Quick and Dirty Example of Converting CG12 formatted data into Precog formatted data.

eg_cg12-to-precog-format.R

# convert cg-12 raw data into generic growth data that can be imported into
# precog-lite

library(tidyverse)
library(lubridate)
# devtools::install_github("npjc/cg12r")
library(cg12r)

# how do you take raw data from the cg-12 and turn it into growth curves

path <- "2018-04-19_800drugscreen_plate-1-of-11_BY4743=replica-plates-1-4-7-10_YPS128=replica-plates-2-5-8-11_YPS138=replica-plate-3-6-9-12.txt"

l <- read_cg12(path) %>% bind_rows()

slim <- l %>% 
    mutate(datetime = ymd_hms(paste(date, time), tz= "Canada/Pacific")) %>% 
    select(-instrument_header, -wavelength, -date, -time)

out <- slim %>% 
    group_by(plate) %>% 
    mutate(secs = as.numeric(datetime),
       min_secs = min(secs),
       t_since_start = secs - min_secs,
       time = as.integer(t_since_start * 10)) %>% 
    select(-datetime, -secs, -min_secs, -t_since_start) %>% 
    ungroup() %>% 
    unite(sample, plate, plate_row_int, plate_col_int)

out %>% 
    select(time, sample, measurment) %>% 
    filter(str_detect(sample, "S1L1")) %>% 
    spread(sample, measurment) %>% 
    write_tsv("sample-precog-input.txt")
    
out %>% 
    select(time, sample, measurment) %>% 
    filter(str_detect(sample, "S1L2")) %>% 
    spread(sample, measurment) %>% 
    write_tsv("sample-precog-input2.txt")