plot_nanodrop_results.R

#!/usr/bin/env Rscript

library(lubridate)
library(tidyverse)
library(ggplot2)

#############
# FUNCTIONS #
#############

FindHeaderLines <- function(nd_data_lines) {
    grep("^Wavelength \\(nm\\)", nd_data_lines)
}

FindSampleNames <- function(nd_data_lines,
                            header_lines) {
    nd_data_lines[header_lines - 2]
}

FindSamplePOSIXct <- function(nd_data_lines,
                              header_lines) {
    dmy_hms(nd_data_lines[header_lines - 1],
            tz = "Pacific/Auckland")
}

FindStopLines <- function(nd_data_lines,
                          header_lines) {
    c((header_lines - 5)[2:length(header_lines)],
      length(nd_data_lines)) 
}

ParseNdDataLines <- function(nd_data_lines) {
    # parse the metadata
    my_header_lines <- FindHeaderLines(nd_data_lines)
    my_stop_lines <- FindStopLines(nd_data_lines, my_header_lines)
    my_sample_names <- FindSampleNames(nd_data_lines, my_header_lines)
    my_sample_dates <- FindSamplePOSIXct(nd_data_lines, my_header_lines)
    # read_tsv on each subset of data
    my_results_list <- lapply(1:length(my_header_lines), function(i)
        read_tsv(
            paste(nd_data_lines[my_header_lines[[i]]:my_stop_lines[[i]]],
                  collapse = "\n")) %>% 
            mutate(Sample = my_sample_names[[i]],
                   Date = my_sample_dates[[i]]))
    # return the full tibble
    bind_rows(my_results_list)
}

########
# MAIN #
########

# read as lines 
my_file <- "2018_07_20_spectra.tsv"
my_path <- normalizePath(my_file)
nd_data_lines <- read_lines(my_path)

# parse lines
nd_data_raw <- ParseNdDataLines(nd_data_lines) %>%
    filter(Date > ymd_hms("2018-07-20 09:41:00", tz = "Pacific/Auckland")) %>%
    mutate(Label = glue::glue("Sample {Sample}\n{Date}"))


# plot
set1 <- RColorBrewer::brewer.pal(9, "Set1")
gp <- ggplot(nd_data_raw,
             aes(x = `Wavelength (nm)`,
                 y = `10mm Absorbance`,
                 group = `Label`)) +
    ggtitle(my_path,
            subtitle = glue::glue("Printed {now()}.")) +
    theme_grey(base_size = 10) +
    facet_wrap( ~ `Label`) +
    geom_vline(xintercept = c(230, 260, 280),
               linetype = 2,
               colour = alpha(set1[2], 0.5)) +
    geom_point(colour = alpha(set1[3], 0.5), shape = 16) +
    geom_smooth(span = 0.25,
                colour = alpha(set1[1], 0.75),
                size = 1,
                se = FALSE)

ggsave("plot.pdf", gp, width = 250, height = 170, units = "mm")