Last updated: 2025-08-07

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Knit directory: Paul_CX_2025/

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📌 Top BP (Cluster Profiler)

### 📦 Load Required Libraries
library(tidyverse)
Warning: package 'tidyverse' was built under R version 4.3.2
Warning: package 'tidyr' was built under R version 4.3.3
Warning: package 'readr' was built under R version 4.3.3
Warning: package 'purrr' was built under R version 4.3.3
Warning: package 'dplyr' was built under R version 4.3.2
Warning: package 'stringr' was built under R version 4.3.2
Warning: package 'lubridate' was built under R version 4.3.3
library(ComplexHeatmap)
Warning: package 'ComplexHeatmap' was built under R version 4.3.1
library(circlize)
Warning: package 'circlize' was built under R version 4.3.3
library(grid)

### 📁 Define CorMotif GO Enrichment Files
go_files <- list(
  "Non response (0.1)"                         = "data/BP/CorMotif_Terms/GO_BP_Non_response_(0.1).csv",
  "CX_DOX_1"             = "data/BP/CorMotif_Terms/GO_BP_CX-DOX_mid-late_response_(0.1).csv",
  "DOX_sp_1"                    = "data/BP/CorMotif_Terms/GO_BP_DOX_only_mid-late_(0.1).csv",
  "Non response (0.5)"                         = "data/BP/CorMotif_Terms/GO_BP_Non_response_(0.5).csv",
  "DOX_sp_2"                = "data/BP/CorMotif_Terms/GO_BP_DOX_specific_response_(0.5).csv",
  "DOX_sp_3"           = "data/BP/CorMotif_Terms/GO_BP_DOX_only_mid-late_response_(0.5).csv",
  "CX_DOX_2"        = "data/BP/CorMotif_Terms/GO_BP_CX_total_+_DOX_early_response_(0.5).csv",
  "CX_DOX_3" = "data/BP/CorMotif_Terms/GO_BP_DOX_early_+_CX-DOX_mid-late_response_(0.5).csv"
)

### 🔍 Step 1: Extract Top 5 GO Terms Per Group Based on Adjusted P-value
top_go_terms <- map(go_files, function(file) {
  df <- tryCatch(read.csv(file), error = function(e) return(NULL))
  if (!is.null(df) && nrow(df) > 0 && all(c("Description", "p.adjust") %in% colnames(df))) {
    df %>%
      as_tibble() %>%
      filter(p.adjust < 0.05) %>%
      arrange(p.adjust) %>%
      dplyr::select(Description) %>%
      slice_head(n = 5) %>%
      pull(Description) %>%
      unique()
  } else {
    character(0)
  }
}) %>% unlist() %>% unique()

### 🔁 Step 2: Collect All Matrix Values for Top GO Terms
go_matrix_df <- map_dfr(names(go_files), function(group) {
  file <- go_files[[group]]
  df <- tryCatch(read.csv(file), error = function(e) return(tibble()))

  if (nrow(df) == 0 || !all(c("Description", "pvalue", "p.adjust") %in% colnames(df))) {
    tibble(Description = top_go_terms, pvalue = NA, p.adjust = NA, log10p = NA, Group = group)
  } else {
    df_filtered <- df %>%
      as_tibble() %>%
      dplyr::select(Description, pvalue, p.adjust) %>%
      filter(Description %in% top_go_terms)

    tibble(Description = top_go_terms) %>%
      left_join(df_filtered, by = "Description") %>%
      mutate(
        log10p = ifelse(!is.na(pvalue), -log10(pvalue), NA),
        Group = group
      )
  }
})

### 🧱 Step 3: Pivot to Heatmap Matrices
heatmap_data <- go_matrix_df %>%
  dplyr::select(Description, Group, log10p) %>%
  pivot_wider(names_from = Group, values_from = log10p) %>%
  column_to_rownames("Description") %>%
  as.matrix()

pval_matrix <- go_matrix_df %>%
  dplyr::select(Description, Group, pvalue) %>%
  pivot_wider(names_from = Group, values_from = pvalue) %>%
  column_to_rownames("Description") %>%
  as.matrix()

p_adj_matrix <- go_matrix_df %>%
  dplyr::select(Description, Group, p.adjust) %>%
  pivot_wider(names_from = Group, values_from = p.adjust) %>%
  column_to_rownames("Description") %>%
  as.matrix()

### 🎨 Step 4: Define Heatmap Color Gradient
breaks <- seq(0, 20, by = 2.5)
palette <- colorRampPalette(c("white", "#fde0dd", "#fa9fb5", "#f768a1", "#c51b8a", "#7a0177", "#49006a"))(length(breaks))
col_fun <- colorRamp2(breaks, palette)

### 🔥 Step 5: Draw Heatmap with Stars for p.adjust < 0.05
ht <- Heatmap(
  heatmap_data,
  name = "-log10(p)",
  col = col_fun,
  na_col = "white",
  rect_gp = gpar(col = "black", lwd = 0.5),
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  row_names_gp = gpar(fontsize = 9),
  column_names_gp = gpar(fontsize = 9),
  column_names_rot = 45,
  cell_fun = function(j, i, x, y, width, height, fill) {
    adj_p <- p_adj_matrix[i, j]
    if (!is.na(adj_p) && adj_p < 0.05) {
      grid.text("*", x, y, gp = gpar(fontsize = 12))
    }
  },
  heatmap_legend_param = list(
    title = "-log10(p value)",
    at = breaks,
    labels = as.character(breaks),
    legend_width = unit(5, "cm"),
    direction = "horizontal",
    title_gp = gpar(fontsize = 10, fontface = "bold"),
    labels_gp = gpar(fontsize = 9)
  )
)

### 🖼️ Final Output
draw(ht, heatmap_legend_side = "top")

📌 Proportion of Heart Specific Genes (Combined)

# ----------------- Load Required Libraries -----------------
library(dplyr)
library(ggplot2)
library(org.Hs.eg.db)
Warning: package 'AnnotationDbi' was built under R version 4.3.2
Warning: package 'BiocGenerics' was built under R version 4.3.1
Warning: package 'Biobase' was built under R version 4.3.1
Warning: package 'IRanges' was built under R version 4.3.1
Warning: package 'S4Vectors' was built under R version 4.3.2
library(AnnotationDbi)

# ----------------- Load Heart-Specific Genes -----------------
heart_genes <- read.csv("data/Human_Heart_Genes.csv", stringsAsFactors = FALSE)
heart_genes$Entrez_ID <- mapIds(
  org.Hs.eg.db,
  keys = heart_genes$Gene,
  column = "ENTREZID",
  keytype = "SYMBOL",
  multiVals = "first"
)
heart_entrez_ids <- na.omit(heart_genes$Entrez_ID)

# ----------------- Load CorrMotif Groups -----------------
# 0.1 µM
prob_1_0.1 <- as.character(read.csv("data/prob_1_0.1.csv")$Entrez_ID)
prob_2_0.1 <- as.character(read.csv("data/prob_2_0.1.csv")$Entrez_ID)
prob_3_0.1 <- as.character(read.csv("data/prob_3_0.1.csv")$Entrez_ID)

# 0.5 µM
prob_1_0.5 <- as.character(read.csv("data/prob_1_0.5.csv")$Entrez_ID)
prob_2_0.5 <- as.character(read.csv("data/prob_2_0.5.csv")$Entrez_ID)
prob_3_0.5 <- as.character(read.csv("data/prob_3_0.5.csv")$Entrez_ID)
prob_4_0.5 <- as.character(read.csv("data/prob_4_0.5.csv")$Entrez_ID)
prob_5_0.5 <- as.character(read.csv("data/prob_5_0.5.csv")$Entrez_ID)

# ----------------- Annotate CorrMotif Groups -----------------
df_0.1 <- data.frame(Entrez_ID = unique(c(prob_1_0.1, prob_2_0.1, prob_3_0.1))) %>%
  mutate(
    Response_Group = case_when(
      Entrez_ID %in% prob_1_0.1 ~ "Non response (0.1)",
      Entrez_ID %in% prob_2_0.1 ~ "CX_DOX_1",
      Entrez_ID %in% prob_3_0.1 ~ "DOX_sp_1"
    ),
    Category = ifelse(Entrez_ID %in% heart_entrez_ids, "Heart-specific Genes", "Non-Heart-specific Genes"),
    Concentration = "0.1"
  )

df_0.5 <- data.frame(Entrez_ID = unique(c(prob_1_0.5, prob_2_0.5, prob_3_0.5, prob_4_0.5, prob_5_0.5))) %>%
  mutate(
    Response_Group = case_when(
      Entrez_ID %in% prob_1_0.5 ~ "Non response (0.5)",
      Entrez_ID %in% prob_2_0.5 ~ "DOX_sp_2",
      Entrez_ID %in% prob_3_0.5 ~ "DOX_sp_3",
      Entrez_ID %in% prob_4_0.5 ~ "CX_DOX_2",
      Entrez_ID %in% prob_5_0.5 ~ "CX_DOX_3"
    ),
    Category = ifelse(Entrez_ID %in% heart_entrez_ids, "Heart-specific Genes", "Non-Heart-specific Genes"),
    Concentration = "0.5"
  )

# ----------------- Combine Data -----------------
df_combined <- bind_rows(df_0.1, df_0.5)

# ----------------- Calculate Proportions -----------------
proportion_data <- df_combined %>%
  group_by(Concentration, Response_Group, Category) %>%
  summarise(Count = n(), .groups = "drop") %>%
  group_by(Concentration, Response_Group) %>%
  mutate(Percentage = Count / sum(Count) * 100)

# ----------------- Fisher's Exact Test -----------------
run_fisher_test <- function(df, ref_group) {
  ref_counts <- df %>%
    filter(Response_Group == ref_group) %>%
    dplyr::select(Category, Count) %>%
    {setNames(.$Count, .$Category)}
  
  df %>%
    filter(Response_Group != ref_group) %>%
    group_by(Response_Group) %>%
    summarise(
      p_value = {
        group_counts <- Count[Category %in% c("Heart-specific Genes", "Non-Heart-specific Genes")]
        if (length(group_counts) < 2) group_counts <- c(group_counts, 0)
        contingency_table <- matrix(c(
          group_counts[1], group_counts[2],
          ref_counts["Heart-specific Genes"], ref_counts["Non-Heart-specific Genes"]
        ), nrow = 2)
        fisher.test(contingency_table)$p.value
      },
      .groups = "drop"
    ) %>%
    mutate(Significance = ifelse(!is.na(p_value) & p_value < 0.05, "*", ""))
}

# Run Fisher's test for each concentration
fisher_0.1 <- run_fisher_test(proportion_data %>% filter(Concentration == "0.1"), "Non response (0.1)")
fisher_0.5 <- run_fisher_test(proportion_data %>% filter(Concentration == "0.5"), "Non response (0.5)")

# Combine results
fisher_all <- bind_rows(
  fisher_0.1 %>% mutate(Concentration = "0.1"),
  fisher_0.5 %>% mutate(Concentration = "0.5")
)

# ----------------- Merge Fisher Results -----------------
proportion_data <- proportion_data %>%
  left_join(fisher_all, by = c("Concentration", "Response_Group"))

# ----------------- Reorder Factor Levels -----------------
proportion_data$Response_Group <- factor(proportion_data$Response_Group, levels = c(
  "Non response (0.1)", "CX_DOX_1", "DOX_sp_1",
  "Non response (0.5)", "DOX_sp_2", "DOX_sp_3", "CX_DOX_2", "CX_DOX_3"
))

# ----------------- Significance Star Labels -----------------
label_data <- proportion_data %>%
  group_by(Concentration, Response_Group) %>%
  summarise(Significance = dplyr::first(Significance), .groups = "drop") %>%
  filter(!is.na(Significance)) %>%
  mutate(y_pos = 100)

# ----------------- Final Plot -----------------
ggplot(proportion_data, aes(x = Response_Group, y = Percentage, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_data,
    aes(x = Response_Group, y = y_pos, label = Significance),
    inherit.aes = FALSE,
    size = 5,
    color = "black"
  ) +
  facet_wrap(~ Concentration, scales = "free_x") +
  scale_fill_manual(values = c(
    "Heart-specific Genes" = "#4daf4a",
    "Non-Heart-specific Genes" = "#377eb8"
  )) +
  scale_y_continuous(limits = c(0, 110), expand = c(0, 0)) +
  labs(
    title = "Heart-Specific Gene Proportions Across CorrMotif Groups",
    x = "Response Groups",
    y = "Percentage of Genes",
    fill = "Gene Category"
  ) +
  theme_minimal(base_size = 14) +
  theme(
    plot.title = element_text(size = 16, hjust = 0.5, face = "bold"),
    axis.title.x = element_text(size = 14, face = "bold"),
    axis.title.y = element_text(size = 14, face = "bold"),
    axis.text.x = element_text(size = 11, angle = 45, hjust = 1),
    axis.text.y = element_text(size = 12),
    legend.title = element_text(size = 13),
    legend.text = element_text(size = 12),
    strip.text = element_text(size = 14, face = "bold"),
    panel.border = element_rect(color = "black", fill = NA, linewidth = 1.2),
    panel.spacing = unit(1.2, "lines")
  )

📌 Tissue Specificity Score

# 📦 Load Required Libraries
library(ggplot2)
library(dplyr)

# ✅ Step 1: Load CorrMotif group assignments
grouped_files <- list(
  "data/prob_1_0.1.csv" = "Non response 0.1",
  "data/prob_2_0.1.csv" = "CX_DOX_1",
  "data/prob_3_0.1.csv" = "DOX_sp_1",
  "data/prob_1_0.5.csv" = "Non response 0.5",
  "data/prob_2_0.5.csv" = "DOX_sp_2",
  "data/prob_3_0.5.csv" = "DOX_sp_3",
  "data/prob_4_0.5.csv" = "CX_DOX_2",
  "data/prob_5_0.5.csv" = "CX_DOX_3"
)

group_order <- unname(unlist(grouped_files))  # group order for consistent plotting

all_groups <- bind_rows(lapply(names(grouped_files), function(f) {
  read.csv(f) %>% mutate(Group = grouped_files[[f]])
})) %>% mutate(Entrez_ID = as.character(Entrez_ID))

# ✅ Step 2: Load TS data
ts_data <- read.csv("data/TS.csv") %>%
  mutate(Entrez_ID = as.character(Entrez_ID))

# ✅ Step 3: Merge and clean
merged_data <- all_groups %>%
  left_join(ts_data, by = "Entrez_ID") %>%
  mutate(
    Heart_Ventricle = as.numeric(Heart_Ventricle),
    Group = factor(Group, levels = group_order)
  ) %>%
  filter(!is.na(Heart_Ventricle))
Warning in left_join(., ts_data, by = "Entrez_ID"): Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 803 of `x` matches multiple rows in `y`.
ℹ Row 10933 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
  "many-to-many"` to silence this warning.
Warning: There was 1 warning in `mutate()`.
ℹ In argument: `Heart_Ventricle = as.numeric(Heart_Ventricle)`.
Caused by warning:
! NAs introduced by coercion
# ✅ Step 4: Define ALL comparisons
comparison_map_1 <- list(
  "CX_DOX_1" = "Non response 0.1",
  "DOX_sp_1" = "Non response 0.1",
  "DOX_sp_2" = "Non response 0.5",
  "DOX_sp_3" = "Non response 0.5",
  "CX_DOX_2" = "Non response 0.5",
  "CX_DOX_3" = "Non response 0.5"
)

comparison_table_2 <- data.frame(
  resp_group = c(
    "DOX_sp_1",
    "DOX_sp_2",
    "DOX_sp_3",
    "DOX_sp_2",
    "DOX_sp_3"
  ),
  control_group = c(
    "CX_DOX_1",
    "CX_DOX_2",
    "CX_DOX_2",
    "CX_DOX_3",
    "CX_DOX_3"
  ),
  stringsAsFactors = FALSE
)

# ✅ Step 5: Run Wilcoxon test for both comparison sets
star_df_1 <- lapply(names(comparison_map_1), function(resp_group) {
  control_group <- comparison_map_1[[resp_group]]
  resp_vals <- merged_data$Heart_Ventricle[merged_data$Group == resp_group]
  control_vals <- merged_data$Heart_Ventricle[merged_data$Group == control_group]
  test_result <- wilcox.test(resp_vals, control_vals)
  pval <- test_result$p.value
  
  if (pval < 0.05) {
    label <- case_when(pval < 0.001 ~ "***", pval < 0.01 ~ "**", TRUE ~ "*")
    y_pos <- max(c(resp_vals, control_vals), na.rm = TRUE) + 0.4
    data.frame(control_group, resp_group, y_pos, label, P_Value = signif(pval, 4))
  } else {
    NULL
  }
}) %>% bind_rows()

star_df_2 <- lapply(1:nrow(comparison_table_2), function(i) {
  resp_group <- comparison_table_2$resp_group[i]
  control_group <- comparison_table_2$control_group[i]
  resp_vals <- merged_data$Heart_Ventricle[merged_data$Group == resp_group]
  control_vals <- merged_data$Heart_Ventricle[merged_data$Group == control_group]
  test_result <- wilcox.test(resp_vals, control_vals)
  pval <- test_result$p.value
  
  if (pval < 0.05) {
    label <- case_when(pval < 0.001 ~ "***", pval < 0.01 ~ "**", TRUE ~ "*")
    y_pos <- max(c(resp_vals, control_vals), na.rm = TRUE) + 0.4
    data.frame(control_group, resp_group, y_pos, label, P_Value = signif(pval, 4))
  } else {
    NULL
  }
}) %>% bind_rows()

star_df <- bind_rows(star_df_1, star_df_2) %>%
  mutate(
    x = as.numeric(factor(control_group, levels = levels(merged_data$Group))),
    xend = as.numeric(factor(resp_group, levels = levels(merged_data$Group))),
    bump = 0.8 * (row_number() - 1),
    y_pos = y_pos + bump
  )

# ✅ Step 6: Define group colors
group_colors <- c(
  "Non response 0.1" = "#33FF33",
  "CX_DOX_1" = "#228B22",
  "DOX_sp_1" = "#003366",
  "Non response 0.5" = "#FF6666",
  "DOX_sp_2" = "#B22222",
  "DOX_sp_3" = "#FF8C00",
  "CX_DOX_2" = "#4682B4",
  "CX_DOX_3" = "#8B008B"
)

# ✅ Step 7: Violin + boxplot with all significance annotations
p <- ggplot(merged_data, aes(x = Group, y = Heart_Ventricle, fill = Group)) +
  geom_violin(trim = FALSE, scale = "width", color = "black", alpha = 0.8) +
  geom_boxplot(width = 0.2, color = "black", fill = "white", outlier.shape = NA) +
  scale_fill_manual(values = group_colors) +
  scale_y_continuous(
    limits = c(-10, max(star_df$y_pos, na.rm = TRUE) + 1),
    breaks = seq(-10, 25, 5)
  ) +
  geom_hline(yintercept = 0, linetype = "dashed", color = "red") +
  geom_segment(data = star_df, aes(x = x, xend = xend, y = y_pos, yend = y_pos),
               inherit.aes = FALSE, color = "black", size = 0.7) +
  geom_text(data = star_df, aes(x = (x + xend)/2, y = y_pos + 0.3, label = label),
            inherit.aes = FALSE, size = 6, fontface = "bold") +
  labs(
    title = "Violin-Boxplot: Heart Ventricle TS (All Comparisons)",
    y = "Tissue specificity score (Heart Ventricle)",
    x = ""
  ) +
  theme_bw() +
  theme(
    axis.text.x = element_text(angle = 45, hjust = 1),
    plot.title = element_text(size = 14, face = "bold", hjust = 0.5),
    legend.position = "none"
  )
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
# ✅ Step 8: Show plot
print(p)


sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats4    grid      stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] org.Hs.eg.db_3.18.0   AnnotationDbi_1.64.1  IRanges_2.36.0       
 [4] S4Vectors_0.40.2      Biobase_2.62.0        BiocGenerics_0.48.1  
 [7] circlize_0.4.16       ComplexHeatmap_2.18.0 lubridate_1.9.4      
[10] forcats_1.0.0         stringr_1.5.1         dplyr_1.1.4          
[13] purrr_1.0.4           readr_2.1.5           tidyr_1.3.1          
[16] tibble_3.2.1          ggplot2_3.5.2         tidyverse_2.0.0      

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1        farver_2.1.2            blob_1.2.4             
 [4] bitops_1.0-9            Biostrings_2.70.3       RCurl_1.98-1.17        
 [7] fastmap_1.2.0           promises_1.3.2          digest_0.6.34          
[10] timechange_0.3.0        lifecycle_1.0.4         cluster_2.1.8.1        
[13] Cairo_1.6-2             KEGGREST_1.42.0         RSQLite_2.3.9          
[16] magrittr_2.0.3          compiler_4.3.0          rlang_1.1.3            
[19] sass_0.4.10             tools_4.3.0             yaml_2.3.10            
[22] knitr_1.50              labeling_0.4.3          bit_4.6.0              
[25] RColorBrewer_1.1-3      workflowr_1.7.1         withr_3.0.2            
[28] git2r_0.36.2            colorspace_2.1-0        scales_1.3.0           
[31] iterators_1.0.14        cli_3.6.1               rmarkdown_2.29         
[34] crayon_1.5.3            generics_0.1.3          rstudioapi_0.17.1      
[37] httr_1.4.7              tzdb_0.5.0              rjson_0.2.23           
[40] DBI_1.2.3               cachem_1.1.0            zlibbioc_1.48.2        
[43] parallel_4.3.0          XVector_0.42.0          matrixStats_1.5.0      
[46] vctrs_0.6.5             jsonlite_2.0.0          hms_1.1.3              
[49] GetoptLong_1.0.5        bit64_4.6.0-1           clue_0.3-66            
[52] magick_2.8.6            foreach_1.5.2           jquerylib_0.1.4        
[55] glue_1.7.0              codetools_0.2-20        stringi_1.8.3          
[58] gtable_0.3.6            shape_1.4.6.1           GenomeInfoDb_1.38.8    
[61] later_1.3.2             munsell_0.5.1           pillar_1.10.2          
[64] htmltools_0.5.8.1       GenomeInfoDbData_1.2.11 R6_2.6.1               
[67] doParallel_1.0.17       rprojroot_2.0.4         evaluate_1.0.3         
[70] png_0.1-8               memoise_2.0.1           httpuv_1.6.15          
[73] bslib_0.9.0             Rcpp_1.0.12             xfun_0.52              
[76] fs_1.6.3                pkgconfig_2.0.3         GlobalOptions_0.1.2