0-general_functions_main.R

# FUnctions to load qPCR data and manipulate it. The functions can be called from another R file

# read in excel file (.xls) of qPCR exported from Quantstudio 3 
  # Make sure to include raw data as well

# Library calling  ----
# calling libraries ; make sure they are installed (install.packages)
library(tidyverse); library(rlang); # tidyverse general tabular stuff. rlang -- unconventional tidyeval stuff
library(plotly) # interactive plots

# library(magrittr); # special chaining functions beyond "%>%"
# library(ggrepel); # for non-overlapping labels of points on plots
# library(lubridate); # for advanced date operations


# google sheets ----
sheeturls <- list(plate_layouts_PK = 'https://docs.google.com/spreadsheets/d/1RffyflHCQ_GzlRHbeH3bAkiYo4zNlnFWx4FXo7xkUt8/edit#gid=0')

# pre-authorization for google sheets: Works if there is only 1 cached account (after first access)
googlesheets4::gs4_auth(email = TRUE) # reference: https://googlesheets4.tidyverse.org/reference/gs4_auth.html

# Convenience function for plotting directory and .png suffix for adhoc plots
plot_as <- function(plt_name, ...)  str_c('qPCR analysis/Archive/', plt_name, ..., '.png')

# dummy data  ---- 
# or test data for testing simple functions 

# dummy test tibble
a <- tibble(a1 = 1:6, a2 = 6:1, a3 = rep(c('a', 'b'),3), a4 = a2 ^2)

# expression to test on plotting
y_namr_test <- list( 'a2' = expression(paste('this is a ', mu, 'L')),
                     'a4' = expression(paste('super large ', sigma, 'L')))

# test ggplot
a_plt <- ggplot(a, aes(a1, a2, colour = a3)) + 
  geom_point() + 
  geom_line() + 
  ylab(y_namr_test[['a4']])



# calling more funs ----

list_of_general_functions <- c("1-reading_files_funs.R",
                               "2-tibble_columns_wrapper_funs.R",
                               "3-obsolete_arcane_funs.R",
                               "4-qPCR_specific_funs.R",
                               "5-mathematical_fitting_funs.R",
                               "6-formatting_plot_funs.R",
                               "7-COVID specific_writing_funs.R",
                               "8-plot_mean_sd_jitter.R",
                               "9-plot_scatter.R",
                               "10-process_qpcr.R",
                               '12-plot_facetted_assay.R',
                               'g.13-std_curve_processing.R',
                               '16-User_parameters.R') # "0-old_general_functions.R"

# Source all the functions listed above
map(str_c('./scripts_general_fns/', list_of_general_functions),
    source)