ENH: Plot multiwell plates

plot-plates.R

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+## Plate sanity checks
+
+suppressPackageStartupMessages({
+    library(platetools)
+    library(ggplot2)
+    library(dplyr)
+    library(viridis)
+})
+
+wells_all <- read.csv("rnai-p_values.csv") %>%
+    mutate(significant = p_value < 0.05)
+binwidth <- 0.025
+
+plot_save <- function(prefix, dir = "plots", extensions = c("png")) {
+    invisible(sapply(file.path(dir, paste(prefix, extensions, sep = ".")),
+                     ggplot2::ggsave, width = 8, height = 5,
+                     units = "in"))
+}
+
+plates <- wells_all$plate %>% unique %>% sort
+for (plate_ in plates) {
+    wells_plate <- filter(wells_all, plate == plate_)
+    data <- platetools::plate_map(wells_plate[["n"]], wells_plate$well)
+    ggplot(data,
+           aes(Column, Row)) +
+        geom_tile(aes(x = Column, y = Row, fill = values), size = 2,
+                  color = "white") +
+        geom_text(aes(label = values), size = 3) +
+        coord_fixed(ratio = 1,
+                    xlim = c(0.5, 24.5),
+                    ylim = c(0.5, 16.5)) +
+        scale_x_continuous(breaks = seq(1, 24), expand = c(0, 0)) +
+        scale_y_reverse(breaks = seq(1, 16), labels = LETTERS[1:16],
+                        expand = c(0, 0)) +
+        scale_fill_distiller(direction = 1) + xlab("") + ylab("") +
+        theme_minimal() +
+        ggtitle(paste0("Plate ", plate_, ": number of cells"))
+    plot_save(paste0("plate_", plate_, "-cell_count"))
+}
+
+## Check repeated RNAi wells.
+wells_repeated <- group_by(wells_all, symbol) %>%
+    summarise(n_symbol = n(), coloc_mean = mean(coloc),
+              coloc_stddev = sd(coloc)) %>%
+    filter(n_symbol > 1)
+
+print(summary(wells_repeated))
+
+wells_repeated %>% merge(wells_all) %>% arrange(-coloc_stddev) %>%
+    write.csv("wells-stddev-descending.csv", row.names = FALSE)
+
+ggplot(wells_repeated, aes(coloc_mean, coloc_stddev)) +
+    geom_point(aes(size = n_symbol), alpha = 0.5)
+plot_save("stddev-scatter")
+
+ggplot(wells_repeated, aes(coloc_mean, coloc_stddev)) +
+    geom_text(aes(label = symbol), check_overlap = TRUE)
+plot_save("stddev-words")