adding responsive column. see readme

README.md

@@ -564,6 +564,12 @@ configs:
       dtype: float64
       description: Benjamini-Hochberg adjusted p-value (DESeq2 output)
       role: quantitative_measure
+    - name: responsive
+      dtype: bool
+      description: >-
+        TRUE/FALSE labeling based on authors recommended threshold on
+        responsiveness where TRUE means that
+        padj < 0.1 & abs(log2FoldChange) >= log2(1.3)
 
 - config_name: degron_counts_meta
   description: Sample-level metadata for auxin-inducible degron perturbation experiments with HTSeq count statistics

rnaseq_reprocessed.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:66a53db51bfadb326f663f90a9da4a64d8e4724da679ad17851a530541ea3fb4
-size 43776387
+oid sha256:2233d75235f0309d8c03ef92e73ecc1c4e3fdb9cc622bd5b7b910cbf12766e69
+size 41622007

scripts/evaluating_zscore_vs_enrichment_vs_peaks_vs_perturbation.R

@@ -0,0 +1,124 @@
+library(tidyverse)
+library(here)
+library(ggExtra)
+library(patchwork)
+library(pROC)
+
+promoters = read_csv("~/code/hf/yeast_genome_resources/mindel_promoters.csv.gz")
+chec_promoter_sums_raw = read_csv("~/projects/ChEC_Target_Selection/data/chec_sumprom.csv")
+chec_promoter_zscores = chec_promoter_sums_raw %>%
+    dplyr::rename(mindel_name = name) %>%
+    # removed because these two loci are merged and considered a -1 frameshift
+    # of the same locus. confusingly labeled promoters in original mindel data
+    filter(!mindel_name %in% c("AAD6", "AAD16", "YAR061W", "YAR062W")) %>%
+    pivot_longer(-mindel_name, names_to = 'mindel_regulator', values_to = 'promoter_score') %>%
+    left_join(promoters %>%
+                  select(mindel_name, target_locus_tag, target_symbol)) %>%
+    select(-mindel_name) %>%
+    left_join(
+        promoters %>%
+            select(mindel_name, target_locus_tag, target_symbol) %>%
+            dplyr::rename(mindel_regulator = mindel_name,
+                          regulator_locus_tag = target_locus_tag,
+                          regulator_symbol = target_symbol) %>%
+            bind_rows(
+                tibble(mindel_regulator = c("COM2", "SDD4"),
+                       regulator_locus_tag = c("YER130C", "YPR022C"),
+                       regulator_symbol = c("COM2", "SDD4")))) %>%
+    select(-mindel_regulator) %>%
+    dplyr::relocate(regulator_locus_tag, regulator_symbol, target_locus_tag, target_symbol) %>%
+    group_by(regulator_locus_tag) %>%
+    mutate(zscore = as.numeric(scale(promoter_score))) %>%
+    ungroup()
+
+chec_enrichment = arrow::read_parquet("~/code/hf/mahendrawada_2025/chec_mahendrawada_m2025_af_combined.parquet") %>%
+    left_join(arrow::read_parquet("~/code/hf/mahendrawada_2025/chec_mahendrawada_m2025_af_combined_meta.parquet")) %>%
+    filter(condition == "standard")
+
+mahendrawada_rnaseq = arrow::read_parquet("~/code/hf/mahendrawada_2025/rnaseq_reprocessed.parquet") %>%
+    filter(env_condition == "standard_30C") %>%
+    replace_na(list(log2FoldChange = 0, padj = 1)) %>%
+    mutate(responsive = abs(log2FoldChange) > 0.5 & padj < 0.05)
+
+comp_df = chec_promoter_zscores %>%
+    select(-c(promoter_score)) %>%
+    left_join(select(chec_enrichment, regulator_locus_tag,
+                     target_locus_tag,
+                     log_poisson_pval)) %>%
+    left_join(select(mahendrawada_rnaseq, regulator_locus_tag, target_locus_tag,
+                     log2FoldChange, padj, responsive)) %>%
+    filter(complete.cases(.)) %>%
+    arrange(regulator_locus_tag, target_locus_tag)
+
+
+comp_plot = function(rsym){
+    p1 = comp_df %>%
+        filter(regulator_symbol == rsym) %>%
+        ggplot(aes(zscore, -log_poisson_pval, color = responsive)) +
+        geom_point(alpha = 0.8) +
+        geom_smooth(aes(group = 1), color = "blue") +
+        geom_vline(xintercept = 3.5) +
+        geom_hline(yintercept = -log(0.05/5331))
+
+    df_reg <- comp_df %>% filter(regulator_symbol == rsym)
+
+    roc_z <- roc(df_reg$responsive, df_reg$zscore, direction = "<")
+    roc_p <- roc(df_reg$responsive, -df_reg$log_poisson_pval, direction = "<")
+
+    roc_plot = ggroc(list(zscore = roc_z, poisson = roc_p)) +
+        geom_abline(slope = 1, intercept = 1, linetype = "dashed") +
+        scale_color_manual(values = c(zscore = "darkgreen", poisson = "purple")) +
+        labs(color = "Method")
+
+    p2 = comp_df %>%
+        filter(regulator_symbol == rsym) %>%
+        ggplot(aes(zscore, color = responsive)) +
+        stat_ecdf() +
+        geom_vline(xintercept = 3.5, linetype = "dashed") +
+        labs(y = "Cumulative fraction")
+
+    p3 = comp_df %>%
+        filter(regulator_symbol == rsym) %>%
+        ggplot(aes(-log_poisson_pval, color = responsive)) +
+        stat_ecdf() +
+        geom_vline(xintercept = -log(0.05/5331), linetype = "dashed") +
+        labs(y = "Cumulative fraction")
+
+    (p1 + roc_plot) / (p2 + p3) + plot_layout(guides = "collect") +
+        plot_annotation(title = paste0("Regulator: ", rsym))
+}
+
+comp_plot("FKH1")
+
+comp_auc = comp_df %>%
+    filter(!regulator_symbol %in% c("STB5", "USV1")) %>%
+    group_by(regulator_symbol) %>%
+    reframe(
+        auc_zscore = as.numeric(auc(responsive, zscore, direction = "<")),
+        auc_poisson = as.numeric(auc(responsive, -log_poisson_pval, direction = "<"))
+    )
+
+
+# summary
+comp_auc %>%
+    reframe(
+        mean_auc_z = mean(auc_zscore),
+        mean_auc_p = mean(auc_poisson),
+        z_wins = sum(auc_zscore > auc_poisson),
+        p_wins = sum(auc_zscore < auc_poisson)
+    )
+
+comp_df_ranked_by_binding = comp_df %>%
+    group_by(regulator_locus_tag) %>%
+    mutate(zscore_rank = rank(-zscore, ties.method = "min"),
+           enrichment_rank = rank(log_poisson_pval, ties.method = "min")) %>%
+    ungroup()
+
+rr_25_summary = comp_df_ranked_by_binding %>%
+    group_by(regulator_locus_tag) %>%
+    reframe(
+        zscore_rr_25 = sum(responsive[zscore_rank <= 25]),
+        zscore_n = length(responsive[zscore_rank <= 25]),
+        enrichment_rr_25 = sum(responsive[enrichment_rank <= 25]),
+        enrichment_n = length(responsive[enrichment_rank <= 25])) %>%
+    pivot_longer(-regulator_locus_tag)