MAINT: Use new directory layout

src/overlap-analysis.R

@@ -7,8 +7,8 @@ suppressPackageStartupMessages({
 })
 
 ## Configuration values.
-file_db <- "cellprofiler_all-plates/all-plates.db"
-files_plate <- "plates/DRSC_TF_Library_Distribution.xls"
+file_db <- file.path("../results/cellprofiler/rnai-screen-tf.db")
+files_plate <- "../data/DRSC_TF_Library_Distribution.xls"
 
 ## Plate 504 was run at the last minute, and so the controls are not
 ## reflected in the Excel spreadsheet provided by the core facility.
@@ -141,4 +141,5 @@ wells_repeated <- group_by(wells_all, symbol) %>%
     filter(n > 1)
 print(summary(wells_repeated))
 
-write_csv(wells_all %>% arrange(p_value), "rnai-p_values.csv")
+write_csv(wells_all %>% arrange(p_value),
+          paste0("../results/tables/rnai-p_values-.csv"))

src/plot-plates.R

@@ -7,11 +7,11 @@ suppressPackageStartupMessages({
     library(viridis)
 })
 
-wells_all <- read.csv("rnai-p_values.csv") %>%
+wells_all <- read.csv("../results/tables/rnai-p_values.csv") %>%
     mutate(significant = p_value < 0.05)
 binwidth <- 0.025
 
-plot_save <- function(prefix, dir = "plots", extensions = c("png")) {
+plot_save <- function(prefix, dir = "../results/plots", extensions = c("png")) {
     invisible(sapply(file.path(dir, paste(prefix, extensions, sep = ".")),
                      ggplot2::ggsave, width = 8, height = 5,
                      units = "in"))
@@ -47,7 +47,7 @@ wells_repeated <- group_by(wells_all, symbol) %>%
 print(summary(wells_repeated))
 
 wells_repeated %>% merge(wells_all) %>% arrange(-coloc_stddev) %>%
-    write.csv("wells-stddev-descending.csv", row.names = FALSE)
+    write.csv("../results/tables/wells-stddev-descending.csv", row.names = FALSE)
 
 ggplot(wells_repeated, aes(coloc_mean, coloc_stddev)) +
     geom_point(aes(size = n_symbol), alpha = 0.5)

src/plots.R

@@ -11,15 +11,15 @@ suppressPackageStartupMessages({
 ## Do not generate Rplots.pdf
 pdf(NULL)
 
-wells_all <- read_csv("rnai-p_values.csv") %>%
+wells_all <- read_csv("../results/tables/rnai-p_values.csv") %>%
     mutate(significant = p_value < 0.05,
            plate = factor(plate))
 binwidth <- 0.025
 
 theme_set(theme_bw())
 
-plot_save <- function(prefix, dir = "plots",
-                      extensions = c("png", "pdf", "svg"),
+plot_save <- function(prefix, dir = "../results/plots",
+                      extensions = c("png", "pdf"),
                       width = 8, height = 5) {
     invisible(sapply(file.path(dir, paste(prefix, extensions, sep = ".")),
                      ggplot2::ggsave, width = width, height = height,