From ce15ed4fa278a973d3098d2454f0bf0c18596f57 Mon Sep 17 00:00:00 2001
From: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: Fri, 3 Nov 2023 20:59:06 +0100
Subject: [PATCH] Fixed bug in Category-to-Class mapping

---
 R/03_expression_partitioning.R | 43 +++++++++++++++++++---------------
 R/utils.R                      |  8 +++----
 R/visualization.R              |  1 -
 3 files changed, 28 insertions(+), 24 deletions(-)

diff --git a/R/03_expression_partitioning.R b/R/03_expression_partitioning.R
index 5403df2..7ab9984 100644
--- a/R/03_expression_partitioning.R
+++ b/R/03_expression_partitioning.R
@@ -34,26 +34,26 @@ expression_partitioning <- function(deg_list) {
     
     # Data frame with classification rules for groups and classes
     cl <- c(
-        "ADD", "ELD_P1", "DOWN", "ELD_P2", "UP", "UP", 
-        "DOWN", "UP", "ELD_P2", "DOWN", "ELD_P1", "ADD"
+        "ADD", "ELD_P2", "DOWN", "ELD_P1", "UP", "UP", 
+        "DOWN", "UP", "ELD_P1", "DOWN", "ELD_P2", "ADD"
     )
     partition_rules <- data.frame(
-        DEG = c(
-            "down-up-up",
-            "unchanged-up-up",
-            "down-down-up",
-            "up-unchanged-down",
-            "up-up-up",
-            "up-up-down",
-            "down-down-unchanged",
-            "up-up-unchanged",
-            "down-unchanged-up",
-            "down-down-down",
-            "unchanged-down-down",
-            "up-down-down"
-        ),
         Category = factor(seq_len(12), levels = seq_len(12)),
-        Class = factor(cl, levels = c("UP", "DOWN", "ADD", "ELD_P1", "ELD_P2"))
+        Class = factor(cl, levels = c("UP", "DOWN", "ADD", "ELD_P1", "ELD_P2")),
+        DEG = c(
+            "down-up-up", #             1
+            "unchanged-up-up", #        2
+            "down-down-up", #           3
+            "up-unchanged-down", #      4
+            "up-up-up", #               5
+            "up-up-down", #             6
+            "down-down-unchanged", #    7
+            "up-up-unchanged", #        8
+            "down-unchanged-up", #      9
+            "down-down-down", #         10
+            "unchanged-down-down", #    11
+            "up-down-down" #            12
+        )
     )
 
     # Classify genes in 12 groups
@@ -70,11 +70,16 @@ expression_partitioning <- function(deg_list) {
         data.frame(
             Gene = rownames(deg_list$F1_vs_P2),
             lFC_F1_vs_P2 = deg_list$F1_vs_P2$log2FoldChange
-        )
+        ),
+        all = TRUE
     )
+    log2fc_df[is.na(log2fc_df)] <- 0
     
     # Combine classification data frame with log2foldchange
-    class_df <- merge(classified_genes[, c("Gene", "Category", "Class")], log2fc_df)
+    class_df <- merge(
+        classified_genes[, c("Gene", "Category", "Class")], log2fc_df,
+        all.x = TRUE
+    )
     class_df <- class_df[!is.na(class_df$Category), ]
     class_df <- class_df[order(class_df$Category), ]
     
diff --git a/R/utils.R b/R/utils.R
index be19436..636760d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -241,11 +241,11 @@ partition_lineplots <- function(
     
     # Data frame of point coordinates for each group
     pline_data <- data.frame(
-        Category = factor(rep(1:12, each = 3)),
+        Category = factor(rep(seq_len(12), each = 3)),
         Class = factor(
             rep(c(
-                "ADD", "ELD_P1", "DOWN", "ELD_P2", "UP", "UP", 
-                "DOWN", "UP", "ELD_P2", "DOWN", "ELD_P1", "ADD"
+                "ADD", "ELD_P2", "DOWN", "ELD_P1", "UP", "UP", 
+                "DOWN", "UP", "ELD_P1", "DOWN", "ELD_P2", "ADD"
             ), each = 3),
             levels = c("UP", "DOWN", "ADD", "ELD_P1", "ELD_P2")),
         x = factor(rep(c("P1", "F1", "P2"), 12), levels = c("P1", "F1", "P2")),
@@ -269,7 +269,7 @@ partition_lineplots <- function(
     pline_data <- split(pline_data, pline_data[[group_by]])
     
     ## Number of genes per level of `group_by`
-    n <- as.numeric(table(partition_table$Category))
+    n <- as.numeric(table(partition_table[[group_by]]))
     
     p_line <- lapply(seq_along(pline_data), function(x) {
         
diff --git a/R/visualization.R b/R/visualization.R
index 3b78f64..9ad31cf 100644
--- a/R/visualization.R
+++ b/R/visualization.R
@@ -112,7 +112,6 @@ plot_expression_partitions <- function(
 ) {
     
     pdata <- partition_table
-    pdata <- pdata[!is.na(pdata$lFC_F1_vs_P1) & !is.na(pdata$lFC_F1_vs_P2), ]
     
     # Define color palette
     pal <- ppal(palette, "partition")[seq_along(levels(pdata[[group_by]]))]