ENH: Plot control derived p-values

analysis-only_overlap.R

@@ -108,6 +108,15 @@ p_value <- function(x) {
     x <- x[1L, 1L]
     phyper(x - 1, m, n, k, lower.tail = FALSE)
 }
+## Apply implementation of Fisher's exact test to large vectors
+p_values <- function(x, y, x_total, y_total) {
+    contingency_matrix <- rbind(x, y,
+                                x_total, y_total)
+    ## Organize array to have 2x2 margin instead of 1x4.
+    dim(contingency_matrix) <- c(2, 2, length(contingency_matrix) / 4)
+    apply(contingency_matrix, 3, p_value) # nolint
+}
+## P-values for RNAi wells.
 wells_all <- merge(wells, wells_layout) %>%
     mutate(coloc = n_coloc / n)
 cells <- filter(wells_all) %>% select(n) %>% unlist
@@ -117,13 +126,19 @@ cells_all <- filter(wells_all, is.na(control)) %>% select(n) %>%
     unlist %>% sum
 overlaps_all <- filter(wells_all, is.na(control)) %>%
     select(n_coloc) %>% unlist %>% sum
-contingency_matrix <- rbind(cells, overlaps,
-                            cells_all, overlaps_all)
-## Organize array to have 2x2 margin instead of 1x4.
-dim(contingency_matrix) <- c(2, 2, length(contingency_matrix) / 4)
-p_values_uncorrected <- apply(contingency_matrix, 3, p_value)
-p_values <- p.adjust(p_values_uncorrected, method = "bonferroni")
-wells_all$p_value <- p_values_uncorrected
+wells_all$p_value <- p_values(cells, overlaps, cells_all, overlaps_all)
+## P-values for control wells.
+cells_all_control <- filter(wells_all,
+                            !is.na(control),
+                            symbol == "LacZ") %>%
+    select(n) %>% unlist %>% sum
+overlaps_all_control <- filter(wells_all,
+                       !is.na(control),
+                       symbol == "LacZ") %>%
+    select(n_coloc) %>% unlist %>% sum
+wells_all$p_value_control <- p_values(cells, overlaps,
+                                      cells_all_control,
+                                      overlaps_all_control)
 
 ## Check repeated RNAi wells.
 wells_repeated <- group_by(wells_all, symbol) %>%

plots.R

@@ -4,10 +4,13 @@ suppressPackageStartupMessages({
     library(ggplot2)
     library(dplyr)
     library(readr)
+    library(forcats)
+    library(varhandle)
 })
 
 wells_all <- read_csv("rnai-p_values.csv") %>%
-    mutate(significant = p_value < 0.05)
+    mutate(significant = p_value < 0.05,
+           plate = factor(plate) %>% fct_relevel("504"))
 binwidth <- 0.025
 
 theme_set(theme_bw())
@@ -37,24 +40,30 @@ ggplot(filter(wells_all,
     xlab("% colocalization")
 
 ggplot(filter(wells_all, !is.na(control)) %>%
-       group_by(well) %>% mutate(ymin = min(coloc), ymax = max(coloc),
-                                 plate = factor(plate)),
+       group_by(well) %>% mutate(ymin = min(coloc), ymax = max(coloc)),
        aes(well, coloc, color = plate)) +
     geom_errorbar(aes(ymin = ymin, ymax = ymax), color = "gray") +
     geom_jitter(aes(shape = plate)) +
     scale_color_brewer(palette = "Set1") +
-    ggtitle(paste("Scatter plot of control well colocalization across plates")) +
+    ggtitle(paste("Scatter plot of control well",
+                  "colocalization across plates")) +
     xlab("well") + ylab("% colocalization")
 
 ggplot(filter(wells_all, !is.na(control)) %>%
-       group_by(well) %>% mutate(ymin = min(p_value), ymax = max(p_value),
-                                 plate = factor(plate)),
-       aes(well, p_value, color = plate)) +
-    geom_errorbar(aes(ymin = ymin, ymax = ymax, color = control)) +
-    geom_jitter(aes(shape = plate, size = n)) +
+       group_by(well) %>% mutate(ymin = min(p_value_control),
+                                 ymax = max(p_value_control),
+                                 ytext = plate %>%
+                                     lvls_revalue(seq(1.5, 1.1, -0.1) %>%
+                                                  as.character) %>%
+                                     unfactor),
+       aes(well, p_value_control, color = plate)) +
+    geom_errorbar(aes(ymin = ymin, ymax = ymax, linetype = control),
+                  color = "grey") +
+    geom_jitter(aes(color = plate), size = 3) +
+    geom_text(aes(label = symbol, y = ytext, color = plate)) +
     scale_color_brewer(palette = "Set1") +
     ggtitle(paste("Scatter plot of control well p-values across plates")) +
-    xlab("well") + ylab("p-value")
+    xlab("well") + ylab("p-value against LacZ")
 
 ggplot(wells_all, aes(coloc, color = type)) +
     geom_freqpoly(binwidth = binwidth) +