 0.5*weights["exprs_ligand"] + 0.5*weights["exprs_receptor"] + weights["ligand_condition_specificity"] + weights["receptor_condition_specificity"]
group_prioritization_tbl = group_prioritization_tbl %>% rowwise() %>%
dplyr::mutate(prioritization_score =
(
(prioritizing_weights["de_ligand"] * ifelse("scaled_p_val_adapted_ligand" %in% names(group_prioritization_tbl), scaled_p_val_adapted_ligand, 0)) +
(prioritizing_weights["de_receptor"] * ifelse("scaled_p_val_adapted_receptor" %in% names(group_prioritization_tbl), scaled_p_val_adapted_receptor, 0)) +
(0.5*prioritizing_weights["de_ligand"] * ifelse("scaled_p_val_adapted_ligand" %in% names(group_prioritization_tbl), scaled_p_val_adapted_ligand, 0)) +
(0.5*prioritizing_weights["de_receptor"] * ifelse("scaled_p_val_adapted_receptor" %in% names(group_prioritization_tbl), scaled_p_val_adapted_receptor, 0)) +
(prioritizing_weights["activity_scaled"] * ifelse("scaled_activity" %in% names(group_prioritization_tbl), scaled_activity, 0)) +
(prioritizing_weights["exprs_ligand"] * ifelse("scaled_avg_exprs_ligand" %in% names(group_prioritization_tbl), scaled_avg_exprs_ligand, 0)) +
(prioritizing_weights["exprs_receptor"] * ifelse("scaled_avg_exprs_receptor" %in% names(group_prioritization_tbl), scaled_avg_exprs_receptor, 0)) +
(0.5*prioritizing_weights["exprs_ligand"] * ifelse("scaled_avg_exprs_ligand" %in% names(group_prioritization_tbl), scaled_avg_exprs_ligand, 0)) +
(0.5*prioritizing_weights["exprs_receptor"] * ifelse("scaled_avg_exprs_receptor" %in% names(group_prioritization_tbl), scaled_avg_exprs_receptor, 0)) +
(prioritizing_weights["ligand_condition_specificity"] * ifelse("scaled_p_val_adapted_ligand_group" %in% names(group_prioritization_tbl), scaled_p_val_adapted_ligand_group, 0)) +
(prioritizing_weights["receptor_condition_specificity"] * ifelse("scaled_p_val_adapted_receptor_group" %in% names(group_prioritization_tbl), scaled_p_val_adapted_receptor_group, 0))
)* (1/sum_prioritization_weights)) %>% dplyr::arrange(-prioritization_score) %>%
Expand Down
9 changes: 5 additions & 4 deletions tests/testthat/test-prioritization.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -274,11 +274,11 @@ test_that("Prioritization scheme works", {
check.attributes = FALSE)

# Check that prioritization score is the same as the sum of the weighted scores
temp_weights = c("de_ligand" = 1,
"de_receptor" = 1,
temp_weights = c("de_ligand" = 0.5,
"de_receptor" = 0.5,
"activity_scaled" = 1,
"exprs_ligand" = 1,
"exprs_receptor" = 1,
"exprs_ligand" = 0.5,
"exprs_receptor" = 0.5,
"ligand_condition_specificity" = 1,
"receptor_condition_specificity" = 1)
expect_equal(prior_table %>% filter(ligand == "Lgals1", sender == "Mono", receptor == "Cd69") %>%
Expand All @@ -300,6 +300,7 @@ test_that("Prioritization scheme works", {
processed_condition_markers,
prioritizing_weights = prioritizing_weights)
temp_weights <- prioritizing_weights
temp_weights[c("de_ligand", "de_receptor", "exprs_ligand", "exprs_receptor")] <- 0.5
expect_equal(prior_table %>% filter(ligand == "Lgals1", sender == "Mono", receptor == "Cd69") %>%
mutate(prioritization_score = rowSums(across(c(scaled_p_val_adapted_ligand, scaled_p_val_adapted_receptor, scaled_activity, scaled_avg_exprs_ligand, scaled_avg_exprs_receptor, scaled_p_val_adapted_ligand_group, scaled_p_val_adapted_receptor_group)) * temp_weights) / sum(temp_weights)) %>% pull(prioritization_score),
prior_table %>% filter(ligand == "Lgals1", sender == "Mono", receptor == "Cd69") %>% pull(prioritization_score),
Expand Down
54 changes: 27 additions & 27 deletions vignettes/seurat_steps_prioritization.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -224,12 +224,12 @@ prior_table %>% head
## # A tibble: 6 × 52
## sender receiver ligand receptor lfc_ligand lfc_receptor ligand_receptor_lfc_avg p_val_ligand p_adj_ligand p_val_receptor p_adj_receptor pct_expressed_sender pct_expressed_receiver avg_ligand
## <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 NK CD8 T Ptprc Dpp4 0.642 0.299 0.471 2.18e- 7 2.96e- 3 0.000663 1 0.894 0.148 16.6
## 2 Mono CD8 T Ptprc Dpp4 0.474 0.299 0.386 3.52e- 5 4.77e- 1 0.000663 1 0.867 0.148 14.9
## 3 Mono CD8 T Cxcl10 Dpp4 4.86 0.299 2.58 2.53e- 79 3.43e- 75 0.000663 1 0.867 0.148 54.8
## 4 Mono CD8 T Cxcl9 Dpp4 6.68 0.299 3.49 3.83e-124 5.19e-120 0.000663 1 0.547 0.148 23.8
## 5 Treg CD8 T Ptprc Dpp4 0.307 0.299 0.303 1.44e- 2 1 e+ 0 0.000663 1 0.685 0.148 13.2
## 6 Mono CD8 T Cxcl11 Dpp4 6.60 0.299 3.45 9.28e-121 1.26e-116 0.000663 1 0.307 0.148 4.37
## 1 NK CD8 T Ptprc Dpp4 0.642 0.299 0.471 2.18e- 7 2.96e- 3 0.000663 1 0.894 0.148 16.6
## 2 Mono CD8 T Ptprc Dpp4 0.474 0.299 0.386 3.52e- 5 4.77e- 1 0.000663 1 0.867 0.148 14.9
## 3 Treg CD8 T Ptprc Dpp4 0.307 0.299 0.303 1.44e- 2 1 e+ 0 0.000663 1 0.685 0.148 13.2
## 4 Mono CD8 T Cxcl10 Dpp4 4.86 0.299 2.58 2.53e-79 3.43e-75 0.000663 1 0.867 0.148 54.8
## 5 B CD8 T Ptprc Dpp4 0.201 0.299 0.250 2.08e- 2 1 e+ 0 0.000663 1 0.669 0.148 12.3
## 6 Mono CD8 T Ebi3 Il6st 4.00 0.141 2.07 9.77e-49 1.32e-44 0.0147 1 0.147 0.09 0.546
## # ℹ 38 more variables: avg_receptor <dbl>, ligand_receptor_prod <dbl>, lfc_pval_ligand <dbl>, p_val_adapted_ligand <dbl>, scaled_lfc_ligand <dbl>, scaled_p_val_ligand <dbl>,
## # scaled_lfc_pval_ligand <dbl>, scaled_p_val_adapted_ligand <dbl>, activity <dbl>, rank <dbl>, activity_zscore <dbl>, scaled_activity <dbl>, lfc_pval_receptor <dbl>,
## # p_val_adapted_receptor <dbl>, scaled_lfc_receptor <dbl>, scaled_p_val_receptor <dbl>, scaled_lfc_pval_receptor <dbl>, scaled_p_val_adapted_receptor <dbl>, scaled_avg_exprs_ligand <dbl>,
Expand All @@ -256,14 +256,14 @@ prior_table %>% select(c('sender', 'receiver', 'ligand', 'receptor', 'scaled_p_v
## <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 NK CD8 T Ptprc Dpp4 0.871 0.846 1.00 1.00 0.844 0.833 0.660
## 2 Mono CD8 T Ptprc Dpp4 0.841 0.846 0.867 1.00 0.844 0.833 0.660
## 3 Mono CD8 T Cxcl10 Dpp4 0.958 0.846 1.00 1.00 0.926 0.833 0.309
## 4 Mono CD8 T Cxcl9 Dpp4 0.974 0.846 1.00 1.00 0.779 0.833 0.263
## 5 Treg CD8 T Ptprc Dpp4 0.754 0.846 0.741 1.00 0.844 0.833 0.660
## 6 Mono CD8 T Cxcl11 Dpp4 0.972 0.846 1.00 1.00 0.721 0.833 0.273
## 7 B CD8 T Ptprc Dpp4 0.747 0.846 0.666 1.00 0.844 0.833 0.660
## 8 DC CD8 T Ccl22 Dpp4 0.997 0.846 1.00 1.00 0.545 0.833 0.361
## 9 DC CD8 T Icam1 Il2rg 0.878 0.723 1.00 0.995 0.713 0.985 0.273
## 10 DC CD8 T Il15 Il2rg 0.964 0.723 1.00 0.995 0.598 0.985 0.214
## 3 Treg CD8 T Ptprc Dpp4 0.754 0.846 0.741 1.00 0.844 0.833 0.660
## 4 Mono CD8 T Cxcl10 Dpp4 0.958 0.846 1.00 1.00 0.926 0.833 0.309
## 5 B CD8 T Ptprc Dpp4 0.747 0.846 0.666 1.00 0.844 0.833 0.660
## 6 Mono CD8 T Ebi3 Il6st 0.937 0.692 1.00 0.635 0.680 0.515 1.00
## 7 Mono CD8 T Cxcl9 Dpp4 0.974 0.846 1.00 1.00 0.779 0.833 0.263
## 8 DC CD8 T Icam1 Il2rg 0.878 0.723 1.00 0.995 0.713 0.985 0.273
## 9 DC CD8 T B2m Tap2 0.862 0.631 1.00 0.781 1 0.864 0.254
## 10 Mono CD8 T Cxcl11 Dpp4 0.972 0.846 1.00 1.00 0.721 0.833 0.273
## # ℹ 1,202 more rows
## # ℹ abbreviated names: ¹​scaled_p_val_adapted_receptor, ²​scaled_avg_exprs_ligand, ³​scaled_avg_exprs_receptor, ⁴​scaled_p_val_adapted_ligand_group, ⁵​scaled_p_val_adapted_receptor_group
```
Expand Down Expand Up @@ -332,12 +332,12 @@ prior_table %>% head
## # A tibble: 6 × 52
## sender receiver ligand receptor lfc_ligand lfc_receptor ligand_receptor_lfc_avg p_val_ligand p_adj_ligand p_val_receptor p_adj_receptor pct_expressed_sender pct_expressed_receiver avg_ligand
## <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 NK CD8 T Ptprc Dpp4 0.642 0.299 0.471 2.18e- 7 2.96e- 3 0.000663 1 0.894 0.148 16.6
## 2 Mono CD8 T Ptprc Dpp4 0.474 0.299 0.386 3.52e- 5 4.77e- 1 0.000663 1 0.867 0.148 14.9
## 3 Mono CD8 T Cxcl10 Dpp4 4.86 0.299 2.58 2.53e- 79 3.43e- 75 0.000663 1 0.867 0.148 54.8
## 4 Mono CD8 T Cxcl9 Dpp4 6.68 0.299 3.49 3.83e-124 5.19e-120 0.000663 1 0.547 0.148 23.8
## 5 Treg CD8 T Ptprc Dpp4 0.307 0.299 0.303 1.44e- 2 1 e+ 0 0.000663 1 0.685 0.148 13.2
## 6 Mono CD8 T Cxcl11 Dpp4 6.60 0.299 3.45 9.28e-121 1.26e-116 0.000663 1 0.307 0.148 4.37
## 1 NK CD8 T Ptprc Dpp4 0.642 0.299 0.471 2.18e- 7 2.96e- 3 0.000663 1 0.894 0.148 16.6
## 2 Mono CD8 T Ptprc Dpp4 0.474 0.299 0.386 3.52e- 5 4.77e- 1 0.000663 1 0.867 0.148 14.9
## 3 Treg CD8 T Ptprc Dpp4 0.307 0.299 0.303 1.44e- 2 1 e+ 0 0.000663 1 0.685 0.148 13.2
## 4 Mono CD8 T Cxcl10 Dpp4 4.86 0.299 2.58 2.53e-79 3.43e-75 0.000663 1 0.867 0.148 54.8
## 5 B CD8 T Ptprc Dpp4 0.201 0.299 0.250 2.08e- 2 1 e+ 0 0.000663 1 0.669 0.148 12.3
## 6 Mono CD8 T Ebi3 Il6st 4.00 0.141 2.07 9.77e-49 1.32e-44 0.0147 1 0.147 0.09 0.546
## # ℹ 38 more variables: avg_receptor <dbl>, ligand_receptor_prod <dbl>, lfc_pval_ligand <dbl>, p_val_adapted_ligand <dbl>, scaled_lfc_ligand <dbl>, scaled_p_val_ligand <dbl>,
## # scaled_lfc_pval_ligand <dbl>, scaled_p_val_adapted_ligand <dbl>, activity <dbl>, rank <dbl>, activity_zscore <dbl>, scaled_activity <dbl>, lfc_pval_receptor <dbl>,
## # p_val_adapted_receptor <dbl>, scaled_lfc_receptor <dbl>, scaled_p_val_receptor <dbl>, scaled_lfc_pval_receptor <dbl>, scaled_p_val_adapted_receptor <dbl>, scaled_avg_exprs_ligand <dbl>,
Expand Down Expand Up @@ -444,11 +444,11 @@ head(prior_table_combined)
## # A tibble: 6 × 52
## sender receiver ligand receptor lfc_ligand lfc_receptor ligand_receptor_lfc_avg p_val_ligand p_adj_ligand p_val_receptor p_adj_receptor pct_expressed_sender pct_expressed_receiver avg_ligand
## <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 NK CD4 T Ptprc Cd4 0.642 1.71 1.18 0.000000218 0.00296 2.63e-34 3.56e-30 0.894 0.226 16.6
## 2 NK CD8 T Ptprc Dpp4 0.642 0.299 0.471 0.000000218 0.00296 6.63e- 4 1 e+ 0 0.894 0.148 16.6
## 3 B CD4 T H2-Eb1 Cd4 5.00 1.71 3.36 0 0 2.63e-34 3.56e-30 0.93 0.226 31.0
## 4 Mono CD4 T Ptprc Cd4 0.474 1.71 1.09 0.0000352 0.477 2.63e-34 3.56e-30 0.867 0.226 14.9
## 5 Mono CD8 T Ptprc Dpp4 0.474 0.299 0.386 0.0000352 0.477 6.63e- 4 1 e+ 0 0.867 0.148 14.9
## 1 NK CD8 T Ptprc Dpp4 0.642 0.299 0.471 0.000000218 0.00296 6.63e- 4 1 e+ 0 0.894 0.148 16.6
## 2 NK CD4 T Ptprc Cd4 0.642 1.71 1.18 0.000000218 0.00296 2.63e-34 3.56e-30 0.894 0.226 16.6
## 3 Mono CD8 T Ptprc Dpp4 0.474 0.299 0.386 0.0000352 0.477 6.63e- 4 1 e+ 0 0.867 0.148 14.9
## 4 B CD4 T H2-Eb1 Cd4 5.00 1.71 3.36 0 0 2.63e-34 3.56e-30 0.93 0.226 31.0
## 5 Mono CD4 T Ptprc Cd4 0.474 1.71 1.09 0.0000352 0.477 2.63e-34 3.56e-30 0.867 0.226 14.9
## 6 NK CD4 T Ptprc Cd247 0.642 0.599 0.620 0.000000218 0.00296 5.61e- 4 1 e+ 0 0.894 0.309 16.6
## # ℹ 38 more variables: avg_receptor <dbl>, ligand_receptor_prod <dbl>, lfc_pval_ligand <dbl>, p_val_adapted_ligand <dbl>, scaled_lfc_ligand <dbl>, scaled_p_val_ligand <dbl>,
## # scaled_lfc_pval_ligand <dbl>, scaled_p_val_adapted_ligand <dbl>, activity <dbl>, rank <dbl>, activity_zscore <dbl>, scaled_activity <dbl>, lfc_pval_receptor <dbl>,
Expand Down Expand Up @@ -556,8 +556,8 @@ sessionInfo()
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
## [11] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4 nichenetr_2.1.7
## [1] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
## [11] tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 nichenetr_2.2.0
##
## loaded via a namespace (and not attached):
## [1] RcppAnnoy_0.0.22 splines_4.3.3 later_1.3.2 bitops_1.0-7 polyclip_1.10-6 hardhat_1.3.1 pROC_1.18.5 rpart_4.1.23
Expand Down
Binary file modified vignettes/seurat_steps_prioritization_files/figure-gfm/lr-circos-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/seurat_steps_prioritization_files/figure-gfm/lr-circos-unused-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/seurat_steps_prioritization_files/figure-gfm/mushroom-plot-1-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/seurat_steps_prioritization_files/figure-gfm/mushroom-plot-2-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

0 comments on commit 395e1c7

Please sign in to comment.