Switch from theme_gray() to theme_foundation()

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -76,15 +76,15 @@ args <- parse_arguments()
 # dir.create(file.path(args$out_dir, "zscores", "qc"), showWarnings = FALSE)
 
 # Define themes and scales
+library(ggthemes)
+
 theme_publication <- function(base_size = 14, base_family = "sans", legend_position = "bottom") {
-  theme_foundation <- ggplot2::theme_grey(base_size = base_size, base_family = base_family)
+  theme_foundation <- ggthemes::theme_foundation(base_size = base_size, base_family = base_family)
   
   theme_foundation %+replace%
     theme(
       plot.title = element_text(face = "bold", size = rel(1.2), hjust = 0.5),
       text = element_text(),
-      panel.background = element_rect(colour = NA),
-      plot.background = element_rect(colour = NA),
       panel.border = element_rect(colour = NA),
       axis.title = element_text(face = "bold", size = rel(1)),
       axis.title.y = element_text(angle = 90, vjust = 2, size = 18),
@@ -1119,7 +1119,7 @@ main <- function() {
         x_var = "delta_bg",
         y_var = NULL,
         plot_type = "density",
-        title = "Plate analysis by Drug Conc for Delta Background before quality control",
+        title = "Density plot for Delta Background by Conc All Data",
         color_var = "conc_num_factor",
         x_label = "Delta Background",
         y_label = "Density",
@@ -1130,7 +1130,7 @@ main <- function() {
         x_var = "delta_bg",
         y_var = NULL,
         plot_type = "bar",
-        title = "Plate analysis by Drug Conc for Delta Background before quality control",
+        title = "Bar plot for Delta Background by Conc All Data",
         color_var = "conc_num_factor",
         x_label = "Delta Background",
         y_label = "Count",
@@ -1215,9 +1215,7 @@ main <- function() {
       )
     )
 
-    message("Generating quality control plots")
-
-    # TODO trying out some parallelization
+    message("Generating quality control plots in parallel")
     # future::plan(future::multicore, workers = parallel::detectCores())
     future::plan(future::multisession, workers = 3) # generate 3 plots in parallel
 
@@ -1368,7 +1366,7 @@ main <- function() {
         file = file.path(out_dir, "zscore_interaction_deletion_enhancers_and_suppressors_K.csv"), row.names = FALSE)
       
       # Handle linear model based enhancers and suppressors
-      lm_threshold <- 2
+      lm_threshold <- 2 # TODO add to study config?
       enhancers_lm_L <- zscore_interactions[zscore_interactions$Z_lm_L >= lm_threshold, ]
       suppressors_lm_L <- zscore_interactions[zscore_interactions$Z_lm_L <= -lm_threshold, ]
       enhancers_lm_K <- zscore_interactions[zscore_interactions$Z_lm_K >= lm_threshold, ]
@@ -1406,19 +1404,20 @@ main <- function() {
         plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
 
       message("Filtering and reranking plots")
+      interaction_threshold <- 2 # TODO add to study config?
       # Formerly X_NArm
       zscore_interactions_filtered <- zscore_interactions_joined %>%
         filter(!is.na(Z_lm_L) & !is.na(Avg_Zscore_L)) %>%
         mutate(
           Overlap = case_when(
-            Z_lm_L >= 2 & Avg_Zscore_L >= 2 ~ "Deletion Enhancer Both",
-            Z_lm_L <= -2 & Avg_Zscore_L <= -2 ~ "Deletion Suppressor Both",
-            Z_lm_L >= 2 & Avg_Zscore_L <= 2 ~ "Deletion Enhancer lm only",
-            Z_lm_L <= 2 & Avg_Zscore_L >= 2 ~ "Deletion Enhancer Avg Zscore only",
-            Z_lm_L <= -2 & Avg_Zscore_L >= -2 ~ "Deletion Suppressor lm only",
-            Z_lm_L >= -2 & Avg_Zscore_L <= -2 ~ "Deletion Suppressor Avg Zscore only",
-            Z_lm_L >= 2 & Avg_Zscore_L <= -2 ~ "Deletion Enhancer lm, Deletion Suppressor Avg Z score",
-            Z_lm_L <= -2 & Avg_Zscore_L >= 2 ~ "Deletion Suppressor lm, Deletion Enhancer Avg Z score",
+            Z_lm_L >= interaction_threshold & Avg_Zscore_L >= interaction_threshold ~ "Deletion Enhancer Both",
+            Z_lm_L <= -interaction_threshold & Avg_Zscore_L <= -interaction_threshold ~ "Deletion Suppressor Both",
+            Z_lm_L >= interaction_threshold & Avg_Zscore_L <= interaction_threshold ~ "Deletion Enhancer lm only",
+            Z_lm_L <= interaction_threshold & Avg_Zscore_L >= interaction_threshold ~ "Deletion Enhancer Avg Zscore only",
+            Z_lm_L <= -interaction_threshold & Avg_Zscore_L >= -interaction_threshold ~ "Deletion Suppressor lm only",
+            Z_lm_L >= -interaction_threshold & Avg_Zscore_L <= -interaction_threshold ~ "Deletion Suppressor Avg Zscore only",
+            Z_lm_L >= interaction_threshold & Avg_Zscore_L <= -interaction_threshold ~ "Deletion Enhancer lm, Deletion Suppressor Avg Z score",
+            Z_lm_L <= -interaction_threshold & Avg_Zscore_L >= interaction_threshold ~ "Deletion Suppressor lm, Deletion Enhancer Avg Z score",
             TRUE ~ "No Effect"
           ),
           lm_R_squared_L = summary(lm(Z_lm_L ~ Avg_Zscore_L))$r.squared,

qhtcp-workflow/qhtcp-workflow

@@ -1430,9 +1430,14 @@ wrapper calculate_interaction_zscores
 # TODO
 #
 # * More variables can be read in from the config file to allow more configuration
+#   * sd thresholds
+#   * lm thresholds
+#   * interaction thresholds
+#   * reference gene(s)
+#   * background genes
 # * Add gene names, other threshold values, etc.
 # * Dataframe columns and output file columns should be standardized in calculate_interactions()
-# * Need to decide if conc_num_factor is numeric or factor 
+# * Need to decide if conc_num_factor is numeric or factor
 #
 # INPUT
 #