plots.R

## See the distribution of % Overlap vs. wells

suppressPackageStartupMessages({
    library(ggplot2)
    library(dplyr)
})

wells_all <- read.csv("rnai-p_values.csv") %>%
    mutate(significant = p_value < 0.05)
binwidth <- 0.025
## Bring RNAi to the front of the level list.
wells_all$type <- relevel(wells_all$type, "RNAi")

theme_set(theme_bw())

plot_save <- function(prefix, dir = "plots",
                      extensions = c("png", "pdf", "svg")) {
    invisible(sapply(file.path(dir, paste(prefix, extensions, sep = ".")),
                     ggplot2::ggsave, width = 8, height = 5,
                     units = "in"))
}

ggplot(filter(wells_all, type == "RNAi"),
       aes(coloc, fill = significant)) +
    geom_histogram(binwidth = binwidth) +
    scale_fill_manual(values = c("grey", "blue")) +
    ggtitle("Histogram of RNAi wells with significant overlap (p-value < 5%)") +
    xlab("% colocalization")
plot_save("rnai-hist-signif")

ggplot(filter(wells_all,
              !is.na(control),
              plate == "160415_015529-V"),
       aes(coloc, fill = significant)) +
    geom_histogram(binwidth = binwidth) +
    facet_wrap(~ control) +
    scale_fill_manual(values = c("grey", "blue")) +
    ggtitle(paste("Histogram of control wells with",
                  "significant overlap (p-value < 5%)")) +
    xlab("% colocalization")

ggplot(wells_all, aes(coloc, color = type)) +
    geom_freqpoly(binwidth = binwidth) +
    scale_y_log10() +
    facet_wrap(~ type) +
    ggtitle("Histogram of all well types") +
    xlab("% colocalization")
plot_save("all-hist")

ggplot(wells_all, aes(coloc, color = type)) +
    geom_density() +
    facet_wrap(~ type) +
    ggtitle("Density plot of wells to show distribution") +
    xlab("% colocalization")
plot_save("all-density")